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Strontium in PDB 3i55: Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit

Protein crystallography data

The structure of Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit, PDB code: 3i55 was solved by G.Gurel, G.Blaha, T.A.Steitz, P.B.Moore, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.98 / 3.11
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 211.324, 299.649, 574.241, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 26

Other elements in 3i55:

The structure of Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit also contains other interesting chemical elements:

Magnesium (Mg) 93 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 - 108;

Binding sites:

The binding sites of Strontium atom in the Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit (pdb code 3i55). This binding sites where shown within 5.0 Angstroms radius around Strontium atom.
In total 108 binding sites of Strontium where determined in the Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit, PDB code: 3i55:
Jump to Strontium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Strontium binding site 1 out of 108 in 3i55

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Strontium binding site 1 out of 108 in the Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit


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Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 1 of Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Sr8901

b:78.1
occ:1.00
N7 0:G824 2.7 48.0 1.0
N7 0:G854 2.8 42.2 1.0
O 0:HOH2936 2.8 40.0 1.0
O 0:HOH3123 2.9 0.4 1.0
O 0:HOH8589 2.9 95.1 1.0
O 0:HOH3276 2.9 0.7 1.0
C8 0:G854 3.2 44.3 1.0
C8 0:G824 3.4 49.9 1.0
OP2 0:G854 3.5 45.2 1.0
OP2 0:U823 3.8 56.5 1.0
C5 0:G824 3.9 49.9 1.0
C5 0:G854 4.0 44.1 1.0
OP2 0:G824 4.2 57.1 1.0
OP2 0:C853 4.3 55.8 1.0
O6 0:G824 4.3 52.1 1.0
C6 0:G824 4.5 50.1 1.0
N9 0:G854 4.5 44.4 1.0
O5' 0:G854 4.6 44.7 1.0
N9 0:G824 4.7 50.0 1.0
P 0:G854 4.7 47.4 1.0
O6 0:G854 4.8 45.6 1.0
C6 0:G854 4.8 43.8 1.0
O5' 0:C853 4.9 50.5 1.0
O 0:HOH8143 4.9 89.5 1.0
C5 0:U823 4.9 52.8 1.0
O5' 0:U823 4.9 55.3 1.0
P 0:U823 5.0 56.8 1.0
C4 0:G824 5.0 49.5 1.0
C4 0:G854 5.0 43.9 1.0

Strontium binding site 2 out of 108 in 3i55

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Strontium binding site 2 out of 108 in the Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 2 of Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Sr8902

b:44.9
occ:1.00
OP1 0:G836 2.6 36.8 1.0
OP1 0:U2615 2.7 42.1 1.0
OE1 B:GLN230 2.8 40.8 1.0
O 0:HOH4152 2.9 44.5 1.0
O B:HOH343 3.0 48.7 1.0
O 0:HOH8403 3.2 0.3 1.0
O 0:HOH6446 3.4 96.8 1.0
CD B:GLN230 3.7 41.5 1.0
P 0:U2615 3.9 42.0 1.0
P 0:G836 4.0 41.0 1.0
CB B:GLN230 4.0 43.3 1.0
CG B:GLN230 4.1 42.3 1.0
O 0:HOH3574 4.1 69.4 1.0
OP2 0:U2615 4.4 41.2 1.0
O 0:HOH4803 4.4 40.7 1.0
O3' 0:C2614 4.5 39.5 1.0
C5' 0:G836 4.5 39.4 1.0
CA B:GLN230 4.6 45.2 1.0
O5' 0:G836 4.6 39.4 1.0
O B:GLN230 4.7 44.3 1.0
OP2 0:G836 4.8 40.6 1.0
C3' 0:U835 4.9 37.9 1.0
NE2 B:GLN230 4.9 39.8 1.0
O3' 0:U835 4.9 37.9 1.0
O 0:HOH3980 4.9 97.6 1.0
OP2 0:G2616 5.0 38.9 1.0
N2 0:G2616 5.0 46.2 1.0

Strontium binding site 3 out of 108 in 3i55

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Strontium binding site 3 out of 108 in the Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 3 of Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Sr8903

b:62.1
occ:1.00
O6 0:G1491 2.7 62.2 1.0
OP2 0:G1489 2.8 51.4 1.0
O 0:HOH5539 2.9 54.0 1.0
O 0:HOH8587 3.0 0.9 1.0
O 0:HOH4273 3.0 63.3 1.0
O 0:HOH8191 3.2 62.8 1.0
P 0:G1489 3.7 51.7 1.0
OP1 0:G1489 3.7 53.3 1.0
C6 0:G1491 3.8 61.6 1.0
N7 0:G1491 4.3 61.8 1.0
OP2 0:A1487 4.4 51.8 1.0
C5 0:G1491 4.4 61.5 1.0
O 0:HOH5552 4.4 56.0 1.0
OP2 0:G1490 4.6 55.6 1.0
O5' 0:G1489 4.7 49.0 1.0
N7 0:G1490 4.7 53.7 1.0
OP1 0:G1453 4.8 51.9 1.0
O3' 0:U1488 4.9 53.2 1.0
N1 0:G1491 4.9 61.2 1.0

