Atomistry » Magnesium » PDB 7zbg-7zke » 7zhg
Atomistry »
  Magnesium »
    PDB 7zbg-7zke »
      7zhg »

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

Go back to Magnesium Binding Sites List in 7zhg
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

Go back to Magnesium Binding Sites List in 7zhg
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

Go back to Magnesium Binding Sites List in 7zhg
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

Go back to Magnesium Binding Sites List in 7zhg
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

Go back to Magnesium Binding Sites List in 7zhg
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

Go back to Magnesium Binding Sites List in 7zhg
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

Go back to Magnesium Binding Sites List in 7zhg
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

Go back to Magnesium Binding Sites List in 7zhg
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

Go back to Magnesium Binding Sites List in 7zhg
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

Go back to Magnesium Binding Sites List in 7zhg
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: Thu Oct 3 16:47:09 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy