Magnesium in PDB 7zah: Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna, AIF1A and AIF5B
Other elements in 7zah:
The structure of Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna, AIF1A and AIF5B also contains other interesting chemical elements:
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 -
63;
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 AIF5B
(pdb code 7zah). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 63 binding sites of Magnesium where determined in the
Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna, AIF1A and AIF5B, PDB code: 7zah:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Magnesium binding site 1 out
of 63 in 7zah
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Magnesium Binding Sites List in 7zah
Magnesium binding site 1 out
of 63 in the Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna, AIF1A and 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 AIF5B within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
2:Mg1601
b:46.2
occ:1.00
|
O
|
2:HOH2004
|
1.9
|
42.4
|
1.0
|
O
|
2:HOH1855
|
1.9
|
42.9
|
1.0
|
O
|
F:HOH404
|
1.9
|
43.9
|
1.0
|
O
|
2:HOH1854
|
1.9
|
41.8
|
1.0
|
O
|
2:HOH1790
|
1.9
|
39.4
|
1.0
|
O
|
2:HOH1993
|
1.9
|
42.3
|
1.0
|
OP1
|
2:A836
|
4.0
|
46.4
|
1.0
|
N7
|
2:G834
|
4.1
|
31.6
|
1.0
|
OP1
|
2:U1043
|
4.4
|
36.4
|
1.0
|
O6
|
2:G834
|
4.6
|
31.6
|
1.0
|
C5
|
2:G834
|
4.8
|
31.6
|
1.0
|
OP2
|
2:A836
|
4.8
|
46.4
|
1.0
|
C8
|
2:G834
|
4.9
|
31.6
|
1.0
|
P
|
2:A836
|
4.9
|
46.4
|
1.0
|
C6
|
2:G834
|
4.9
|
31.6
|
1.0
|
|
Magnesium binding site 2 out
of 63 in 7zah
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Magnesium Binding Sites List in 7zah
Magnesium binding site 2 out
of 63 in the Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna, AIF1A and 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 AIF5B within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
2:Mg1602
b:71.6
occ:1.00
|
O
|
2:HOH1734
|
1.8
|
76.6
|
1.0
|
OP2
|
2:A209
|
1.9
|
63.8
|
1.0
|
O
|
2:HOH1958
|
1.9
|
74.2
|
1.0
|
O
|
2:HOH1716
|
1.9
|
68.2
|
1.0
|
O
|
2:HOH1840
|
1.9
|
69.0
|
1.0
|
P
|
2:A209
|
3.3
|
63.8
|
1.0
|
O4
|
2:U177
|
3.7
|
73.2
|
1.0
|
C2'
|
2:G208
|
3.9
|
62.5
|
1.0
|
C3'
|
2:G208
|
4.0
|
62.5
|
1.0
|
O5'
|
2:A209
|
4.1
|
63.8
|
1.0
|
O3'
|
2:G208
|
4.2
|
62.5
|
1.0
|
C5'
|
2:A209
|
4.2
|
63.8
|
1.0
|
OP1
|
2:A209
|
4.3
|
63.8
|
1.0
|
N7
|
2:A176
|
4.4
|
76.5
|
1.0
|
N9
|
2:G208
|
4.6
|
62.5
|
1.0
|
C4
|
2:G208
|
4.7
|
62.5
|
1.0
|
O2'
|
2:G208
|
4.8
|
62.5
|
1.0
|
C4
|
2:U177
|
4.8
|
73.2
|
1.0
|
C1'