Strontium binding site 4 out of 108 in 3i55

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Strontium binding site 4 out of 108 in the Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 4 of Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Sr8904

b:65.8
occ:1.00
OP1 0:G1354 2.8 46.1 1.0
O 0:HOH4394 2.8 14.1 1.0
OP2 0:A643 2.8 45.3 1.0
O 0:HOH6104 3.3 48.5 1.0
OP1 0:C1353 3.5 53.2 1.0
O3' 0:C1353 3.8 46.9 1.0
O 0:HOH7247 3.8 67.3 1.0
P 0:G1354 3.8 46.6 1.0
P 0:A643 3.9 44.7 1.0
O5' 0:C1353 4.0 53.5 1.0
OP1 0:A643 4.1 43.9 1.0
C5' 0:C1353 4.2 50.5 1.0
O 0:HOH7482 4.4 0.1 1.0
P 0:C1353 4.4 56.2 1.0
O5' 0:A643 4.5 39.9 1.0
O4 0:U904 4.6 42.7 1.0
C3' 0:C1353 4.6 48.8 1.0
N3 0:U904 4.7 37.7 1.0
OP2 0:G1354 4.8 46.4 1.0
O2' 0:A1352 4.8 62.0 1.0
OP1 0:G642 4.8 43.8 1.0
OP2 0:G642 4.8 43.1 1.0
N6 0:A1355 4.9 39.5 1.0
C4' 0:C1353 4.9 49.7 1.0
N1 0:A1355 4.9 39.3 1.0
NH2 L:ARG8 4.9 48.0 1.0
O5' 0:G1354 5.0 45.6 1.0

Strontium binding site 5 out of 108 in 3i55

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Strontium binding site 5 out of 108 in the Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 5 of Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Sr8905

b:78.9
occ:1.00
OP1 0:A1755 2.8 49.4 1.0
O 0:HOH6927 3.1 70.4 1.0
O 0:HOH7509 3.1 0.0 1.0
O 0:HOH6117 3.3 0.4 1.0
O3' 0:A1754 3.9 48.0 1.0
P 0:A1755 3.9 50.9 1.0
O 0:HOH7035 4.0 54.6 1.0
N2 0:G834 4.1 42.6 1.0
O 0:HOH6844 4.4 50.0 1.0
OP1 0:C1738 4.6 49.0 1.0
N3 0:G834 4.6 40.5 1.0
OP2 0:C1738 4.7 48.9 1.0
O2' 0:G834 4.8 36.9 1.0
O2 0:C849 4.8 53.7 1.0
C2 0:G834 4.8 42.0 1.0
OP2 0:A1755 4.9 50.7 1.0

Strontium binding site 6 out of 108 in 3i55

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Strontium binding site 6 out of 108 in the Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 6 of Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Sr8906

b:64.4
occ:1.00
O2' 0:C893 2.8 43.6 1.0
O 0:HOH7378 2.9 70.3 1.0
O2 0:C893 2.9 47.2 1.0
O 0:HOH5674 3.0 40.6 1.0
O 0:HOH4776 3.2 89.6 1.0
O 0:HOH3970 3.6 34.4 1.0
C2 0:C893 3.9 43.8 1.0
O 0:HOH6325 3.9 38.9 1.0
C2' 0:C893 4.0 41.3 1.0
C1' 0:C893 4.1 41.6 1.0
O 0:HOH3095 4.2 47.5 1.0
O3' 0:C893 4.3 38.8 1.0
N7 0:G892 4.3 29.6 1.0
N1 0:C893 4.4 42.8 1.0
OP2 0:G892 4.6 42.3 1.0
O 0:HOH3250 4.8 66.1 1.0
C3' 0:C893 4.8 40.7 1.0
NZ 1:LYS53 4.8 49.0 1.0
N3 0:C893 4.8 41.5 1.0
O 0:HOH5824 4.9 86.4 1.0
O 0:HOH3602 4.9 16.6 1.0
C8 0:G892 4.9 31.5 1.0
OP2 0:A895 5.0 40.6 1.0

Strontium binding site 7 out of 108 in 3i55

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Strontium binding site 7 out of 108 in the Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 7 of Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Sr8907

b:59.0
occ:1.00
O 0:HOH5761 3.0 61.1 1.0
O 0:HOH8389 3.0 68.9 1.0
O6 0:G1055 3.1 59.1 1.0
O H:HOH714 3.1 0.5 1.0
O H:ASP13 3.1 65.0 1.0
O 0:HOH3682 3.2 90.5 1.0
O 0:HOH6511 3.4 58.4 1.0
O 0:HOH8683 3.6 94.2 1.0
C H:ASP13 3.9 63.4 1.0
CB H:ASP13 3.9 64.8 1.0
C6 0:G1055 4.2 57.4 1.0
OP2 0:G1054 4.5 52.0 1.0
N7 0:G1055 4.5 56.0 1.0
CA H:ASP13 4.5 64.3 1.0
N7 0:G1054 4.6 58.2 1.0
CG H:ASP13 4.6 66.0 1.0
N H:LYS14 4.7 61.8 1.0
C5 0:G1055 4.7 56.4 1.0
CD H:LYS14 4.8 55.1 1.0
O 0:HOH7301 4.8 33.2 1.0
CA H:LYS14 4.9 59.9 1.0
OD1 H:ASP13 5.0 67.0 1.0
OP2 0:G1053 5.0 50.5 1.0

Strontium binding site 8 out of 108 in 3i55

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Strontium binding site 8 out of 108 in the Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 8 of Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Sr8908

b:0.6
occ:1.00
O 0:HOH8265 2.7 34.5 1.0
OD2 M:ASP157 2.8 67.6 1.0
OP1 0:G147 3.1 53.0 1.0
O3' 0:U146 3.2 51.0 1.0
OP1 0:A183 3.3 53.2 1.0
O 0:HOH7525 3.4 55.1 1.0
CG M:ASP157 3.7 67.3 1.0
P 0:G147 3.8 51.5 1.0
OD1 M:ASP157 3.8 68.5 1.0
O M:HOH5483 3.9 36.0 1.0
O3' 0:G182 4.2 52.7 1.0
P 0:A183 4.4 54.1 1.0
C3' 0:U146 4.4 52.0 1.0
C4' 0:U146 4.4 52.3 1.0
C5' 0:G147 4.7 51.2 1.0
O 0:HOH6495 4.7 63.9 1.0
O2' 0:U146 4.8 49.9 1.0
O M:HOH2174 4.8 49.7 1.0
O5' 0:G147 4.8 52.1 1.0
C5' 0:U146 4.8 52.8 1.0
OP2 0:G147 4.9 50.6 1.0
C5' 0:A183 4.9 53.0 1.0

Strontium binding site 9 out of 108 in 3i55

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Strontium binding site 9 out of 108 in the Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 9 of Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Sr8909

b:0.5
occ:1.00
O 0:HOH7824 2.9 70.0 1.0
O 0:HOH4603 3.1 66.2 1.0
O 0:HOH8329 3.3 0.0 1.0
O 0:HOH6121 3.3 0.9 1.0
O 0:HOH5508 3.3 0.1 1.0
O 0:HOH6543 3.6 0.7 1.0
O 0:HOH8886 3.6 0.4 1.0
O 0:HOH5546 4.3 70.7 1.0
O 0:HOH7825 4.3 0.0 1.0
OP2 0:C2077 4.3 49.7 1.0
O 0:HOH6103 4.4 96.8 1.0
O 0:HOH8680 4.6 0.9 1.0
O6 0:G2080 4.7 52.0 1.0
N7 0:G2079 4.8 44.1 1.0
OP2 0:U2078 5.0 47.7 1.0

Strontium binding site 10 out of 108 in 3i55

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Strontium binding site 10 out of 108 in the Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 10 of Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Sr8910

b:0.1
occ:1.00
OP1 0:G2585 2.7 50.5 1.0
O4 0:U1749 2.8 51.2 1.0
OP2 0:U1748 2.9 44.3 1.0
OP2 0:A1747 3.0 45.9 1.0
OP2 0:G2585 3.4 51.4 1.0
O 0:HOH8378 3.4 0.7 1.0
P 0:G2585 3.5 50.4 1.0
C4 0:U1749 3.5 51.1 1.0
O 0:HOH5256 3.7 0.7 1.0
OP2 0:U2586 3.8 44.4 1.0
C5 0:U1749 3.8 51.5 1.0
O 0:HOH5622 3.8 56.4 1.0
P 0:U1748 4.2 46.8 1.0
O5' 0:G2585 4.2 47.3 1.0
O 0:HOH7731 4.3 95.7 1.0
O 0:HOH3830 4.4 0.9 1.0
OP1 0:G1751 4.4 39.8 1.0
P 0:A1747 4.5 45.3 1.0
SR 0:SR8982 4.5 0.0 1.0
OP1 0:U1748 4.5 44.1 1.0
P 0:U2586 4.6 44.4 1.0
OP1 0:U2586 4.7 44.7 1.0
O 0:HOH7944 4.7 65.5 1.0
N3 0:U1749 4.7 51.4 1.0
C5' 0:G2585 4.7 44.4 1.0
O3' 0:G2584 4.8 48.2 1.0
O 0:HOH4869 5.0 0.3 1.0

Reference:

G.Gurel, G.Blaha, T.A.Steitz, P.B.Moore. Structures of Triacetyloleandomycin and Mycalamide A Bind to the Large Ribosomal Subunit of Haloarcula Marismortui. Antimicrob.Agents Chemother. V. 53 5010 2009.
ISSN: ISSN 0066-4804
PubMed: 19738021
DOI: 10.1128/AAC.00817-09
Page generated: Wed Dec 16 02:22:04 2020

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