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Strontium in PDB 1vqm: The Structure of the Transition State Analogue "Dan" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui

Protein crystallography data

The structure of The Structure of the Transition State Analogue "Dan" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1vqm was solved by T.M.Schmeing, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.30
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 211.445, 298.564, 574.493, 90.00, 90.00, 90.00
R / Rfree (%) 21.4 / 24.7

Other elements in 1vqm:

The structure of The Structure of the Transition State Analogue "Dan" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui also contains other interesting chemical elements:

Magnesium (Mg) 94 atoms
Potassium (K) 2 atoms
Cadmium (Cd) 5 atoms
Chlorine (Cl) 22 atoms
Sodium (Na) 75 atoms

Strontium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 70; Page 8, Binding sites: 71 - 80; Page 9, Binding sites: 81 - 90; Page 10, Binding sites: 91 - 100; Page 11, Binding sites: 101 - 110; Page 12, Binding sites: 111 - 114;

Binding sites:

The binding sites of Strontium atom in the The Structure of the Transition State Analogue "Dan" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui (pdb code 1vqm). This binding sites where shown within 5.0 Angstroms radius around Strontium atom.
In total 114 binding sites of Strontium where determined in the The Structure of the Transition State Analogue "Dan" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1vqm:
Jump to Strontium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Strontium binding site 1 out of 114 in 1vqm

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Strontium binding site 1 out of 114 in the The Structure of the Transition State Analogue "Dan" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 1 of The Structure of the Transition State Analogue "Dan" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Sr9405

b:59.4
occ:1.00
N7 0:G854 2.2 33.8 1.0
O 0:HOH4552 2.3 42.6 1.0
N7 0:G824 2.3 37.9 1.0
O 0:HOH4874 2.4 46.6 1.0
O 0:HOH5104 2.6 43.5 1.0
C8 0:G824 3.1 37.0 1.0
C8 0:G854 3.1 31.0 1.0
C5 0:G854 3.3 31.1 1.0
C5 0:G824 3.5 35.5 1.0
O6 0:G854 3.7 36.4 1.0
C6 0:G854 3.9 33.6 1.0
O6 0:G824 3.9 38.1 1.0
OP2 0:G824 4.0 49.3 1.0
OP2 0:G854 4.0 38.0 1.0
C6 0:G824 4.0 37.3 1.0
OP2 0:U823 4.3 43.0 1.0
N9 0:G854 4.3 32.8 1.0
N9 0:G824 4.4 38.7 1.0
C4 0:G854 4.4 31.3 1.0
C4 0:G824 4.5 36.9 1.0
OP2 0:C853 4.5 43.1 1.0
C5 0:C853 4.7 32.6 1.0
C5 0:U823 4.8 34.8 1.0
O5' 0:G824 4.9 44.6 1.0
O5' 0:G854 4.9 36.3 1.0
O 0:HOH4186 4.9 65.7 1.0
C6 0:C853 5.0 36.1 1.0

Strontium binding site 2 out of 114 in 1vqm

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Strontium binding site 2 out of 114 in the The Structure of the Transition State Analogue "Dan" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 2 of The Structure of the Transition State Analogue "Dan" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Sr9406

b:36.4
occ:1.00
O 0:HOH9987 2.4 27.6 1.0
OP1 0:U2615 2.4 35.6 1.0
OP1 0:G836 2.5 36.3 1.0
OE1 B:GLN230 2.6 31.0 1.0
O 0:HOH9896 2.6 29.2 1.0
O 0:HOH4433 2.8 36.2 1.0
CD B:GLN230 3.6 30.8 1.0
P 0:U2615 3.8 32.2 1.0
CB B:GLN230 3.9 33.2 1.0
P 0:G836 4.0 34.9 1.0
CG B:GLN230 4.0 28.5 1.0
O 0:HOH3173 4.3 51.6 1.0
CA B:GLN230 4.5 34.0 1.0
OP2 0:U2615 4.5 35.0 1.0
C5' 0:G836 4.6 34.6 1.0
O3' 0:C2614 4.6 33.1 1.0
O 0:HOH7329 4.6 52.0 1.0
C3' 0:U835 4.6 34.7 1.0
O B:GLN230 4.6 33.5 1.0
O5' 0:G836 4.6 36.5 1.0
O 0:HOH5602 4.6 56.7 1.0
O3' 0:U835 4.7 34.3 1.0
O 0:HOH9831 4.8 32.1 1.0
NE2 B:GLN230 4.8 28.9 1.0
O5' 0:U2615 4.8 34.0 1.0
OP2 0:G2616 4.9 35.1 1.0
N2 0:G2616 4.9 36.7 1.0
OP2 0:G836 5.0 39.0 1.0

