Magnesium in PDB 7zhg: High-Resolution Cryo-Em Structure of Pyrococcus Abyssi 30S Ribosomal Subunit Bound to Mrna and Initiator Trna Anticodon Stem-Loop

Other elements in 7zhg:

The structure of High-Resolution Cryo-Em Structure of Pyrococcus Abyssi 30S Ribosomal Subunit Bound to Mrna and Initiator Trna Anticodon Stem-Loop also contains other interesting chemical elements:

Zinc (Zn) 6 atoms

Magnesium 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;

Binding sites:

The binding sites of Magnesium atom in the High-Resolution Cryo-Em Structure of Pyrococcus Abyssi 30S Ribosomal Subunit Bound to Mrna and Initiator Trna Anticodon Stem-Loop (pdb code 7zhg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 90 binding sites of Magnesium where determined in the High-Resolution Cryo-Em Structure of Pyrococcus Abyssi 30S Ribosomal Subunit Bound to Mrna and Initiator Trna Anticodon Stem-Loop, PDB code: 7zhg:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 90 in 7zhg

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Magnesium binding site 1 out of 90 in the High-Resolution Cryo-Em Structure of Pyrococcus Abyssi 30S Ribosomal Subunit Bound to Mrna and Initiator Trna Anticodon Stem-Loop


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of High-Resolution Cryo-Em Structure of Pyrococcus Abyssi 30S Ribosomal Subunit Bound to Mrna and Initiator Trna Anticodon Stem-Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1601

b:12.5
occ:1.00
 O 2:HOH2148 2.0 10.6 1.0
O F:HOH444 2.3 12.9 1.0
O 2:HOH2955 2.4 10.1 1.0
O 2:HOH3397 2.4 13.6 1.0
O 2:HOH3396 2.4 14.9 1.0
O 2:HOH2380 2.5 10.1 1.0
N7 2:G1042 4.1 12.6 1.0
OP1 2:G1044 4.2 12.6 1.0
OP2 2:G1044 4.4 12.6 1.0
O 2:HOH1708 4.6 9.8 1.0
O6 2:G1042 4.6 12.6 1.0
P 2:G1044 4.7 12.6 1.0
C5 2:G1042 4.8 12.6 1.0
C8 2:G1042 4.9 12.6 1.0
C6 2:G1042 5.0 12.6 1.0

Magnesium binding site 2 out of 90 in 7zhg

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Magnesium binding site 2 out of 90 in the High-Resolution Cryo-Em Structure of Pyrococcus Abyssi 30S Ribosomal Subunit Bound to Mrna and Initiator Trna Anticodon Stem-Loop


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of High-Resolution Cryo-Em Structure of Pyrococcus Abyssi 30S Ribosomal Subunit Bound to Mrna and Initiator Trna Anticodon Stem-Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1602

b:10.5
occ:1.00
 O 2:HOH3063 2.1 12.6 1.0
OP2 2:A1370 2.1 12.6 1.0
O 2:HOH1951 2.1 8.8 1.0
O 2:HOH2183 2.3 10.6 1.0
O 2:HOH3349 2.4 12.2 1.0
O 2:HOH2271 2.6 10.8 1.0
P 2:A1370 3.5 12.6 1.0
O5' 2:A1370 4.0 12.6 1.0
OP1 2:G22 4.1 12.6 1.0
OP1 2:A1370 4.2 12.6 1.0
C8 2:A1370 4.4 12.6 1.0
O 2:HOH2312 4.5 9.0 1.0
OP2 2:C1369 4.5 12.6 1.0
O3' 2:C1369 4.6 12.6 1.0
O 2:HOH2673 4.7 11.8 1.0
OP1 2:C1369 4.7 12.6 1.0
C3' 2:C1369 4.8 12.6 1.0
O3' 2:U21 4.8 12.6 1.0
O 2:HOH3377 4.9 12.3 1.0
C2' 2:A1370 4.9 12.6 1.0
N7 2:A1370 4.9 12.6 1.0
P 2:C1369 4.9 12.6 1.0

Magnesium binding site 3 out of 90 in 7zhg

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Magnesium binding site 3 out of 90 in the High-Resolution Cryo-Em Structure of Pyrococcus Abyssi 30S Ribosomal Subunit Bound to Mrna and Initiator Trna Anticodon Stem-Loop


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of High-Resolution Cryo-Em Structure of Pyrococcus Abyssi 30S Ribosomal Subunit Bound to Mrna and Initiator Trna Anticodon Stem-Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1603

b:12.8
occ:1.00
 O 2:HOH2784 2.0 13.3 1.0
O 2:HOH2613 2.0 10.7 1.0
OP1 2:A949 2.1 9.1 1.0
O 2:HOH2319 2.3 11.5 1.0
OP2 2:A950 2.4 12.8 1.0
O 2:HOH2864 2.5 13.3 1.0
P 2:A949 3.2 9.1 1.0
OP2 2:A949 3.5 9.1 1.0
P 2:A950 3.8 12.8 1.0
O 2:HOH3133 4.2 11.8 1.0
O5' 2:A949 4.3 9.1 1.0
O2 2:C1336 4.3 11.1 1.0
O3' 2:G948 4.4 13.6 1.0
C5' 2:A949 4.4 9.1 1.0
O3' 2:A949 4.5 9.1 1.0
C3' 2:A949 4.5 9.1 1.0
OP1 2:A950 4.6 12.8 1.0
C2' 2:G948 4.6 13.6 1.0
O2' 2:G948 4.7 13.6 1.0
N3 2:A949 4.9 9.1 1.0
C3' 2:G948 4.9 13.6 1.0
C5' 2:A950 4.9 12.8 1.0
O5' 2:A950 4.9 12.8 1.0
C2 2:A949 5.0 9.1 1.0

Magnesium binding site 4 out of 90 in 7zhg

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Magnesium binding site 4 out of 90 in the High-Resolution Cryo-Em Structure of Pyrococcus Abyssi 30S Ribosomal Subunit Bound to Mrna and Initiator Trna Anticodon Stem-Loop


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of High-Resolution Cryo-Em Structure of Pyrococcus Abyssi 30S Ribosomal Subunit Bound to Mrna and Initiator Trna Anticodon Stem-Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1604

b:9.7
occ:1.00
 OP1 2:U1198 2.0 10.1 1.0
O 2:HOH2607 2.1 10.8 1.0
O 2:HOH2813 2.3 10.4 1.0
O 2:HOH3328 2.3 11.5 1.0
O 2:HOH2145 2.4 10.8 1.0
O 2:HOH2230 2.5 9.8 1.0
P 2:U1198 3.3 10.1 1.0
OP2 2:U1198 3.9 10.1 1.0
O2' 2:C1197 4.1 10.3 1.0
O3' 2:C1197 4.2 10.3 1.0
O 2:HOH2837 4.3 12.8 1.0
C2' 2:C1197 4.4 10.3 1.0
OP2 2:C924 4.4 12.6 1.0
O5' 2:U1198 4.4 10.1 1.0
O 2:HOH1802 4.6 13.2 1.0
OP1 2:G923 4.6 11.0 1.0
N7 2:A949 4.6 9.1 1.0
O 2:HOH3262 4.7 11.9 1.0
N2 2:G947 4.7 9.3 1.0
N6 2:A949 4.7 9.1 1.0
O 2:HOH3065 4.8 11.0 1.0
C3' 2:C1197 4.8 10.3 1.0

Magnesium binding site 5 out of 90 in 7zhg

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Magnesium binding site 5 out of 90 in the High-Resolution Cryo-Em Structure of Pyrococcus Abyssi 30S Ribosomal Subunit Bound to Mrna and Initiator Trna Anticodon Stem-Loop


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of High-Resolution Cryo-Em Structure of Pyrococcus Abyssi 30S Ribosomal Subunit Bound to Mrna and Initiator Trna Anticodon Stem-Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1605

b:11.6
occ:1.00
 O 2:HOH2122 2.0 8.9 1.0
O6 2:G1196 2.2 13.3 1.0
OP2 2:C952 2.2 13.8 1.0
O 2:HOH2700 2.3 11.1 1.0
O4 2:U953 2.5 13.8 1.0
OP1 2:C951 2.6 13.4 1.0
P 2:C952 3.3 13.8 1.0
C6 2:G1196 3.3 13.3 1.0
OP1 2:C952 3.4 13.8 1.0
C4 2:U953 3.5 13.8 1.0
P 2:C951 3.9 13.4 1.0
C5 2:U953 3.9 13.8 1.0
O6 2:G1195 4.1 11.0 1.0
C5 2:G1196 4.2 13.3 1.0
N1 2:G1196 4.3 13.3 1.0
N3 2:C954 4.3 11.9 1.0
N4 2:C1197 4.3 10.3 1.0
O2 2:C954 4.3 11.9 1.0
O5' 2:C951 4.4 13.4 1.0
O3' 2:C951 4.4 13.4 1.0
O5' 2:C952 4.4 13.8 1.0
N7 2:G1196 4.5 13.3 1.0
C5' 2:C951 4.5 13.4 1.0
OP2 2:C951 4.6 13.4 1.0
C2 2:C954 4.6 11.9 1.0
N3 2:U953 4.7 13.8 1.0
C3' 2:C951 5.0 13.4 1.0

