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Strontium in PDB 1vqn: The Structure of Cc-Hpmn and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui

Protein crystallography data

The structure of The Structure of Cc-Hpmn and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1vqn 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 / 2.40
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 211.721, 298.782, 575.272, 90.00, 90.00, 90.00
R / Rfree (%) 21.2 / 24.8

Other elements in 1vqn:

The structure of The Structure of Cc-Hpmn and Cca-Phe-Cap-Bio 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 Cc-Hpmn and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui (pdb code 1vqn). 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 Cc-Hpmn and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1vqn:
Jump to Strontium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Strontium binding site 1 out of 114 in 1vqn

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Strontium binding site 1 out of 114 in the The Structure of Cc-Hpmn and Cca-Phe-Cap-Bio 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 Cc-Hpmn and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Sr9405

b:59.6
occ:1.00
O 0:HOH4547 2.3 44.0 1.0
N7 0:G824 2.3 40.3 1.0
N7 0:G854 2.4 32.6 1.0
O 0:HOH4874 2.4 50.6 1.0
O 0:HOH5101 2.5 52.7 1.0
C8 0:G824 3.1 39.1 1.0
C8 0:G854 3.2 32.2 1.0
C5 0:G854 3.4 32.7 1.0
C5 0:G824 3.5 37.7 1.0
O6 0:G854 3.7 35.7 1.0
O6 0:G824 3.9 39.7 1.0
C6 0:G854 4.0 32.8 1.0
OP2 0:G824 4.0 48.1 1.0
OP2 0:G854 4.0 39.0 1.0
C6 0:G824 4.1 38.1 1.0
OP2 0:U823 4.1 46.1 1.0
N9 0:G824 4.3 38.1 1.0
OP2 0:C853 4.5 41.3 1.0
N9 0:G854 4.5 33.0 1.0
C4 0:G824 4.5 36.4 1.0
C4 0:G854 4.6 31.8 1.0
C5 0:C853 4.8 28.9 1.0
C5 0:U823 4.8 34.1 1.0
O5' 0:G824 4.9 44.9 1.0
O5' 0:G854 5.0 36.7 1.0
C6 0:U823 5.0 37.1 1.0
O5' 0:U823 5.0 43.6 1.0
O 0:HOH4181 5.0 57.5 1.0

Strontium binding site 2 out of 114 in 1vqn

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Strontium binding site 2 out of 114 in the The Structure of Cc-Hpmn and Cca-Phe-Cap-Bio 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 Cc-Hpmn and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Sr9406

b:35.6
occ:1.00
O 0:HOH9985 2.4 21.6 1.0
OP1 0:U2615 2.4 34.6 1.0
OP1 0:G836 2.4 36.3 1.0
O 0:HOH9894 2.5 28.7 1.0
OE1 B:GLN230 2.6 32.5 1.0
O 0:HOH4430 2.9 37.3 1.0
CD B:GLN230 3.7 30.0 1.0
P 0:U2615 3.9 30.4 1.0
CB B:GLN230 3.9 31.5 1.0
P 0:G836 3.9 34.9 1.0
O 0:HOH3171 4.0 45.1 1.0
CG B:GLN230 4.1 27.8 1.0
C5' 0:G836 4.5 33.6 1.0
CA B:GLN230 4.5 32.2 1.0
O5' 0:G836 4.6 34.9 1.0
O3' 0:C2614 4.6 32.1 1.0
OP2 0:U2615 4.6 34.7 1.0
O 0:HOH5595 4.6 55.7 1.0
C3' 0:U835 4.6 34.3 1.0
O 0:HOH9831 4.6 28.3 1.0
O B:GLN230 4.7 33.4 1.0
O3' 0:U835 4.7 33.1 1.0
O 0:HOH7314 4.7 46.6 1.0
O5' 0:U2615 4.8 31.4 1.0
NE2 B:GLN230 4.8 29.1 1.0
OP2 0:G2616 4.9 32.4 1.0
N2 0:G2616 4.9 34.6 1.0
OP2 0:G836 4.9 38.9 1.0
C5' 0:U835 5.0 35.0 1.0