Strontium binding site 3 out of 114 in 1vqm

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Strontium binding site 3 out of 114 in the The Structure of the Transition State Analogue "Dan" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 3 of The Structure of the Transition State Analogue "Dan" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Sr9407

b:46.8
occ:1.00
O6 0:G1491 2.5 39.9 1.0
O 0:HOH4550 2.6 65.8 1.0
OP2 0:G1489 2.6 43.0 1.0
O 0:HOH3024 2.7 34.8 1.0
O 0:HOH4232 2.7 41.3 1.0
O 0:HOH6707 3.1 62.7 1.0
C6 0:G1491 3.7 41.0 1.0
P 0:G1489 3.8 47.2 1.0
O 0:HOH6815 4.1 38.6 1.0
OP1 0:G1489 4.1 49.9 1.0
OP2 0:A1487 4.3 40.9 1.0
N7 0:G1491 4.4 41.0 1.0
C5 0:G1491 4.4 41.2 1.0
N7 0:G1490 4.7 39.3 1.0
O 0:HOH9785 4.7 49.6 1.0
O5' 0:G1489 4.7 44.5 1.0
OP1 0:G1453 4.8 43.5 1.0
OP2 0:G1490 4.8 42.7 1.0
N1 0:G1491 4.8 38.5 1.0
O3' 0:U1488 4.9 48.4 1.0

Strontium binding site 4 out of 114 in 1vqm

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Strontium binding site 4 out of 114 in the The Structure of the Transition State Analogue "Dan" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 4 of The Structure of the Transition State Analogue "Dan" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Sr9408

b:41.7
occ:1.00
OP1 0:A1839 2.4 37.4 1.0
O 0:HOH3960 2.5 55.4 1.0
OP2 0:A1840 2.5 29.9 1.0
OP2 0:U832 2.5 37.6 1.0
O 0:HOH8300 2.6 41.6 1.0
O 0:HOH9635 2.7 30.1 1.0
O 0:HOH9727 2.9 50.1 1.0
P 0:U832 3.7 40.1 1.0
P 0:A1839 3.7 34.9 1.0
P 0:A1840 3.7 35.2 1.0
OP1 0:U832 4.1 38.1 1.0
OP1 0:A1840 4.1 34.6 1.0
O 0:HOH3257 4.1 36.1 1.0
O 0:HOH5573 4.2 81.0 1.0
OP2 0:A1839 4.3 36.0 1.0
O 0:HOH6871 4.3 74.1 1.0
O3' 0:U1838 4.6 35.8 1.0
O5' 0:A1839 4.7 34.7 1.0
O3' 0:A1839 4.7 34.7 1.0
O3' 0:U831 4.7 38.6 1.0
O 0:HOH8383 4.7 39.5 1.0
C3' 0:U831 4.7 40.3 1.0
O5' 0:U832 4.8 41.4 1.0
O5' 0:A1840 4.9 33.7 1.0
C5' 0:A1839 5.0 32.7 1.0
C3' 0:A1839 5.0 34.1 1.0

