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Magnesium in PDB 7zag: Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna,Mrna, AIF1A and the C-Terminal Domain of AIF5B.

Other elements in 7zag:

The structure of Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna,Mrna, AIF1A and the C-Terminal Domain of AIF5B. 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 - 62;

Binding sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna,Mrna, AIF1A and the C-Terminal Domain of AIF5B. (pdb code 7zag). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 62 binding sites of Magnesium where determined in the Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna,Mrna, AIF1A and the C-Terminal Domain of AIF5B., PDB code: 7zag:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 62 in 7zag

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Magnesium binding site 1 out of 62 in the Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna,Mrna, AIF1A and the C-Terminal Domain of AIF5B.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna,Mrna, AIF1A and the C-Terminal Domain of AIF5B. within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1601

b:80.8
occ:1.00
 O 2:HOH1932 1.9 75.2 1.0
O 2:HOH1723 1.9 74.2 1.0
O F:HOH403 1.9 78.2 1.0
O F:HOH402 1.9 75.7 1.0
O 2:HOH1883 2.0 75.8 1.0
O 2:HOH2020 2.0 79.4 1.0
OP1 2:A836 4.0 65.7 1.0
N7 2:G834 4.3 66.8 1.0
N F:GLY150 4.7 67.0 1.0
OP2 2:A836 4.7 65.7 1.0
OE2 F:GLU149 4.7 69.2 1.0
O6 2:G834 4.8 66.8 1.0
OP1 2:U1043 4.8 68.2 1.0
P 2:A836 4.9 65.7 1.0
C5 2:G834 4.9 66.8 1.0

Magnesium binding site 2 out of 62 in 7zag

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Magnesium binding site 2 out of 62 in the Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna,Mrna, AIF1A and the C-Terminal Domain of AIF5B.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna,Mrna, AIF1A and the C-Terminal Domain of AIF5B. within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1602

b:114.2
occ:1.00
 O 2:HOH1760 1.9 109.0 1.0
O 2:HOH1931 2.0 112.6 1.0
O 2:HOH1841 2.0 111.7 1.0
OP2 2:A209 2.0 105.9 1.0
O 2:HOH1702 2.1 110.0 1.0
P 2:A209 3.3 105.9 1.0
O5' 2:A209 3.9 105.9 1.0
O4 2:U177 4.0 111.0 1.0
OP1 2:A209 4.1 105.9 1.0
N7 2:A176 4.1 112.0 1.0
C5' 2:A209 4.3 105.9 1.0
O3' 2:G208 4.5 105.0 1.0
C2' 2:G208 4.6 105.0 1.0
C3' 2:G208 4.6 105.0 1.0
N6 2:A176 4.7 112.0 1.0
OP2 2:C175 4.8 113.2 1.0
C5 2:C175 4.9 113.2 1.0
C8 2:A176 5.0 112.0 1.0
C4 2:U177 5.0 111.0 1.0

Magnesium binding site 3 out of 62 in 7zag

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Magnesium binding site 3 out of 62 in the Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna,Mrna, AIF1A and the C-Terminal Domain of AIF5B.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna,Mrna, AIF1A and the C-Terminal Domain of AIF5B. within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1603

b:103.2
occ:1.00
 O 2:HOH1894 2.0 97.0 1.0
O 2:HOH1984 2.0 97.3 1.0
O 2:HOH2027 2.0 97.2 1.0
O 2:HOH1854 2.0 95.3 1.0
O 2:HOH1904 2.0 96.3 1.0
O6 2:G652 4.4 87.7 1.0
OP1 2:A671 4.4 88.0 1.0
N7 2:G650 4.6 87.7 1.0
OP2 2:G650 4.8 87.7 1.0