Strontium binding site 3 out of 114 in 1vqn

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Strontium binding site 3 out of 114 in the The Structure of Cc-Hpmn and Cca-Phe-Cap-Bio 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 Cc-Hpmn and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Sr9407

b:47.6
occ:1.00
O 0:HOH3021 2.4 34.1 1.0
O6 0:G1491 2.5 43.6 1.0
OP2 0:G1489 2.5 43.7 1.0
O 0:HOH4545 2.6 57.9 1.0
O 0:HOH4228 2.7 42.0 1.0
O 0:HOH6704 2.9 80.0 1.0
O 0:HOH6693 3.3 58.3 1.0
C6 0:G1491 3.6 42.4 1.0
P 0:G1489 3.8 45.2 1.0
O 0:HOH6805 4.1 35.0 1.0
OP1 0:G1489 4.3 49.7 1.0
N7 0:G1491 4.4 41.6 1.0
C5 0:G1491 4.4 42.4 1.0
OP2 0:A1487 4.4 39.3 1.0
O 0:HOH9786 4.5 48.1 1.0
N7 0:G1490 4.7 39.4 1.0
OP1 0:G1453 4.7 43.3 1.0
N1 0:G1491 4.7 41.9 1.0
O5' 0:G1489 4.8 42.7 1.0
OP2 0:G1490 4.8 43.3 1.0
O3' 0:U1488 4.9 48.5 1.0

Strontium binding site 4 out of 114 in 1vqn

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Strontium binding site 4 out of 114 in the The Structure of Cc-Hpmn and Cca-Phe-Cap-Bio 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 Cc-Hpmn and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Sr9408

b:36.7
occ:1.00
OP1 0:A1839 2.4 35.0 1.0
O 0:HOH3956 2.4 54.2 1.0
OP2 0:A1840 2.5 28.9 1.0
OP2 0:U832 2.5 36.5 1.0
O 0:HOH8291 2.6 34.9 1.0
O 0:HOH9635 2.6 29.7 1.0
O 0:HOH9728 2.9 39.4 1.0
P 0:A1840 3.7 33.7 1.0
P 0:U832 3.7 37.3 1.0
P 0:A1839 3.7 33.0 1.0
O 0:HOH6864 3.9 66.9 1.0
OP1 0:A1840 4.0 32.2 1.0
OP1 0:U832 4.1 35.7 1.0
O 0:HOH3257 4.2 35.3 1.0
OP2 0:A1839 4.3 34.8 1.0
O3' 0:U831 4.6 37.0 1.0
O 0:HOH8375 4.6 38.8 1.0
C3' 0:U831 4.7 39.0 1.0
O3' 0:A1839 4.7 35.0 1.0
O3' 0:U1838 4.7 34.4 1.0
O5' 0:A1839 4.7 35.2 1.0
O5' 0:A1840 4.8 32.4 1.0
O5' 0:U832 4.8 38.3 1.0

Strontium binding site 5 out of 114 in 1vqn

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Strontium binding site 5 out of 114 in the The Structure of Cc-Hpmn and Cca-Phe-Cap-Bio 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 Cc-Hpmn and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Sr9410