Strontium binding site 5 out of 114 in 1vqm

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Strontium binding site 5 out of 114 in the The Structure of the Transition State Analogue "Dan" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 5 of The Structure of the Transition State Analogue "Dan" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Sr9410

b:41.1
occ:1.00
O 0:HOH8445 2.4 27.1 1.0
O 0:HOH3058 2.4 31.7 1.0
O 0:HOH7098 2.5 25.0 1.0
OP1 0:G1354 2.6 39.0 1.0
OP2 0:A643 2.8 28.6 1.0
OP1 0:C1353 3.2 53.9 1.0
O3' 0:C1353 3.5 33.9 1.0
P 0:G1354 3.6 33.8 1.0
P 0:A643 3.8 32.5 1.0
OP1 0:A643 3.9 34.9 1.0
O5' 0:C1353 4.2 48.7 1.0
P 0:C1353 4.3 51.9 1.0
O4 0:U904 4.4 30.6 1.0
OP2 0:G1354 4.5 34.4 1.0
OP1 0:G642 4.5 36.1 1.0
N3 0:U904 4.5 27.7 1.0
C5' 0:C1353 4.6 39.7 1.0
C3' 0:C1353 4.6 36.5 1.0
OP2 0:G642 4.6 37.5 1.0
O5' 0:A643 4.7 30.4 1.0
N1 0:A1355 4.7 33.7 1.0
O5' 0:G1354 4.8 32.6 1.0
P 0:G642 4.9 36.4 1.0
O5' 0:G642 4.9 37.1 1.0
N6 0:A1355 4.9 30.7 1.0
C5' 0:G1354 5.0 29.6 1.0
C4 0:U904 5.0 30.2 1.0
OP2 0:C1353 5.0 51.0 1.0

Strontium binding site 6 out of 114 in 1vqm

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Strontium binding site 6 out of 114 in the The Structure of the Transition State Analogue "Dan" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 6 of The Structure of the Transition State Analogue "Dan" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Sr9411

b:46.9
occ:1.00
OP1 0:A1755 2.6 38.4 1.0
O 0:HOH7660 2.6 49.8 1.0
O 0:HOH7106 2.7 58.6 1.0
O 0:HOH8136 2.8 35.5 1.0
O3' 0:A1754 3.5 36.5 1.0
P 0:A1755 3.6 36.8 1.0
C5' 0:A1755 4.5 36.4 1.0
OP2 0:C1738 4.6 46.7 1.0
O5' 0:A1755 4.6 37.2 1.0
O 0:HOH3640 4.8 49.8 1.0
N2 0:G834 4.8 29.8 1.0
OP2 0:A1755 4.8 34.8 1.0
OP1 0:C1738 4.8 44.9 1.0
C3' 0:A1754 4.9 36.9 1.0
O2' 0:G834 5.0 32.4 1.0

Strontium binding site 7 out of 114 in 1vqm

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Strontium binding site 7 out of 114 in the The Structure of the Transition State Analogue "Dan" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 7 of The Structure of the Transition State Analogue "Dan" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Sr9412

b:46.3
occ:1.00
O C:HOH9148 2.4 39.2 1.0
O 0:HOH8444 2.5 39.3 1.0
O2 0:C893 2.5 34.7 1.0
O 0:HOH6181 2.7 26.0 1.0
O2' 0:C893 2.7 35.7 1.0
C2 0:C893 3.7 30.7 1.0
O 0:HOH6798 3.7 35.4 1.0
C2' 0:C893 3.8 34.9 1.0
C1' 0:C893 3.9 32.6 1.0
O3' 0:C893 4.2 36.8 1.0
N1 0:C893 4.3 31.3 1.0
N7 0:G892 4.4 28.7 1.0
O C:HOH9213 4.5 58.0 1.0
O 0:HOH4485 4.5 38.5 1.0
O C:HOH9117 4.7 32.8 1.0
OP2 0:G892 4.7 29.5 1.0
O 0:HOH4984 4.7 49.2 1.0
OP2 0:A895 4.7 41.3 1.0
N3 0:C893 4.7 28.2 1.0
C3' 0:C893 4.7 34.9 1.0
NZ 1:LYS53 5.0 40.7 1.0
C8 0:G892 5.0 28.4 1.0