Magnesium binding site 6 out of 90 in 7zhg

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Magnesium binding site 6 out of 90 in the High-Resolution Cryo-Em Structure of Pyrococcus Abyssi 30S Ribosomal Subunit Bound to Mrna and Initiator Trna Anticodon Stem-Loop


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of High-Resolution Cryo-Em Structure of Pyrococcus Abyssi 30S Ribosomal Subunit Bound to Mrna and Initiator Trna Anticodon Stem-Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1606

b:14.6
occ:1.00
 O 2:HOH3359 1.9 12.8 1.0
O 2:HOH2269 2.0 11.7 1.0
O 2:HOH1904 2.1 13.5 1.0
O 2:HOH3369 2.7 13.2 1.0
O 2:HOH2737 2.8 12.4 1.0
O 2:HOH1856 2.8 12.9 1.0
O 2:HOH2394 3.6 13.3 1.0
O 2:HOH2046 3.8 11.1 1.0
O 2:HOH2410 4.1 11.7 1.0
N7 2:OMG934 4.2 10.6 1.0
O 2:HOH2145 4.3 10.8 1.0
O 2:HOH2185 4.4 11.2 1.0
O 2:HOH2511 4.5 13.4 1.0
OP1 2:G925 4.6 11.7 1.0
OP2 2:OMG934 4.7 10.6 1.0
OP2 2:G925 4.7 11.7 1.0
OP1 2:U933 4.8 11.6 1.0
C8 2:OMG934 4.9 10.6 1.0
OP1 2:C924 5.0 12.6 1.0

Magnesium binding site 7 out of 90 in 7zhg

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Magnesium binding site 7 out of 90 in the High-Resolution Cryo-Em Structure of Pyrococcus Abyssi 30S Ribosomal Subunit Bound to Mrna and Initiator Trna Anticodon Stem-Loop


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of High-Resolution Cryo-Em Structure of Pyrococcus Abyssi 30S Ribosomal Subunit Bound to Mrna and Initiator Trna Anticodon Stem-Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1607

b:10.7
occ:1.00
 OP2 2:A909 1.9 8.6 1.0
O 2:HOH2422 1.9 13.6 1.0
O 2:HOH2585 2.0 13.9 1.0
O 2:HOH3035 2.1 12.2 1.0
O 2:HOH2366 2.1 11.4 1.0
O 2:HOH1812 3.0 10.3 1.0
P 2:A909 3.3 8.6 1.0
O5' 2:A909 3.9 8.6 1.0
OP1 2:A909 4.1 8.6 1.0
O3' 2:C908 4.4 8.5 1.0
O 2:HOH2520 4.5 8.6 1.0
N7 2:A910 4.6 9.7 1.0
C3' 2:C908 4.7 8.5 1.0
N7 2:G911 4.8 12.6 1.0
OP2 2:A910 4.9 9.7 1.0
O6 2:G911 4.9 12.6 1.0
C8 2:A909 5.0 8.6 1.0

Magnesium binding site 8 out of 90 in 7zhg

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Magnesium binding site 8 out of 90 in the High-Resolution Cryo-Em Structure of Pyrococcus Abyssi 30S Ribosomal Subunit Bound to Mrna and Initiator Trna Anticodon Stem-Loop


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of High-Resolution Cryo-Em Structure of Pyrococcus Abyssi 30S Ribosomal Subunit Bound to Mrna and Initiator Trna Anticodon Stem-Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1608

