Zinc in PDB 8sev: Cryo-Em Structure of RYR1 + Atp-Gamma-S (Local Refinement of Tmd)
Zinc Binding Sites:
The binding sites of Zinc atom in the Cryo-Em Structure of RYR1 + Atp-Gamma-S (Local Refinement of Tmd)
(pdb code 8sev). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Cryo-Em Structure of RYR1 + Atp-Gamma-S (Local Refinement of Tmd), PDB code: 8sev:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 8sev
Go back to
Zinc Binding Sites List in 8sev
Zinc binding site 1 out
of 4 in the Cryo-Em Structure of RYR1 + Atp-Gamma-S (Local Refinement of Tmd)
![](/pictures/ZN/pdb/se/8sev-ZN-sphere_01.jpg) Mono view
![](/pictures/ZN/pdb/se/8sev-ZN-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Cryo-Em Structure of RYR1 + Atp-Gamma-S (Local Refinement of Tmd) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn5102
b:72.9
occ:1.00
|
ND1
|
A:HIS4983
|
2.0
|
61.5
|
1.0
|
NE2
|
A:HIS4978
|
2.0
|
64.3
|
1.0
|
SG
|
A:CYS4958
|
2.3
|
62.8
|
1.0
|
SG
|
A:CYS4961
|
2.3
|
61.9
|
1.0
|
CE1
|
A:HIS4978
|
2.7
|
64.3
|
1.0
|
CE1
|
A:HIS4983
|
2.9
|
61.5
|
1.0
|
CG
|
A:HIS4983
|
3.0
|
61.5
|
1.0
|
CB
|
A:CYS4958
|
3.1
|
62.8
|
1.0
|
CD2
|
A:HIS4978
|
3.3
|
64.3
|
1.0
|
CB
|
A:CYS4961
|
3.3
|
61.9
|
1.0
|
CB
|
A:HIS4983
|
3.4
|
61.5
|
1.0
|
N
|
A:CYS4961
|
3.8
|
61.9
|
1.0
|
ND1
|
A:HIS4978
|
3.9
|
64.3
|
1.0
|
NE2
|
A:HIS4983
|
4.0
|
61.5
|
1.0
|
CD2
|
A:HIS4983
|
4.1
|
61.5
|
1.0
|
CA
|
A:CYS4961
|
4.1
|
61.9
|
1.0
|
CG
|
A:HIS4978
|
4.2
|
64.3
|
1.0
|
CZ
|
A:PHE4968
|
4.4
|
66.1
|
1.0
|
CA
|
A:CYS4958
|
4.5
|
62.8
|
1.0
|
CE2
|
A:PHE4968
|
4.8
|
66.1
|
1.0
|
CB
|
A:ILE4960
|
4.8
|
59.9
|
1.0
|
N
|
A:GLY4962
|
4.9
|
63.9
|
1.0
|
C
|
A:CYS4961
|
4.9
|
61.9
|
1.0
|
C
|
A:ILE4960
|
4.9
|
59.9
|
1.0
|
CA
|
A:HIS4983
|
4.9
|
61.5
|
1.0
|
N
|
A:ILE4960
|
5.0
|
59.9
|
1.0
|
C
|
A:CYS4958
|
5.0
|
62.8
|
1.0
|
|
Zinc binding site 2 out
of 4 in 8sev
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Zinc Binding Sites List in 8sev
Zinc binding site 2 out
of 4 in the Cryo-Em Structure of RYR1 + Atp-Gamma-S (Local Refinement of Tmd)
![](/pictures/ZN/pdb/se/8sev-ZN-sphere_02.jpg) Mono view
![](/pictures/ZN/pdb/se/8sev-ZN-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Cryo-Em Structure of RYR1 + Atp-Gamma-S (Local Refinement of Tmd) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn5102
