Zinc 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:
Zinc Binding Sites:
The binding sites of Zinc 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 Zinc atom.
In total 6 binding sites of Zinc 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 Zinc binding site number:
1;
2;
3;
4;
5;
6;
Zinc binding site 1 out
of 6 in 7zah
Go back to
Zinc Binding Sites List in 7zah
Zinc binding site 1 out
of 6 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 Zinc with other atoms in the Zn 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
|
C:Zn101
b:115.7
occ:1.00
|
SG
|
C:CYS35
|
2.3
|
65.1
|
1.0
|
SG
|
C:CYS58
|
2.3
|
71.2
|
1.0
|
SG
|
C:CYS55
|
2.3
|
65.2
|
1.0
|
SG
|
C:CYS32
|
2.7
|
56.9
|
1.0
|
CB
|
C:CYS35
|
3.3
|
65.1
|
1.0
|
CB
|
C:CYS55
|
3.3
|
65.2
|
1.0
|
CB
|
C:CYS58
|
3.3
|
71.2
|
1.0
|
CB
|
C:CYS32
|
3.5
|
56.9
|
1.0
|
N
|
C:CYS58
|
3.6
|
71.2
|
1.0
|
N
|
C:CYS35
|
4.0
|
65.1
|
1.0
|
CA
|
C:CYS58
|
4.0
|
71.2
|
1.0
|
CA
|
C:CYS35
|
4.3
|
65.1
|
1.0
|
CB
|
C:LYS57
|
4.3
|
71.4
|
1.0
|
C
|
C:LYS57
|
4.6
|
71.4
|
1.0
|
CA
|
C:CYS55
|
4.7
|
65.2
|
1.0
|
N
|
C:LYS57
|
4.7
|
71.4
|
1.0
|
CA
|
C:LYS57
|
4.8
|
71.4
|
1.0
|
ND2
|
C:ASN34
|
4.9
|
61.1
|
1.0
|
N
|
C:GLY36
|
4.9
|
63.1
|
1.0
|
C
|
C:CYS58
|
4.9
|
71.2
|
1.0
|
N
|
C:GLY59
|
4.9
|
64.2
|
1.0
|
CA
|
C:CYS32
|
5.0
|
56.9
|
1.0
|
C
|
C:CYS35
|
5.0
|
65.1
|
1.0
|
|
Zinc binding site 2 out
of 6 in 7zah
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Zinc Binding Sites List in 7zah
Zinc binding site 2 out
of 6 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 Zinc with other atoms in the Zn 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
|
C:Zn102
b:71.0
occ:1.00
|
SG
|
C:CYS14
|
2.3
|
41.1
|
1.0
|
SG
|
C:CYS46
|
2.3
|
39.0
|
1.0
|
SG
|
C:CYS43
|
2.3
|
39.4
|
1.0
|
SG
|
C:CYS17
|
2.3
|
43.8
|
1.0
|
CB
|
C:CYS14
|
3.3
|
41.1
|
1.0
|
CB
|
C:CYS17
|
3.3
|
43.8
|
1.0
|
CB
|
C:CYS46
|
3.5
|
39.0
|
1.0
|
CB
|
C:CYS43
|
3.6
|
39.4
|
1.0
|
N
|
C:CYS17
|
3.7
|
43.8
|
1.0
|
CA
|
C:CYS17
|
4.1
|
43.8
|
1.0
|
N
|
C:CYS43
|
4.1
|
39.4
|
1.0
|
N
|
C:CYS46
|
4.4
|
39.0
|
1.0
|
CA
|
C:CYS43
|
4.4
|
39.4
|
1.0
|
CA
|
C:CYS46
|
4.5
|
39.0
|
1.0
|
CB
|
C:SER16
|
4.6
|
42.6
|
1.0
|
CA
|
C:CYS14
|
4.7
|
41.1
|
1.0
|
C
|
C:SER16
|
4.8
|
42.6
|
1.0
|
C
|
C:CYS17
|
4.9
|
43.8
|
1.0
|
OG
|
C:SER16
|
4.9
