Magnesium in PDB 7zai: Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna and AIF1A.
Other elements in 7zai:
The structure of Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna and AIF1A. also contains other interesting chemical elements:
Magnesium Binding Sites:
Magnesium binding site 1 out
of 62 in 7zai
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Magnesium Binding Sites List in 7zai
Magnesium binding site 1 out
of 62 in the Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna and AIF1A.
 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 and AIF1A. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
2:Mg1601
b:65.4
occ:1.00
|
O
|
2:HOH1952
|
1.9
|
61.0
|
1.0
|
O
|
2:HOH1770
|
2.0
|
60.7
|
1.0
|
O
|
2:HOH1855
|
2.0
|
60.1
|
1.0
|
O
|
F:HOH402
|
2.0
|
63.3
|
1.0
|
O
|
2:HOH2015
|
2.0
|
64.0
|
1.0
|
O
|
F:HOH401
|
2.0
|
61.7
|
1.0
|
OP1
|
2:A836
|
3.9
|
50.5
|
1.0
|
N7
|
2:G834
|
4.3
|
52.4
|
1.0
|
OP1
|
2:U1043
|
4.7
|
54.9
|
1.0
|
OE2
|
F:GLU149
|
4.7
|
55.9
|
1.0
|
N
|
F:GLY150
|
4.8
|
54.1
|
1.0
|
OP2
|
2:A836
|
4.9
|
50.5
|
1.0
|
O6
|
2:G834
|
4.9
|
52.4
|
1.0
|
P
|
2:A836
|
4.9
|
50.5
|
1.0
|
C5
|
2:G834
|
5.0
|
52.4
|
1.0
|
|
Magnesium binding site 2 out
of 62 in 7zai
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Magnesium Binding Sites List in 7zai
Magnesium binding site 2 out
of 62 in the Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna and AIF1A.
 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 and AIF1A. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
2:Mg1602
b:96.4
occ:1.00
|
OP2
|
2:A209
|
1.9
|
90.6
|
1.0
|
O
|
2:HOH1894
|
1.9
|
97.4
|
1.0
|
O
|
2:HOH1917
|
2.0
|
94.7
|
1.0
|
O
|
2:HOH1849
|
2.0
|
95.4
|
1.0
|
O
|
2:HOH1735
|
2.0
|
96.5
|
1.0
|
P
|
2:A209
|
3.1
|
90.6
|
1.0
|
OP1
|
2:A209
|
3.5
|
90.6
|
1.0
|
OP2
|
2:C175
|
3.9
|
98.9
|
1.0
|
C3'
|
2:G208
|
4.1
|
89.6
|
1.0
|
O3'
|
2:G208
|
4.1
|
89.6
|
1.0
|
O5'
|
2:A209
|
4.2
|
90.6
|
1.0
|
C2'
|
2:G208
|
4.4
|
89.6
|
1.0
|
C5'
|
2:A209
|
4.9
|
90.6
|
1.0
|
|
Magnesium binding site 3 out
of 62 in 7zai
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Magnesium Binding Sites List in 7zai
Magnesium binding site 3 out
of 62 in the Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna and AIF1A.
 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 and AIF1A. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
2:Mg1603
b:85.0
occ:1.00
|
O
|
2:HOH1812
|
2.0
|
80.8
|
1.0
|
O
|
2:HOH2005
|
2.0
|
83.6
|
1.0
|
O
|
2:HOH1889
|
2.0
|
82.4
|
1.0
|
O
|
2:HOH1725
|
2.0
|
82.5
|
1.0
|
O
|
2:HOH2019
|
2.0
|
83.0
|
1.0
|
O6
|
2:G652
|
3.8
|
75.8
|
1.0
|
N7
|
2:G650
|
3.8
|
75.2
|
1.0
|
N7
|
2:G651
|
3.9
|
74.2
|
1.0
|
O6
|
2:G650
|
4.0
|
75.2
|
1.0
|
O6
|
2:G651
|
4.0
|
74.2
|
1.0
|
C5
|
2:G650
|
4.2
|
75.2
|
1.0
|
C6
|
2:G650
|
4.3
|
75.2
|
1.0
|
C8
|
2:G650
|
4.6
|
75.2
|
1.0
|
C6
|
2:G652
|
4.6
|
75.8
|
1.0
|
C5
|
2:G651
|
4.7
|
74.2
|
1.0
|
C6
|
2:G651
|
4.7
|
74.2
|
1.0
|
OP1
|
2:A671
|
4.8
|
76.0
|
1.0
|
OP2
|
2:A671
|
4.8
|
76.0
|
1.0
|
N1
|
2:G652
|
5.0
|
75.8
|
1.0
|
C8
|
2:G651
|
5.0
|
74.2
|
1.0
|
|
Magnesium binding site 4 out
of 62 in 7zai
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Magnesium Binding Sites List in 7zai
Magnesium binding site 4 out
of 62 in the Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna and AIF1A.
 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 and AIF1A. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
2:Mg1604
b:67.2
occ:1.00
|
OP1
|
2:C1048
|
1.9
|
55.2
|
1.0
|
O
|
2:HOH1915
|
1.9
|
64.6
|
1.0
|
O
|
2:HOH1976
|
1.9
|
66.2
|
1.0
|
O
|
2:HOH1959
|
2.0
|
65.1
|
1.0
|
O
|
2:HOH1820
|
2.0
|
62.8
|
1.0
|
O
|
2:HOH1776
|
2.0
|
62.9
|
1.0
|
P
|
2:C1048
|
3.2
|
55.2
|
1.0
|
O3'
|
2:G1047
|
3.6
|
54.4
|
1.0
|
C5'
|
2:C1048
|
3.6
|
55.2
|
1.0
|
O5'
|
2:C1048
|
3.8
|
55.2
|
1.0
|
OP2
|
2:C1048
|
4.4
|
55.2
|
1.0
|
OP2
|
2:G1049
|
4.6
|
56.3
|
1.0
|
C3'
|
2:G1047
|
5.0
|
54.4
|
1.0
|
|
Magnesium binding site 5 out
of 62 in 7zai
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Magnesium Binding Sites List in 7zai
Magnesium binding site 5 out
of 62 in the Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna and AIF1A.
 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 and AIF1A. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
2:Mg1605
b:70.2
occ:1.00
|
O4
|
2:U825
|
1.9
|
60.9
|
1.0
|
O
|
2:HOH1934
|
1.9
|
69.1
|
1.0
|
O
|
2:HOH1977
|
2.0
|
67.1
|
1.0
|
O
|
2:HOH1873
|
2.0
|
69.5
|
1.0
|
O
|
2:HOH1804
|
2.0
|
66.0
|
1.0
|
O
|
2:HOH2003
|
2.0
|
69.0
|
1.0
|
C4
|
2:U825
|
3.0
|
60.9
|
1.0
|
C5
|
2:U825
|
3.6
|
60.9
|
1.0
|
N7
|
2:G824
|
3.6
|
59.6
|
1.0
|
N3
|
2:U825
|
4.1
|
60.9
|
1.0
|
C8
|
2:G824
|
4.3
|
59.6
|
1.0
|
C5
|
2:G824
|
4.4
|
59.6
|
1.0
|
O6
|
2:G824
|
4.6
|
59.6
|
1.0
|
C6
|
2:G824
|
4.8
|
59.6
|
1.0
|
C6
|
2:U825
|
4.9
|
60.9
|
1.0
|
OP1
|
2:U842
|
4.9
|
60.2
|
1.0
|
C5
|
2:U842
|
5.0
|
60.2
|
1.0
|
|
Magnesium binding site 6 out
of 62 in 7zai
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Magnesium Binding Sites List in 7zai
Magnesium binding site 6 out
of 62 in the Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna and AIF1A.
 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 and AIF1A. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
2:Mg1606
b:68.5
occ:1.00
|
OP1
|
2:G948
|
2.0
|
65.1
|
1.0
|
O
|
2:HOH1884
|
2.0
|
66.0
|
1.0
|
O
|
2:HOH1801
|
2.0
|
67.2
|
1.0
|
O
|
2:HOH1983
|
2.0
|
67.1
|
1.0
|
O
|
2:HOH1709
|
2.2
|
65.8
|
1.0
|
O5'
|
2:G948
|
2.6
|
65.1
|
1.0
|
P
|
2:G948
|
2.8
|
65.1
|
1.0
|
OP2
|
2:G948
|
3.9
|
65.1
|
1.0
|
O3'
|
2:G947
|
3.9
|
65.5
|
1.0
|
C5'
|
2:G948
|
4.0
|
65.1
|
1.0
|
C3'
|
2:G947
|
4.0
|
65.5
|
1.0
|
O4'
|
2:G948
|
4.1
|
65.1
|
1.0
|
N6
|
2:A1337
|
4.2
|
64.5
|
1.0
|
OP2
|
2:G947
|
4.2
|
65.5
|
1.0
|
N1
|
2:A1337
|
4.3
|
64.5
|
1.0
|
O5'
|
2:G947
|
4.5
|
65.5
|
1.0
|
C4'
|
2:G948
|
4.6
|
65.1
|
1.0
|
O3'
|
2:G946
|
4.7
|
65.3
|
1.0
|
N2
|
2:G943
|
4.7
|
62.4
|
1.0
|
O2'
|
2:G946
|
4.8
|
65.3
|
1.0
|
C6
|
2:A1337
|
4.8
|
64.5
|
1.0
|
P
|
2:G947
|
4.8
|
65.5
|
1.0
|
C4'
|
2:G947
|
4.9
|
65.5
|
1.0
|
|
Magnesium binding site 7 out
of 62 in 7zai
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Magnesium Binding Sites List in 7zai
Magnesium binding site 7 out
of 62 in the Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna and AIF1A.
 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 and AIF1A. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
2:Mg1607
b:72.4
occ:1.00
|
O
|
2:HOH1707
|
2.0
|
68.0
|
1.0
|
O
|
2:HOH1701
|
2.0
|
67.6
|
1.0
|
O
|
2:HOH1986
|
2.0
|
70.1
|
1.0
|
OP1
|
2:A1210
|
2.1
|
64.8
|
1.0
|
O
|
2:HOH1904
|
3.3
|
67.8
|
1.0
|
P
|
2:A1210
|
3.4
|
64.8
|
1.0
|
OE2
|
U:GLU88
|
3.9
|
63.5
|
1.0
|
OP2
|
2:A1210
|
4.0
|
64.8
|
1.0
|
O5'
|
2:A1210
|
4.3
|
64.8
|
1.0
|
OP1
|
2:G1216
|
4.4
|
69.9
|
1.0
|
O3'
|
2:U1209
|
4.5
|
61.8
|
1.0
|
CE1
|
H:HIS90
|
4.6
|
67.6
|
1.0
|
ND1
|
H:HIS90
|
4.6
|
67.6
|
1.0
|
CD
|
U:GLU88
|
4.9
|
63.5
|
1.0
|
C5'
|
2:A1210
|
4.9
|
64.8
|
1.0
|
|
Magnesium binding site 8 out
of 62 in 7zai
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Magnesium Binding Sites List in 7zai
Magnesium binding site 8 out
of 62 in the Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna and AIF1A.
 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 and AIF1A. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
2:Mg1608
b:69.4
occ:1.00
|
OP1
|
2:G916
|
1.9
|
65.2
|
1.0
|
O
|
2:HOH1875
|
1.9
|
66.8
|
1.0
|
O
|
2:HOH1706
|
2.0
|
67.3
|
1.0
|
OP2
|
2:G917
|
2.0
|
65.9
|
1.0
|
O
|
2:HOH1806
|
2.0
|
66.4
|
1.0
|
O
|
2:HOH1773
|
2.0
|
66.8
|
1.0
|
P
|
2:G916
|
2.5
|
65.2
|
1.0
|
OP2
|
2:G916
|
2.8
|
65.2
|
1.0
|
O5'
|
2:G916
|
3.0
|
65.2
|
1.0
|
C5'
|
2:G916
|
3.4
|
65.2
|
1.0
|
P
|
2:G917
|
3.5
|
65.9
|
1.0
|
O3'
|
2:U915
|
4.0
|
63.2
|
1.0
|
O5'
|
2:G917
|
4.1
|
65.9
|
1.0
|
C3'
|
2:G916
|
4.3
|
65.2
|
1.0
|
O3'
|
2:G916
|
4.3
|
65.2
|
1.0
|
C4'
|
2:G916
|
4.4
|
65.2
|
1.0
|
OP1
|
2:G917
|
4.4
|
65.9
|
1.0
|
N7
|
2:A918
|
4.7
|
64.0
|
1.0
|
N7
|
2:G917
|
4.8
|
65.9
|
1.0
|
|
Magnesium binding site 9 out
of 62 in 7zai
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Magnesium Binding Sites List in 7zai
Magnesium binding site 9 out
of 62 in the Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna and AIF1A.
 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 and AIF1A. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
2:Mg1609
b:73.8
occ:1.00
|
OP2
|
2:A59
|
1.9
|
64.4
|
1.0
|
O
|
2:HOH1951
|
2.0
|
69.7
|
1.0
|
O
|
2:HOH1789
|
2.0
|
70.2
|
1.0
|
O
|
2:HOH1991
|
2.0
|
70.9
|
1.0
|
O
|
2:HOH1717
|
2.0
|
69.0
|
1.0
|
O
|
2:HOH1968
|
2.0
|
69.9
|
1.0
|
P
|
2:A59
|
3.2
|
64.4
|
1.0
|
O3'
|
2:A58
|
3.6
|
68.0
|
1.0
|
N7
|
2:G60
|
3.7
|
67.9
|
1.0
|
O5'
|
2:A59
|
4.1
|
64.4
|
1.0
|
OP1
|
2:A59
|
4.4
|
64.4
|
1.0
|
C8
|
2:G60
|
4.4
|
67.9
|
1.0
|
C5'
|
2:A59
|
4.6
|
64.4
|
1.0
|
O2'
|
2:A58
|
4.7
|
68.0
|
1.0
|
C3'
|
2:A58
|
4.9
|
68.0
|
1.0
|
C5
|
2:G60
|
4.9
|
67.9
|
1.0
|
|
Magnesium binding site 10 out
of 62 in 7zai
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Magnesium Binding Sites List in 7zai
Magnesium binding site 10 out
of 62 in the Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna and AIF1A.
 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 and AIF1A. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
2:Mg1610
b:77.5
occ:1.00
|
O
|
2:HOH1738
|
2.0
|
74.1
|
1.0
|
O
|
0:HOH103
|
2.0
|
75.3
|
1.0
|
O
|
2:HOH1981
|
2.0
|
73.4
|
1.0
|
O
|
2:HOH2023
|
2.0
|
75.2
|
1.0
|
O
|
2:HOH1906
|
2.0
|
74.1
|
1.0
|
N7
|
2:G866
|
3.9
|
68.5
|
1.0
|
O6
|
2:G866
|
3.9
|
68.5
|
1.0
|
N7
|
2:G865
|
4.1
|
68.3
|
1.0
|
C5
|
2:G866
|
4.6
|
68.5
|
1.0
|
C6
|
2:G866
|
4.6
|
68.5
|
1.0
|
O6
|
2:G865
|
4.7
|
68.3
|
1.0
|
O
|
2:HOH1911
|
4.7
|
69.9
|
1.0
|
C5
|
2:G865
|
4.7
|
68.3
|
1.0
|
C8
|
2:G865
|
4.9
|
68.3
|
1.0
|
C8
|
2:G866
|
4.9
|
68.5
|
1.0
|
C6
|
2:G865
|
5.0
|
68.3
|
1.0
|
N4
|
2:C867
|
5.0
|
67.6
|
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 16:20:52 2024
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