|
2:G208
|
4.9
|
62.5
|
1.0
|
N3
|
2:G208
|
4.9
|
62.5
|
1.0
|
C8
|
2:G208
|
5.0
|
62.5
|
1.0
|
|
Magnesium binding site 3 out
of 63 in 7zah
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Magnesium Binding Sites List in 7zah
Magnesium binding site 3 out
of 63 in the Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna, AIF1A and 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 AIF5B within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
2:Mg1603
b:61.7
occ:1.00
|
O
|
2:HOH1947
|
1.9
|
56.8
|
1.0
|
O
|
2:HOH2005
|
1.9
|
56.3
|
1.0
|
O
|
2:HOH1862
|
2.0
|
56.1
|
1.0
|
O
|
2:HOH1924
|
2.0
|
55.8
|
1.0
|
O
|
2:HOH2014
|
2.0
|
59.5
|
1.0
|
N7
|
2:G650
|
3.5
|
47.0
|
1.0
|
O6
|
2:G650
|
3.8
|
47.0
|
1.0
|
C5
|
2:G650
|
4.2
|
47.0
|
1.0
|
C6
|
2:G650
|
4.3
|
47.0
|
1.0
|
C8
|
2:G650
|
4.4
|
47.0
|
1.0
|
N7
|
2:G649
|
4.5
|
48.4
|
1.0
|
N7
|
2:G651
|
4.5
|
45.5
|
1.0
|
O6
|
2:G651
|
4.5
|
45.5
|
1.0
|
O6
|
2:G649
|
4.5
|
48.4
|
1.0
|
C5
|
2:G649
|
4.8
|
48.4
|
1.0
|
C6
|
2:G649
|
4.8
|
48.4
|
1.0
|
O6
|
2:G652
|
4.8
|
47.3
|
1.0
|
OP1
|
2:A671
|
4.9
|
48.5
|
1.0
|
|
Magnesium binding site 4 out
of 63 in 7zah
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Magnesium Binding Sites List in 7zah
Magnesium binding site 4 out
of 63 in the Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna, AIF1A and 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 AIF5B within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
2:Mg1604
b:38.0
occ:1.00
|
OP1
|
2:C1048
|
1.9
|
26.5
|
1.0
|
O
|
2:HOH1822
|
1.9
|
34.3
|
1.0
|
O
|
2:HOH1962
|
1.9
|
37.6
|
1.0
|
O
|
2:HOH1831
|
1.9
|
37.5
|
1.0
|
O
|
2:HOH1773
|
2.0
|
36.5
|
1.0
|
O
|
2:HOH1985
|
2.2
|
36.0
|
1.0
|
P
|
2:C1048
|
3.3
|
26.5
|
1.0
|
C5'
|
2:C1048
|
3.7
|
26.5
|
1.0
|
O3'
|
2:G1047
|
3.8
|
27.1
|
1.0
|
O5'
|
2:C1048
|
3.8
|
26.5
|
1.0
|
OP2
|
2:G1049
|
4.4
|
26.1
|
1.0
|
OP2
|
2:C1048
|
4.4
|
26.5
|
1.0
|
OP1
|
2:U1364
|
4.9
|
28.3
|
1.0
|
|
Magnesium binding site 5 out
of 63 in 7zah
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Magnesium Binding Sites List in 7zah
Magnesium binding site 5 out
of 63 in the Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna, AIF1A and 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 AIF5B within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
2:Mg1605
b:44.5
occ:1.00
|
O4
|
2:U825
|
1.9
|
33.6
|
1.0
|
O
|
2:HOH1997
|
1.9
|
44.6
|
1.0
|
O
|
2:HOH1793
|
1.9
|
43.2
|
1.0
|
O
|
2:HOH1813
|
1.9
|
41.6
|
1.0
|
O
|
2:HOH1941
|
1.9
|
41.6
|
1.0
|
O
|
2:HOH1973
|
2.0
|
44.5
|
1.0
|
C4
|
2:U825