b:41.8
occ:1.00
O 0:HOH7092 2.4 21.6 1.0
O 0:HOH8437 2.5 26.6 1.0
O 0:HOH3054 2.5 25.0 1.0
OP1 0:G1354 2.6 38.6 1.0
OP2 0:A643 2.8 27.6 1.0
OP1 0:C1353 3.2 47.6 1.0
O3' 0:C1353 3.6 33.1 1.0
P 0:G1354 3.6 32.2 1.0
P 0:A643 3.8 31.2 1.0
OP1 0:A643 3.8 30.7 1.0
P 0:C1353 4.2 46.8 1.0
O5' 0:C1353 4.3 45.6 1.0
O4 0:U904 4.3 28.6 1.0
OP2 0:G1354 4.5 32.5 1.0
OP1 0:G642 4.5 34.8 1.0
N3 0:U904 4.5 30.4 1.0
OP2 0:G642 4.6 34.6 1.0
C5' 0:C1353 4.6 37.9 1.0
C3' 0:C1353 4.6 34.8 1.0
OP2 0:C1353 4.6 44.8 1.0
O5' 0:A643 4.7 27.2 1.0
N1 0:A1355 4.7 32.1 1.0
O5' 0:G1354 4.8 29.6 1.0
P 0:G642 4.8 34.6 1.0
O5' 0:G642 4.9 35.0 1.0
C4 0:U904 4.9 28.8 1.0
O2' 0:A1352 4.9 53.5 1.0
N6 0:A1355 5.0 28.8 1.0

Strontium binding site 6 out of 114 in 1vqn

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Strontium binding site 6 out of 114 in the The Structure of Cc-Hpmn and Cca-Phe-Cap-Bio 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 Cc-Hpmn and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Sr9411

b:43.1
occ:1.00
OP1 0:A1755 2.6 34.5 1.0
O 0:HOH8127 2.7 43.9 1.0
O 0:HOH7641 2.7 47.2 1.0
O 0:HOH7100 2.9 54.0 1.0
O3' 0:A1754 3.5 35.3 1.0
P 0:A1755 3.6 34.1 1.0
C5' 0:A1755 4.6 35.9 1.0
O5' 0:A1755 4.6 36.2 1.0
OP1 0:C1738 4.6 43.4 1.0
OP2 0:A1755 4.7 34.4 1.0
O 0:HOH3636 4.7 50.0 1.0
O 0:HOH7715 4.8 78.0 1.0
OP2 0:C1738 4.8 43.8 1.0
N2 0:G834 4.8 28.7 1.0
C3' 0:A1754 4.9 35.6 1.0
O2' 0:G834 4.9 31.1 1.0

Strontium binding site 7 out of 114 in 1vqn

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Strontium binding site 7 out of 114 in the The Structure of Cc-Hpmn and Cca-Phe-Cap-Bio 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 Cc-Hpmn and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Sr9412

b:45.5
occ:1.00
O C:HOH9150 2.4 48.9 1.0
O 0:HOH8436 2.5 32.0 1.0
O2 0:C893 2.5 33.9 1.0
O 0:HOH6173 2.6 23.8 1.0
O2' 0:C893 2.7 35.3 1.0
C2 0:C893 3.6 30.8 1.0
C2' 0:C893 3.8 31.7 1.0
C1' 0:C893 3.8 32.0 1.0
O 0:HOH6788 3.8 28.3 1.0
O3' 0:C893 4.2 32.5 1.0
N1 0:C893 4.2 31.1 1.0
O 0:HOH4481 4.3 44.4 1.0
N7 0:G892 4.4 29.5 1.0
O C:HOH9215 4.6 43.5 1.0
OP2 0:A895 4.7 40.8 1.0
N3 0:C893 4.7 29.1 1.0
C3' 0:C893 4.7 33.0 1.0
OP2 0:G892 4.7 29.2 1.0
O C:HOH9119 4.7 34.6 1.0
O 0:HOH4982 4.8 38.2 1.0
O C:HOH9256 5.0 53.9 1.0
O 0:HOH6897 5.0 51.5 1.0
C8 0:G892 5.0 29.8 1.0