|
42.6
|
1.0
|
N
|
C:SER16
|
4.9
|
42.6
|
1.0
|
N
|
C:GLY18
|
5.0
|
41.4
|
1.0
|
|
Zinc binding site 3 out
of 6 in 7zah
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Zinc Binding Sites List in 7zah
Zinc binding site 3 out
of 6 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 Zinc with other atoms in the Zn 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
|
F:Zn301
b:49.5
occ:1.00
|
NE2
|
F:HIS139
|
2.1
|
32.3
|
1.0
|
SG
|
F:CYS135
|
2.3
|
37.3
|
1.0
|
SG
|
F:CYS128
|
2.3
|
33.3
|
1.0
|
SG
|
F:CYS133
|
2.3
|
38.3
|
1.0
|
CE1
|
F:HIS139
|
2.9
|
32.3
|
1.0
|
CD2
|
F:HIS139
|
3.3
|
32.3
|
1.0
|
CB
|
F:CYS128
|
3.3
|
33.3
|
1.0
|
CB
|
F:CYS135
|
3.6
|
37.3
|
1.0
|
CB
|
F:CYS133
|
3.7
|
38.3
|
1.0
|
N
|
F:CYS135
|
4.0
|
37.3
|
1.0
|
O
|
F:CYS133
|
4.0
|
38.3
|
1.0
|
ND1
|
F:HIS139
|
4.1
|
32.3
|
1.0
|
C
|
F:CYS133
|
4.2
|
38.3
|
1.0
|
CG
|
F:HIS139
|
4.3
|
32.3
|
1.0
|
CA
|
F:CYS135
|
4.3
|
37.3
|
1.0
|
CB
|
F:ARG161
|
4.4
|
34.7
|
1.0
|
N
|
F:ARG161
|
4.6
|
34.7
|
1.0
|
CA
|
F:CYS133
|
4.6
|
38.3
|
1.0
|
CA
|
F:CYS128
|
4.6
|
33.3
|
1.0
|
NH1
|
F:ARG161
|
4.6
|
34.7
|
1.0
|
N
|
F:ARG134
|
4.7
|
34.6
|
1.0
|
O
|
F:ARG137
|
4.8
|
35.9
|
1.0
|
C
|
F:CYS135
|
4.9
|
37.3
|
1.0
|
N
|
F:ARG136
|
4.9
|
37.4
|
1.0
|
C
|
F:ARG134
|
5.0
|
34.6
|
1.0
|
CD
|
F:ARG161
|
5.0
|
34.7
|
1.0
|
O
|
F:GLY159
|
5.0
|
31.0
|
1.0
|
CA
|
F:ARG161
|
5.0
|
34.7
|
1.0
|
|
Zinc binding site 4 out
of 6 in 7zah
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Zinc Binding Sites List in 7zah
Zinc binding site 4 out
of 6 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 Zinc with other atoms in the Zn 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
|
P:Zn101
b:57.9
occ:1.00
|
SG
|
P:CYS24
|
2.2
|
44.0
|
1.0
|
SG
|
P:CYS42
|
2.3
|
38.7
|
1.0
|
SG
|
P:CYS21
|
2.4
|
42.6
|
1.0
|
SG
|
P:CYS39
|
2.8
|
40.7
|
1.0
|
CB
|
P:CYS39
|
3.0
|
40.7
|
1.0
|
CB
|
P:CYS21
|
3.3
|
42.6
|
1.0
|
CB
|
P:CYS42
|
3.3
|
38.7
|
1.0
|
CB
|
P:CYS24
|
3.6
|
44.0
|
1.0
|
N
|
P:CYS39
|
3.8
|
40.7
|
1.0
|
CA
|
P:CYS39
|
4.0
|
40.7
|
1.0
|
N
|
P:CYS24
|
4.1
|
44.0
|
1.0
|
N
|
P:CYS42
|
4.3
|
38.7
|
1.0
|
CA
|
P:CYS42
|
4.4
|
38.7
|
1.0
|
CA
|
P:CYS24
|
4.4
|
44.0
|
1.0
|
OE1
|
P:GLN26
|
4.7
|
41.6
|
1.0
|
CA
|
P:CYS21
|
4.8
|
42.6
|
1.0
|
CB
|
P:ARG23
|
4.9
|
43.9
|
1.0
|
C
|
P:ARG23
|
4.9
|
43.9
|
1.0
|
CB
|
P:GLN26
|
4.9
|
41.6
|
1.0
|
C
|
P:CYS39
|
5.0
|
40.7
|
1.0
|
O2'
|
2:G1176
|
5.0
|
35.0
|
1.0
|
|
Zinc binding site 5 out
of 6 in 7zah
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Zinc Binding Sites List in 7zah
Zinc binding site 5 out
of 6 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 Zinc with other atoms in the Zn 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
|
R:Zn201
b:86.7
occ:1.00
|
ND1
|
R:HIS24
|
2.1
|
62.1
|
1.0
|
SG
|
R:CYS77
|
2.2
|
57.3
|
1.0
|
SG
|
R:CYS16
|
2.2
|
69.8
|
1.0
|
SG
|
R:CYS21
|
2.3
|
57.4
|
1.0
|
CE1
|
R:HIS24
|
2.8
|
62.1
|
1.0
|
CG
|
R:HIS24
|
3.2
|
62.1
|
1.0
|
CB
|
R:CYS77
|
3.3
|
57.3
|
1.0
|
CB
|
R:CYS21
|
3.4
|
57.4
|
1.0
|
CB
|
R:CYS16
|
3.5
|
69.8
|
1.0
|
CB
|
R:HIS24
|
3.7
|
62.1
|
1.0
|
NE2
|
R:HIS24
|
4.0
|
62.1
|
1.0
|
N
|
R:CYS16
|
4.2
|
69.8
|
1.0
|
CD2
|
R:HIS24
|
4.2
|
62.1
|
1.0
|
N
|
R:HIS24
|
4.2
|
62.1
|
1.0
|
CB
|
R:TRP23
|
4.4
|
56.4
|
1.0
|
CA
|
R:CYS16
|
4.4
|
69.8
|
1.0
|
CA
|
R:CYS77
|
4.5
|
57.3
|
1.0
|
N
|
R:CYS77
|
4.6
|
57.3
|
1.0
|
CA
|
R:HIS24
|
4.6
|
62.1
|
1.0
|
CB
|
R:PRO75
|
4.7
|
48.1
|
1.0
|
CA
|
R:CYS21
|
4.8
|
57.4
|
1.0
|
C
|
R:LYS15
|
4.9
|
72.9
|
1.0
|
C
|
R:TRP23
|
4.9
|
56.4
|
1.0
|
|
Zinc binding site 6 out
of 6 in 7zah
Go back to
Zinc Binding Sites List in 7zah
Zinc binding site 6 out
of 6 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 Zinc with other atoms in the Zn 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
|
W:Zn101
b:112.6
occ:1.00
|
SG
|
W:CYS42
|
2.3
|
82.1
|
1.0
|
SG
|
W:CYS20
|
2.4
|
86.7
|
1.0
|
SG
|
W:CYS39
|
2.4
|
72.5
|
1.0
|
CB
|
W:CYS23
|
2.5
|
94.4
|
1.0
|
CB
|
W:CYS20
|
3.2
|
86.7
|
1.0
|
CB
|
W:CYS39
|
3.3
|
72.5
|
1.0
|
N
|
W:CYS23
|
3.4
|
94.4
|
1.0
|
CA
|
W:CYS23
|
3.5
|
94.4
|
1.0
|
CB
|
W:CYS42
|
3.5
|
82.1
|
1.0
|
SG
|
W:CYS23
|
3.8
|
94.4
|
1.0
|
N
|
W:CYS42
|
4.0
|
82.1
|
1.0
|
CA
|
W:CYS42
|
4.4
|
82.1
|
1.0
|
C
|
W:CYS23
|
4.4
|
94.4
|
1.0
|
CB
|
W:ASN25
|
4.4
|
82.3
|
1.0
|
N
|
W:GLY24
|
4.6
|
90.0
|
1.0
|
C
|
W:ASP22
|
4.6
|
94.1
|
1.0
|
CA
|
W:CYS20
|
4.7
|
86.7
|
1.0
|
N
|
W:ASN25
|
4.7
|
82.3
|
1.0
|
CA
|
W:CYS39
|
4.8
|
72.5
|
1.0
|
CB
|
W:VAL41
|
4.9
|
77.5
|
1.0
|
CB
|
W:ASP22
|
4.9
|
94.1
|
1.0
|
N
|
W:GLY43
|
5.0
|
76.7
|
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: Wed Oct 30 16:21:12 2024
|