|
2.9
|
33.6
|
1.0
|
C5
|
2:U825
|
3.4
|
33.6
|
1.0
|
N7
|
2:G824
|
3.9
|
31.9
|
1.0
|
N3
|
2:U825
|
4.1
|
33.6
|
1.0
|
C8
|
2:G824
|
4.5
|
31.9
|
1.0
|
OP1
|
2:U842
|
4.6
|
34.7
|
1.0
|
C5
|
2:G824
|
4.7
|
31.9
|
1.0
|
C6
|
2:U825
|
4.7
|
33.6
|
1.0
|
C5
|
2:U842
|
4.7
|
34.7
|
1.0
|
O6
|
2:G824
|
4.9
|
31.9
|
1.0
|
OP2
|
2:U842
|
4.9
|
34.7
|
1.0
|
|
Magnesium binding site 6 out
of 63 in 7zah
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Magnesium Binding Sites List in 7zah
Magnesium binding site 6 out
of 63 in the Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna, AIF1A and 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 AIF5B within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
2:Mg1606
b:37.1
occ:1.00
|
O
|
2:HOH1799
|
1.9
|
35.4
|
1.0
|
O
|
2:HOH1957
|
1.9
|
36.6
|
1.0
|
O
|
2:HOH1875
|
2.0
|
37.9
|
1.0
|
O
|
2:HOH1713
|
2.0
|
37.4
|
1.0
|
OP1
|
2:G948
|
2.0
|
34.5
|
1.0
|
P
|
2:G948
|
3.1
|
34.5
|
1.0
|
O5'
|
2:G948
|
3.1
|
34.5
|
1.0
|
O3'
|
2:G947
|
4.2
|
36.6
|
1.0
|
OP2
|
2:G948
|
4.2
|
34.5
|
1.0
|
C3'
|
2:G947
|
4.2
|
36.6
|
1.0
|
N6
|
2:A1337
|
4.3
|
33.2
|
1.0
|
OP2
|
2:G947
|
4.4
|
36.6
|
1.0
|
N1
|
2:A1337
|
4.4
|
33.2
|
1.0
|
C5'
|
2:G948
|
4.5
|
34.5
|
1.0
|
O4'
|
2:G948
|
4.5
|
34.5
|
1.0
|
O5'
|
2:G947
|
4.6
|
36.6
|
1.0
|
O2'
|
2:G946
|
4.6
|
37.4
|
1.0
|
O2
|
2:C1339
|
4.8
|
30.9
|
1.0
|
O3'
|
2:G946
|
4.9
|
37.4
|
1.0
|
C6
|
2:A1337
|
4.9
|
33.2
|
1.0
|
N2
|
2:G943
|
4.9
|
30.8
|
1.0
|
P
|
2:G947
|
4.9
|
36.6
|
1.0
|
|
Magnesium binding site 7 out
of 63 in 7zah
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Magnesium Binding Sites List in 7zah
Magnesium binding site 7 out
of 63 in the Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna, AIF1A and 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 AIF5B within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
2:Mg1607
b:41.5
occ:1.00
|
O
|
2:HOH1867
|
1.9
|
38.1
|
1.0
|
O
|
2:HOH1710
|
1.9
|
36.9
|
1.0
|
O
|
2:HOH1988
|
1.9
|
40.2
|
1.0
|
O
|
2:HOH1844
|
1.9
|
36.1
|
1.0
|
OP1
|
2:A1210
|
2.0
|
30.9
|
1.0
|
P
|
2:A1210
|
3.3
|
30.9
|
1.0
|
OE2
|
U:GLU88
|
3.9
|
33.5
|
1.0
|
O5'
|
2:A1210
|
4.0
|
30.9
|
1.0
|
OP2
|
2:A1210
|
4.0
|
30.9
|
1.0
|
O3'
|
2:U1209
|
4.4
|
28.4
|
1.0
|
OP1
|
2:G1216
|
4.4
|
38.2
|
1.0
|
CE1
|
H:HIS90
|
4.7
|
38.4
|
1.0
|
C5'
|
2:A1210
|
4.7
|
30.9
|
1.0
|
ND1
|
H:HIS90
|
5.0
|
38.4
|
1.0
|
CD
|
U:GLU88
|
5.0
|
33.5
|
1.0
|
|
Magnesium binding site 8 out
of 63 in 7zah
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Magnesium Binding Sites List in 7zah