Strontium binding site 8 out of 114 in 1vqm

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Strontium binding site 8 out of 114 in the The Structure of the Transition State Analogue "Dan" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 8 of The Structure of the Transition State Analogue "Dan" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Sr9413

b:50.6
occ:1.00
O H:ASP10 2.5 49.3 1.0
O6 0:G1055 2.6 41.9 1.0
O 0:HOH5398 2.7 39.9 1.0
O 0:HOH6855 2.7 41.0 1.0
O 0:HOH4644 2.7 38.2 1.0
O 0:HOH4421 2.8 53.4 1.0
C H:ASP10 3.7 52.1 1.0
C6 0:G1055 3.7 38.1 1.0
O 0:HOH3888 3.9 47.0 1.0
CB H:ASP10 4.2 57.4 1.0
CG H:LYS11 4.2 55.5 1.0
N7 0:G1055 4.3 38.6 1.0
C5 0:G1055 4.4 37.1 1.0
CA H:ASP10 4.5 54.1 1.0
OD1 H:ASP10 4.6 62.5 1.0
OP2 0:G1054 4.6 42.0 1.0
N7 0:G1054 4.6 45.4 1.0
CG H:ASP10 4.6 61.2 1.0
N H:LYS11 4.7 51.3 1.0
CA H:LYS11 4.8 51.9 1.0
N1 0:G1055 4.9 39.5 1.0
CE H:LYS11 4.9 58.2 1.0

Strontium binding site 9 out of 114 in 1vqm

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Strontium binding site 9 out of 114 in the The Structure of the Transition State Analogue "Dan" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 9 of The Structure of the Transition State Analogue "Dan" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Sr9414

b:58.3
occ:1.00
OP1 0:A183 2.6 48.1 1.0
OP1 0:G147 2.6 43.2 1.0
O M:HOH9440 2.7 44.2 1.0
OD2 M:ASP157 2.7 59.8 1.0
O3' 0:U146 3.4 39.6 1.0
O3' 0:G182 3.5 41.1 1.0
CG M:ASP157 3.5 56.1 1.0
OD1 M:ASP157 3.6 54.7 1.0
P 0:A183 3.6 42.5 1.0
P 0:G147 3.6 37.7 1.0
O 0:HOH7363 4.1 72.8 1.0
C5' 0:G147 4.3 41.0 1.0
O5' 0:G147 4.4 40.8 1.0
OP2 0:A183 4.6 44.5 1.0
O 0:HOH3714 4.7 65.8 1.0
O5' 0:A183 4.7 45.5 1.0
C3' 0:U146 4.7 43.1 1.0
C3' 0:G182 4.7 41.5 1.0
C5' 0:A183 4.8 45.9 1.0
OP2 0:G147 4.8 36.0 1.0
O2' 0:U146 4.9 44.1 1.0
CB M:ASP157 4.9 52.9 1.0
C5' 0:G182 5.0 40.6 1.0

Strontium binding site 10 out of 114 in 1vqm

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Strontium binding site 10 out of 114 in the The Structure of the Transition State Analogue "Dan" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 10 of The Structure of the Transition State Analogue "Dan" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Sr9415

b:58.3
occ:1.00
O 0:HOH4363 2.5 68.0 1.0
O 0:HOH6062 2.5 89.0 1.0
O 0:HOH7110 2.6 78.3 1.0
O 0:HOH6689 2.6 48.4 1.0
O 0:HOH8381 2.8 59.8 1.0
O 0:HOH8382 3.0 42.7 1.0
O 0:HOH7398 3.4 91.8 1.0
O 0:HOH6713 3.5 0.7 1.0
OP2 0:C2077 4.4 45.9 1.0
O6 0:G2080 4.5 42.8 1.0
O 0:HOH4641 4.5 88.8 1.0
O 0:HOH4281 4.6 46.0 1.0
N6 0:A536 4.8 45.7 1.0
N7 0:G2079 4.8 39.1 1.0
OP2 0:U2078 5.0 44.2 1.0
O 0:HOH4834 5.0 74.3 1.0

Reference:

T.M.Schmeing, K.S.Huang, D.E.Kitchen, S.A.Strobel, T.A.Steitz. Structural Insights Into the Roles of Water and the 2' Hydroxyl of the P Site Trna in the Peptidyl Transferase Reaction. Mol.Cell V. 20 437 2005.
ISSN: ISSN 1097-2765
PubMed: 16285925
DOI: 10.1016/J.MOLCEL.2005.09.006
Page generated: Wed Dec 16 02:11:21 2020

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