Strontium binding site 8 out of 114 in 1vqn

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Strontium binding site 8 out of 114 in the The Structure of Cc-Hpmn and Cca-Phe-Cap-Bio 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 Cc-Hpmn and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Sr9413

b:49.1
occ:1.00
O H:ASP10 2.5 49.1 1.0
O 0:HOH5388 2.6 38.3 1.0
O6 0:G1055 2.6 42.2 1.0
O 0:HOH4419 2.7 53.8 1.0
O 0:HOH6846 2.7 42.7 1.0
O H:HOH9509 2.7 40.0 1.0
C H:ASP10 3.7 51.4 1.0
C6 0:G1055 3.7 36.1 1.0
O 0:HOH3883 4.1 39.9 1.0
CB H:ASP10 4.2 55.2 1.0
CG H:LYS11 4.2 52.8 1.0
N7 0:G1055 4.3 36.6 1.0
C5 0:G1055 4.4 36.1 1.0
OD1 H:ASP10 4.5 59.1 1.0
CA H:ASP10 4.5 53.2 1.0
CG H:ASP10 4.6 59.0 1.0
N7 0:G1054 4.6 45.9 1.0
OP2 0:G1054 4.6 40.8 1.0
N H:LYS11 4.7 51.1 1.0
CA H:LYS11 4.8 51.1 1.0
N1 0:G1055 4.9 37.2 1.0
CE H:LYS11 5.0 55.5 1.0

Strontium binding site 9 out of 114 in 1vqn

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Strontium binding site 9 out of 114 in the The Structure of Cc-Hpmn and Cca-Phe-Cap-Bio 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 Cc-Hpmn and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Sr9414

b:57.2
occ:1.00
OP1 0:A183 2.5 50.5 1.0
O M:HOH9441 2.6 45.6 1.0
OP1 0:G147 2.6 40.5 1.0
OD2 M:ASP157 2.6 57.6 1.0
O3' 0:U146 3.4 38.3 1.0
O3' 0:G182 3.5 43.6 1.0
P 0:A183 3.6 44.8 1.0
CG M:ASP157 3.6 54.1 1.0
P 0:G147 3.6 37.4 1.0
OD1 M:ASP157 4.0 53.3 1.0
O 0:HOH7348 4.0 67.3 1.0
C5' 0:G147 4.3 39.2 1.0
O5' 0:G147 4.4 39.1 1.0
OP2 0:A183 4.5 48.4 1.0
O 0:HOH3710 4.7 60.5 1.0
O5' 0:A183 4.7 46.9 1.0
C3' 0:G182 4.7 44.5 1.0
C3' 0:U146 4.7 41.1 1.0
C5' 0:A183 4.8 47.6 1.0
O2' 0:U146 4.8 40.1 1.0
OP2 0:G147 4.9 36.8 1.0
CB M:ASP157 4.9 52.1 1.0
C5' 0:G182 5.0 43.0 1.0

Strontium binding site 10 out of 114 in 1vqn

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Strontium binding site 10 out of 114 in the The Structure of Cc-Hpmn and Cca-Phe-Cap-Bio 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 Cc-Hpmn and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Sr9415

b:56.4
occ:1.00
O 0:HOH4360 2.4 53.5 1.0
O 0:HOH6054 2.5 85.2 1.0
O 0:HOH6676 2.7 51.4 1.0
O 0:HOH7104 2.7 60.7 1.0
O 0:HOH8373 2.8 68.6 1.0
O 0:HOH7383 2.9 67.2 1.0
O 0:HOH8374 3.1 46.1 1.0
O 0:HOH4834 3.8 94.2 1.0
O 0:HOH6699 4.0 91.0 1.0
O 0:HOH4639 4.2 87.9 1.0
O6 0:G2080 4.4 42.2 1.0
OP2 0:C2077 4.4 44.2 1.0
O 0:HOH4278 4.6 41.9 1.0
N6 0:A536 4.8 44.1 1.0
N7 0:G2079 4.8 37.6 1.0

Reference:

T.M.Schmeing, K.S.Huang, S.A.Strobel, T.A.Steitz. An Induced-Fit Mechanism to Promote Peptide Bond Formation and Exclude Hydrolysis of Peptidyl-Trna. Nature V. 438 520 2005.
ISSN: ISSN 0028-0836
PubMed: 16306996
DOI: 10.1038/NATURE04152
Page generated: Wed Dec 16 02:11:20 2020

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