b:7.7
occ:1.00
 O 2:HOH3195 2.0 9.0 1.0
OP1 2:G544 2.0 12.2 1.0
OP2 2:C542 2.3 12.6 1.0
O 2:HOH2868 2.4 9.3 1.0
O 2:HOH2248 2.6 7.4 1.0
O 2:HOH1804 2.7 7.8 1.0
P 2:G544 3.2 12.2 1.0
P 2:C542 3.5 12.6 1.0
O3' 2:G543 3.6 12.6 1.0
O3' 2:G541 3.6 12.6 1.0
OP2 2:G544 3.8 12.2 1.0
O 2:HOH2089 4.0 11.1 1.0
O 2:HOH3290 4.1 11.8 1.0
O 2:HOH2549 4.2 12.2 1.0
OP1 2:C542 4.4 12.6 1.0
O2' 2:G541 4.5 12.6 1.0
OP1 2:OMU787 4.5 12.6 1.0
O5' 2:G544 4.5 12.2 1.0
O 2:HOH3383 4.5 11.7 1.0
O5' 2:C542 4.6 12.6 1.0
O 2:HOH2796 4.7 12.2 1.0
C5' 2:G788 4.8 12.8 1.0
C5' 2:C542 4.9 12.6 1.0
C3' 2:G541 4.9 12.6 1.0
C3' 2:G543 4.9 12.6 1.0
C5' 2:G544 4.9 12.2 1.0
C4' 2:G788 4.9 12.8 1.0

Magnesium binding site 9 out of 90 in 7zhg

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Magnesium binding site 9 out of 90 in the High-Resolution Cryo-Em Structure of Pyrococcus Abyssi 30S Ribosomal Subunit Bound to Mrna and Initiator Trna Anticodon Stem-Loop


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of High-Resolution Cryo-Em Structure of Pyrococcus Abyssi 30S Ribosomal Subunit Bound to Mrna and Initiator Trna Anticodon Stem-Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1609

b:11.3
occ:1.00
 O 2:HOH2105 2.1 9.3 1.0
OP1 2:C1316 2.2 9.1 1.0
O 2:HOH2794 2.3 8.8 1.0
OP2 2:A907 2.4 10.0 1.0
O 2:HOH3032 2.4 13.0 1.0
O K:HOH305 2.5 7.9 1.0
P 2:C1316 3.4 9.1 1.0
P 2:A907 3.6 10.0 1.0
O3' 2:U906 3.8 10.4 1.0
OP2 2:C1316 3.9 9.1 1.0
O5' 2:C1316 3.9 9.1 1.0
O 2:HOH2644 4.0 10.3 1.0
OP2 2:C1317 4.2 12.6 1.0
OH K:TYR134 4.4 10.7 1.0
C5' 2:C1316 4.4 9.1 1.0
OP1 2:A907 4.5 10.0 1.0
O3' 2:U1315 4.7 9.2 1.0
OP1 2:C908 4.8 8.5 1.0
O5' 2:A907 4.8 10.0 1.0
C5' 2:A907 4.9 10.0 1.0

Magnesium binding site 10 out of 90 in 7zhg

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Magnesium binding site 10 out of 90 in the High-Resolution Cryo-Em Structure of Pyrococcus Abyssi 30S Ribosomal Subunit Bound to Mrna and Initiator Trna Anticodon Stem-Loop


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of High-Resolution Cryo-Em Structure of Pyrococcus Abyssi 30S Ribosomal Subunit Bound to Mrna and Initiator Trna Anticodon Stem-Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1610

b:10.1
occ:1.00
 O 2:HOH3386 2.2 10.0 1.0
O 0:HOH113 2.2 8.5 1.0
O 2:HOH2454 2.2 7.3 1.0
O 2:HOH2397 2.3 6.7 1.0
O 2:HOH2082 2.4 7.9 1.0
O 2:HOH1946 2.8 8.3 1.0
O 2:HOH2590 3.8 11.1 1.0
O 2:HOH2762 3.9 8.0 1.0
O 2:HOH2059 4.0 10.3 1.0
N7 2:G887 4.2 12.6 1.0
O6 2:G887 4.3 12.6 1.0
O 2:HOH2469 4.4 10.9 1.0
O2' 2:OMU20 4.5 12.6 1.0
O 2:HOH2697 4.6 9.0 1.0
N7 2:G888 4.6 12.6 1.0
C5 2:G887 4.7 12.6 1.0
C6 2:G887 4.7 12.6 1.0
O6 2:G888 4.7 12.6 1.0

Reference:

R.Kazan, G.Bourgeois, C.Lazennec-Schurdevin, E.Larquet, Y.Mechulam, P.D.Coureux, E.Schmitt. Role of AIF5B in Archaeal Translation Initiation. Nucleic Acids Res. V. 50 6532 2022.
ISSN: ESSN 1362-4962
PubMed: 35694843
DOI: 10.1093/NAR/GKAC490
Page generated: Fri Apr 7 04:31:54 2023

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