Magnesium binding site 4 out of 62 in 7zag

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Magnesium binding site 4 out of 62 in the Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna,Mrna, AIF1A and the C-Terminal Domain of AIF5B.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna,Mrna, AIF1A and the C-Terminal Domain of AIF5B. within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1604

b:81.1
occ:1.00
 OP1 2:C1048 1.9 70.0 1.0
O 2:HOH1835 1.9 78.2 1.0
O 2:HOH1829 1.9 78.6 1.0
O 2:HOH1943 1.9 80.0 1.0
O 2:HOH1761 1.9 77.3 1.0
O 2:HOH1925 2.0 80.1 1.0
P 2:C1048 3.3 70.0 1.0
C5' 2:C1048 3.7 70.0 1.0
OP2 2:G1049 3.7 70.8 1.0
O5' 2:C1048 3.8 70.0 1.0
O3' 2:G1047 4.1 69.0 1.0
OP2 2:C1048 4.4 70.0 1.0
O4' 2:C1051 4.5 77.6 1.0
C4' 2:C1051 4.6 77.6 1.0
C5' 2:C1051 4.7 77.6 1.0
P 2:G1049 4.8 70.8 1.0
C4' 2:C1048 4.9 70.0 1.0

Magnesium binding site 5 out of 62 in 7zag

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Magnesium binding site 5 out of 62 in the Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna,Mrna, AIF1A and the C-Terminal Domain of AIF5B.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna,Mrna, AIF1A and the C-Terminal Domain of AIF5B. within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1605

b:87.3
occ:1.00
 O 2:HOH1833 1.9 81.7 1.0
O 2:HOH1997 2.0 84.2 1.0
O 2:HOH1818 2.0 83.6 1.0
O4 2:U825 2.0 75.5 1.0
O 2:HOH1959 2.0 82.6 1.0
C4 2:U825 2.9 75.5 1.0
C5 2:U825 3.4 75.5 1.0
O 2:HOH1992 3.6 79.7 1.0
N7 2:G824 3.7 73.7 1.0
N3 2:U825 4.1 75.5 1.0
C8 2:G824 4.2 73.7 1.0
C5 2:G824 4.5 73.7 1.0
C6 2:U825 4.7 75.5 1.0
OP1 2:U842 4.7 74.7 1.0
O6 2:G824 4.8 73.7 1.0
C5 2:U842 4.8 74.7 1.0
C6 2:G824 4.9 73.7 1.0

Magnesium binding site 6 out of 62 in 7zag

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Magnesium binding site 6 out of 62 in the Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna,Mrna, AIF1A and the C-Terminal Domain of AIF5B.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna,Mrna, AIF1A and the C-Terminal Domain of AIF5B. within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1606

b:84.7
occ:1.00
 O 2:HOH1762 1.9 82.7 1.0
O 2:HOH1743 2.0 83.3 1.0
O 2:HOH1949 2.0 84.2 1.0
OP1 2:G948 2.0 79.9 1.0
O5' 2:G948 2.5 79.9 1.0
P 2:G948 2.8 79.9 1.0
O 2:HOH1845 2.9 83.9 1.0
C5' 2:G948 3.8 79.9 1.0
O3' 2:G947 3.9 79.3 1.0
OP2 2:G948 3.9 79.9 1.0
C3' 2:G947 3.9 79.3 1.0
O4' 2:G948 4.0 79.9 1.0
OP2 2:G947 4.0 79.3 1.0
N6 2:A1337 4.1 79.3 1.0
O5' 2:G947 4.2 79.3 1.0
N1 2:A1337 4.3 79.3 1.0
C4' 2:G948 4.4 79.9 1.0
O3' 2:G946 4.6 79.7 1.0
P 2:G947 4.6 79.3 1.0
C6 2:A1337 4.7 79.3 1.0
O2' 2:G946 4.7 79.7 1.0
N2 2:G943 4.8 75.5 1.0
C4' 2:G947 4.8 79.3 1.0

