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Magnesium in PDB 6ys5: Acinetobacter Baumannii Ribosome-Amikacin Complex - 30S Subunit Head

Magnesium Binding Sites:

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>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Magnesium atom in the Acinetobacter Baumannii Ribosome-Amikacin Complex - 30S Subunit Head (pdb code 6ys5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 24 binding sites of Magnesium where determined in the Acinetobacter Baumannii Ribosome-Amikacin Complex - 30S Subunit Head, PDB code: 6ys5:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 24 in 6ys5

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Magnesium binding site 1 out of 24 in the Acinetobacter Baumannii Ribosome-Amikacin Complex - 30S Subunit Head


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Acinetobacter Baumannii Ribosome-Amikacin Complex - 30S Subunit Head within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Mg1601

b:20.0
occ:1.00
 OP1 3:C931 2.4 19.6 1.0
P 3:C931 3.8 19.6 1.0
OP2 3:U1342 3.9 18.6 1.0
C5' 3:C931 4.0 19.6 1.0
OP1 3:U1342 4.2 18.6 1.0
O5' 3:C931 4.3 19.6 1.0
P 3:U1342 4.4 18.6 1.0
O3' 3:G930 4.5 26.5 1.0
O5' 3:U1342 4.6 18.6 1.0
OP2 3:C931 4.9 19.6 1.0
C2' 3:U1342 4.9 18.6 1.0

Magnesium binding site 2 out of 24 in 6ys5

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Magnesium binding site 2 out of 24 in the Acinetobacter Baumannii Ribosome-Amikacin Complex - 30S Subunit Head


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Acinetobacter Baumannii Ribosome-Amikacin Complex - 30S Subunit Head within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Mg1602

b:17.3
occ:1.00
 O o:LEU60 3.9 15.3 1.0
O o:VAL58 4.0 15.6 1.0
O2 3:C977 4.2 21.4 1.0
OP1 3:A1357 4.3 21.4 1.0
O6 3:G1358 4.4 21.4 1.0
NE o:ARG61 4.5 12.7 1.0
O3' 3:C1356 4.5 21.4 1.0
N7 3:A1357 4.5 21.4 1.0
N3 3:C977 4.5 21.4 1.0
C2 3:C977 4.8 21.4 1.0
N4 3:C976 4.9 21.4 1.0
C o:LEU60 4.9 15.3 1.0
CD o:ARG61 5.0 12.7 1.0

Magnesium binding site 3 out of 24 in 6ys5

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Magnesium binding site 3 out of 24 in the Acinetobacter Baumannii Ribosome-Amikacin Complex - 30S Subunit Head


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Acinetobacter Baumannii Ribosome-Amikacin Complex - 30S Subunit Head within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Mg1603

b:20.3
occ:1.00
 OP1 3:U1046 3.6 18.4 1.0
OP1 3:G1045 4.0 22.6 1.0
OP2 3:A1201 4.3 18.5 1.0
O o:ALA2 4.4 13.2 1.0
OP1 3:C1200 4.5 17.1 1.0
P 3:U1046 4.7 18.4 1.0
OP2 3:G1045 4.7 22.6 1.0
OP2 3:U1046 4.7 18.4 1.0
P 3:G1045 4.8 22.6 1.0
OP1 3:A1201 4.9 18.5 1.0

Magnesium binding site 4 out of 24 in 6ys5

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Magnesium binding site 4 out of 24 in the Acinetobacter Baumannii Ribosome-Amikacin Complex - 30S Subunit Head


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Acinetobacter Baumannii Ribosome-Amikacin Complex - 30S Subunit Head within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Mg1604

b:20.0
occ:1.00
 OP2 3:C1051 2.3 19.5 1.0
OP2 3:A1194 2.4 16.2 1.0
P 3:C1051 3.6 19.5 1.0
P 3:A1194 3.7 16.2 1.0
O3' 3:G1050 3.9 17.8 1.0
O3' 3:A1193 4.2 23.1 1.0
O4 3:U1196 4.3 21.4 1.0
N7 3:G1195 4.3 15.6 1.0
O2' 3:G1050 4.4 17.8 1.0
OP1 3:A1194 4.4 16.2 1.0
OP1 3:C1051 4.6 19.5 1.0
O5' 3:C1051 4.6 19.5 1.0
OP2 3:G1195 4.8 15.6 1.0
O5' 3:A1194 4.9 16.2 1.0
C5' 3:C1051 4.9 19.5 1.0
C8 3:G1195 5.0 15.6 1.0
N7 3:A1194 5.0 16.2 1.0

Magnesium binding site 5 out of 24 in 6ys5

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Magnesium binding site 5 out of 24 in the Acinetobacter Baumannii Ribosome-Amikacin Complex - 30S Subunit Head


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Acinetobacter Baumannii Ribosome-Amikacin Complex - 30S Subunit Head within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Mg1605

b:17.3
occ:1.00
 OP1 3:A1194 2.1 16.2 1.0
OP2 3:G1195 2.4 15.6 1.0
OP1 3:C1051 2.5 19.5 1.0
P 3:G1195 3.4 15.6 1.0
P 3:A1194 3.6 16.2 1.0
OP1 3:G1195 3.7 15.6 1.0
P 3:C1051 3.7 19.5 1.0
O2' 3:A1193 3.8 23.1 1.0
OP2 3:C1051 4.0 19.5 1.0
O3' 3:A1194 4.1 16.2 1.0
C5' 3:A1194 4.2 16.2 1.0
OP2 3:A1194 4.2 16.2 1.0
O5' 3:A1194 4.4 16.2 1.0
O3' 3:A1193 4.5 23.1 1.0
O5' 3:C1051 4.5 19.5 1.0
C3' 3:A1194 4.6 16.2 1.0
C2' 3:A1193 4.7 23.1 1.0
C3' 3:A1193 4.7 23.1 1.0
O5' 3:G1195 4.7 15.6 1.0
C4' 3:A1194 4.9 16.2 1.0
O3' 3:G1050 4.9 17.8 1.0

Magnesium binding site 6 out of 24 in 6ys5

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Magnesium binding site 6 out of 24 in the Acinetobacter Baumannii Ribosome-Amikacin Complex - 30S Subunit Head


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Acinetobacter Baumannii Ribosome-Amikacin Complex - 30S Subunit Head within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Mg1606

b:14.3
occ:1.00
 OP1 3:U1196 2.0 21.4 1.0
OP1 3:A961 2.2 17.0 1.0
P 3:U1196 3.2 21.4 1.0
P 3:A961 3.6 17.0 1.0
OP2 3:U1196 3.7 21.4 1.0
O3' 3:G1195 4.0 15.6 1.0
O3' 3:G960 4.1 16.3 1.0
O5' 3:U1196 4.4 21.4 1.0
C5' 3:A961 4.4 17.0 1.0
O5' 3:A961 4.5 17.0 1.0
OP2 3:A961 4.6 17.0 1.0
OP1 3:G1195 4.6 15.6 1.0
OP2 3:U962 4.7 22.7 1.0

Magnesium binding site 7 out of 24 in 6ys5

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Magnesium binding site 7 out of 24 in the Acinetobacter Baumannii Ribosome-Amikacin Complex - 30S Subunit Head


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Acinetobacter Baumannii Ribosome-Amikacin Complex - 30S Subunit Head within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Mg1607

b:11.9
occ:1.00
 O4 3:U1196 2.7 21.4 1.0
O6 3:G1055 2.9 19.6 1.0
O6 3:G1195 3.4 15.6 1.0
N2 3:G1050 3.4 17.8 1.0
N4 3:C1056 3.5 14.2 1.0
C4 3:U1196 3.7 21.4 1.0
N3 3:U1196 3.9 21.4 1.0
C6 3:G1055 4.0 19.6 1.0
C2 3:G1050 4.1 17.8 1.0
C6 3:G1195 4.3 15.6 1.0
OP2 3:G1054 4.3 9.1 1.0
N3 3:G1050 4.4 17.8 1.0
N7 3:G1055 4.5 19.6 1.0
C4 3:C1056 4.5 14.2 1.0
C5 3:G1055 4.7 19.6 1.0
N1 3:G1050 4.9 17.8 1.0
N1 3:G1195 4.9 15.6 1.0
N3 3:C1056 5.0 14.2 1.0