Magnesium binding site 8 out
of 63 in the Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna, AIF1A and 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 AIF5B within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
2:Mg1608
b:32.9
occ:1.00
|
O
|
2:HOH1754
|
1.9
|
31.5
|
1.0
|
O
|
2:HOH1845
|
1.9
|
32.8
|
1.0
|
O
|
2:HOH1892
|
1.9
|
30.8
|
1.0
|
OP2
|
2:G917
|
2.1
|
31.3
|
1.0
|
OP1
|
2:G916
|
2.7
|
30.9
|
1.0
|
O
|
2:HOH1967
|
3.3
|
33.2
|
1.0
|
P
|
2:G917
|
3.4
|
31.3
|
1.0
|
P
|
2:G916
|
3.8
|
30.9
|
1.0
|
OP1
|
2:G917
|
3.9
|
31.3
|
1.0
|
O5'
|
2:G917
|
4.1
|
31.3
|
1.0
|
OP2
|
2:G916
|
4.1
|
30.9
|
1.0
|
O5'
|
2:G916
|
4.2
|
30.9
|
1.0
|
N7
|
2:A918
|
4.3
|
30.6
|
1.0
|
OP2
|
2:A918
|
4.4
|
30.6
|
1.0
|
C5'
|
2:G916
|
4.4
|
30.9
|
1.0
|
O3'
|
2:G916
|
4.6
|
30.9
|
1.0
|
C8
|
2:A918
|
4.9
|
30.6
|
1.0
|
C3'
|
2:G916
|
5.0
|
30.9
|
1.0
|
|
Magnesium binding site 9 out
of 63 in 7zah
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Magnesium Binding Sites List in 7zah
Magnesium binding site 9 out
of 63 in the Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna, AIF1A and 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 AIF5B within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
2:Mg1609
b:45.4
occ:1.00
|
O
|
2:HOH1945
|
1.9
|
43.3
|
1.0
|
OP2
|
2:A59
|
1.9
|
36.0
|
1.0
|
O
|
2:HOH1865
|
1.9
|
41.5
|
1.0
|
O
|
2:HOH1841
|
1.9
|
40.6
|
1.0
|
O
|
2:HOH1954
|
1.9
|
43.3
|
1.0
|
O
|
2:HOH1772
|
1.9
|
41.8
|
1.0
|
P
|
2:A59
|
3.1
|
36.0
|
1.0
|
O3'
|
2:A58
|
3.7
|
42.3
|
1.0
|
OP1
|
2:A59
|
3.8
|
36.0
|
1.0
|
O5'
|
2:A59
|
4.3
|
36.0
|
1.0
|
N7
|
2:G60
|
4.5
|
39.8
|
1.0
|
OP1
|
2:C56
|
4.7
|
41.1
|
1.0
|
OP2
|
2:A55
|
4.7
|
35.5
|
1.0
|
C5'
|
2:A59
|
4.8
|
36.0
|
1.0
|
O2'
|
2:A58
|
4.8
|
42.3
|
1.0
|
C3'
|
2:A58
|
4.8
|
42.3
|
1.0
|
|
Magnesium binding site 10 out
of 63 in 7zah
Go back to
Magnesium Binding Sites List in 7zah
Magnesium binding site 10 out
of 63 in the Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna, AIF1A and 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 AIF5B within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
2:Mg1610
b:54.9
occ:1.00
|
O
|
2:HOH1794
|
1.9
|
47.7
|
1.0
|
O
|
0:HOH103
|
1.9
|
58.9
|
1.0
|
O
|
2:HOH1969
|
1.9
|
49.1
|
1.0
|
O
|
2:HOH1971
|
1.9
|
48.0
|
1.0
|
O
|
2:HOH2019
|
2.0
|
45.9
|
1.0
|
O
|
2:HOH1876
|
3.7
|
39.9
|
1.0
|
O6
|
2:G866
|
4.4
|
40.5
|
1.0
|
N7
|
2:G865
|
4.7
|
40.3
|
1.0
|
O6
|
2:G865
|
4.8
|
40.3
|
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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