Magnesium binding site 7 out of 62 in 7zag

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Magnesium binding site 7 out of 62 in the Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna,Mrna, AIF1A and the C-Terminal Domain of AIF5B.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna,Mrna, AIF1A and the C-Terminal Domain of AIF5B. within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1607

b:85.7
occ:1.00
 O 2:HOH1748 1.9 81.8 1.0
O 2:HOH1958 2.0 83.0 1.0
O 2:HOH1703 2.0 81.0 1.0
OP1 2:A1210 2.1 77.1 1.0
O 2:HOH1889 2.9 80.7 1.0
P 2:A1210 3.3 77.1 1.0
OP2 2:A1210 3.7 77.1 1.0
OE2 U:GLU88 3.8 76.5 1.0
O5' 2:A1210 4.2 77.1 1.0
O3' 2:U1209 4.4 73.8 1.0
O 2:HOH1816 4.5 79.2 1.0
OP1 2:G1216 4.6 81.1 1.0
CD U:GLU88 4.8 76.5 1.0
C5' 2:A1210 4.8 77.1 1.0

Magnesium binding site 8 out of 62 in 7zag

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Magnesium binding site 8 out of 62 in the Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna,Mrna, AIF1A and the C-Terminal Domain of AIF5B.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna,Mrna, AIF1A and the C-Terminal Domain of AIF5B. within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1608

b:82.6
occ:1.00
 OP1 2:G916 1.8 77.5 1.0
O 2:HOH1824 1.9 81.0 1.0
O 2:HOH1844 1.9 79.7 1.0
OP2 2:G917 2.0 78.8 1.0
O 2:HOH1758 2.0 78.8 1.0
P 2:G916 2.4 77.5 1.0
OP2 2:G916 2.6 77.5 1.0
O5' 2:G916 2.9 77.5 1.0
C5' 2:G916 3.5 77.5 1.0
P 2:G917 3.5 78.8 1.0
O3' 2:U915 3.9 75.6 1.0
O5' 2:G917 4.2 78.8 1.0
O3' 2:G916 4.2 77.5 1.0
C3' 2:G916 4.2 77.5 1.0
C4' 2:G916 4.4 77.5 1.0
OP1 2:G917 4.4 78.8 1.0
N7 2:A918 4.8 76.6 1.0
N7 2:G917 4.8 78.8 1.0
O 2:HOH1948 4.9 79.8 1.0
C3' 2:U915 5.0 75.6 1.0

Magnesium binding site 9 out of 62 in 7zag

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Magnesium binding site 9 out of 62 in the Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna,Mrna, AIF1A and the C-Terminal Domain of AIF5B.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna,Mrna, AIF1A and the C-Terminal Domain of AIF5B. within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1609

b:91.2
occ:1.00
 O 2:HOH1887 1.9 87.3 1.0
OP2 2:A59 1.9 79.6 1.0
O 2:HOH1741 1.9 87.6 1.0
O 2:HOH1964 1.9 87.1 1.0
O 2:HOH1966 2.0 88.2 1.0
O 2:HOH1704 2.1 85.6 1.0
P 2:A59 3.2 79.6 1.0
O3' 2:A58 3.5 84.0 1.0
N7 2:G60 3.8 83.4 1.0
O5' 2:A59 4.1 79.6 1.0
OP1 2:A59 4.3 79.6 1.0
C8 2:G60 4.4 83.4 1.0
O2' 2:A58 4.6 84.0 1.0
C5' 2:A59 4.7 79.6 1.0
C3' 2:A58 4.8 84.0 1.0
C5 2:G60 5.0 83.4 1.0

Magnesium binding site 10 out of 62 in 7zag

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Magnesium binding site 10 out of 62 in the Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna,Mrna, AIF1A and the C-Terminal Domain of AIF5B.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna,Mrna, AIF1A and the C-Terminal Domain of AIF5B. within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1610

b:106.9
occ:1.00
 O 2:HOH2038 1.9 108.6 1.0
O 0:HOH103 1.9 104.9 1.0
O 2:HOH1785 2.0 98.2 1.0
O 2:HOH1902 2.0 100.0 1.0
O 2:HOH2031 2.0 103.9 1.0
O 2:HOH1962 2.0 99.9 1.0
N7 2:G865 4.3 83.2 1.0
O6 2:G866 4.8 83.5 1.0
OP2 2:C864 4.9 82.5 1.0
O6 2:G865 5.0 83.2 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 16:20:30 2024

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