Magnesium binding site 8 out of 24 in 6ys5

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Magnesium binding site 8 out of 24 in the Acinetobacter Baumannii Ribosome-Amikacin Complex - 30S Subunit Head


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Acinetobacter Baumannii Ribosome-Amikacin Complex - 30S Subunit Head within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Mg1608

b:25.1
occ:1.00
 O6 3:G1105 1.9 22.4 1.0
OP2 3:U1092 2.5 35.8 1.0
C6 3:G1105 3.0 22.4 1.0
N1 3:G1105 3.7 22.4 1.0
P 3:U1092 3.9 35.8 1.0
C5 3:G1105 4.2 22.4 1.0
C5' 3:U1092 4.5 35.8 1.0
N3 3:C1106 4.5 19.8 1.0
O5' 3:U1092 4.5 35.8 1.0
O2' 3:G1091 4.6 30.9 1.0
O3' 3:G1091 4.6 30.9 1.0
OP2 3:C1093 4.7 44.8 1.0
N7 3:G1105 4.7 22.4 1.0
N4 3:C1104 4.7 25.0 1.0
C4 3:C1106 4.7 19.8 1.0
C2 3:C1106 4.8 19.8 1.0
OP1 3:U1092 4.9 35.8 1.0
N4 3:C1106 5.0 19.8 1.0

Magnesium binding site 9 out of 24 in 6ys5

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Magnesium binding site 9 out of 24 in the Acinetobacter Baumannii Ribosome-Amikacin Complex - 30S Subunit Head


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Acinetobacter Baumannii Ribosome-Amikacin Complex - 30S Subunit Head within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Mg1609

b:17.8
occ:1.00
 OP2 3:A1107 2.4 23.4 1.0
P 3:A1107 3.6 23.4 1.0
O2 3:C1186 3.9 15.2 1.0
O5' 3:A1107 3.9 23.4 1.0
N7 3:A1108 4.0 21.5 1.0
OP1 3:A1107 4.4 23.4 1.0
OP2 3:C1106 4.4 19.8 1.0
N6 3:A1108 4.4 21.5 1.0
N7 3:A1107 4.6 23.4 1.0
C8 3:A1107 4.6 23.4 1.0
OP1 3:C1106 4.6 19.8 1.0
OP2 3:A1108 4.7 21.5 1.0
C2 3:C1186 4.8 15.2 1.0
N3 3:C1186 4.8 15.2 1.0
N4 3:C1109 4.8 22.5 1.0
O3' 3:C1106 4.9 19.8 1.0
C5 3:A1108 4.9 21.5 1.0
C8 3:A1108 4.9 21.5 1.0
P 3:C1106 5.0 19.8 1.0

Magnesium binding site 10 out of 24 in 6ys5

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Magnesium binding site 10 out of 24 in the Acinetobacter Baumannii Ribosome-Amikacin Complex - 30S Subunit Head


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Acinetobacter Baumannii Ribosome-Amikacin Complex - 30S Subunit Head within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Mg1610

b:30.6
occ:1.00
 N7 3:G1382 3.5 24.6 1.0
O6 3:G1382 3.9 24.6 1.0
O6 3:G1383 3.9 31.4 1.0
N7 3:G1383 3.9 31.4 1.0
C5 3:G1382 4.1 24.6 1.0
C6 3:G1382 4.2 24.6 1.0
C8 3:G1382 4.4 24.6 1.0
C6 3:G1383 4.6 31.4 1.0
C5 3:G1383 4.7 31.4 1.0
C8 3:G1383 5.0 31.4 1.0

Reference:

D.Nicholson, T.A.Edwards, A.J.O'neill, N.A.Ranson. Structure of the 70S Ribosome From the Human Pathogen Acinetobacter Baumannii in Complex with Clinically Relevant Antibiotics. Structure V. 28 1087 2020.
ISSN: ISSN 0969-2126
PubMed: 32857965
DOI: 10.1016/J.STR.2020.08.004
Page generated: Wed Oct 2 01:05:33 2024

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