b:72.8
occ:1.00
|
ND1
|
B:HIS4983
|
2.0
|
61.2
|
1.0
|
NE2
|
B:HIS4978
|
2.0
|
64.4
|
1.0
|
SG
|
B:CYS4961
|
2.3
|
62.3
|
1.0
|
SG
|
B:CYS4958
|
2.3
|
63.2
|
1.0
|
CE1
|
B:HIS4978
|
2.7
|
64.4
|
1.0
|
CE1
|
B:HIS4983
|
2.9
|
61.2
|
1.0
|
CG
|
B:HIS4983
|
3.0
|
61.2
|
1.0
|
CB
|
B:CYS4958
|
3.1
|
63.2
|
1.0
|
CD2
|
B:HIS4978
|
3.3
|
64.4
|
1.0
|
CB
|
B:CYS4961
|
3.3
|
62.3
|
1.0
|
CB
|
B:HIS4983
|
3.4
|
61.2
|
1.0
|
N
|
B:CYS4961
|
3.8
|
62.3
|
1.0
|
ND1
|
B:HIS4978
|
3.9
|
64.4
|
1.0
|
NE2
|
B:HIS4983
|
4.0
|
61.2
|
1.0
|
CD2
|
B:HIS4983
|
4.1
|
61.2
|
1.0
|
CA
|
B:CYS4961
|
4.1
|
62.3
|
1.0
|
CG
|
B:HIS4978
|
4.2
|
64.4
|
1.0
|
CZ
|
B:PHE4968
|
4.4
|
66.7
|
1.0
|
CA
|
B:CYS4958
|
4.5
|
63.2
|
1.0
|
CE2
|
B:PHE4968
|
4.8
|
66.7
|
1.0
|
CB
|
B:ILE4960
|
4.8
|
60.2
|
1.0
|
N
|
B:GLY4962
|
4.9
|
64.4
|
1.0
|
C
|
B:CYS4961
|
4.9
|
62.3
|
1.0
|
C
|
B:ILE4960
|
4.9
|
60.2
|
1.0
|
CA
|
B:HIS4983
|
4.9
|
61.2
|
1.0
|
N
|
B:ILE4960
|
5.0
|
60.2
|
1.0
|
C
|
B:CYS4958
|
5.0
|
63.2
|
1.0
|
|
Zinc binding site 3 out
of 4 in 8sev
Go back to
Zinc Binding Sites List in 8sev
Zinc binding site 3 out
of 4 in the Cryo-Em Structure of RYR1 + Atp-Gamma-S (Local Refinement of Tmd)
![](/pictures/ZN/pdb/se/8sev-ZN-sphere_03.jpg) Mono view
![](/pictures/ZN/pdb/se/8sev-ZN-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Cryo-Em Structure of RYR1 + Atp-Gamma-S (Local Refinement of Tmd) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn5102
b:73.8
occ:1.00
|
ND1
|
C:HIS4983
|
2.0
|
61.8
|
1.0
|
NE2
|
C:HIS4978
|
2.0
|
65.2
|
1.0
|
SG
|
C:CYS4961
|
2.3
|
63.2
|
1.0
|
SG
|
C:CYS4958
|
2.3
|
64.1
|
1.0
|
CE1
|
C:HIS4978
|
2.7
|
65.2
|
1.0
|
CE1
|
C:HIS4983
|
2.9
|
61.8
|
1.0
|
CG
|
C:HIS4983
|
3.0
|
61.8
|
1.0
|
CB
|
C:CYS4958
|
3.0
|
64.1
|
1.0
|
CD2
|
C:HIS4978
|
3.3
|
65.2
|
1.0
|
CB
|
C:CYS4961
|
3.3
|
63.2
|
1.0
|
CB
|
C:HIS4983
|
3.4
|
61.8
|
1.0
|
N
|
C:CYS4961
|
3.8
|
63.2
|
1.0
|
ND1
|
C:HIS4978
|
3.9
|
65.2
|
1.0
|
NE2
|
C:HIS4983
|
4.0
|
61.8
|
1.0
|
CD2
|
C:HIS4983
|
4.1
|
61.8
|
1.0
|
CA
|
C:CYS4961
|
4.1
|
63.2
|
1.0
|
CG
|
C:HIS4978
|
4.2
|
65.2
|
1.0
|
CZ
|
C:PHE4968
|
4.4
|
67.7
|
1.0
|
CA
|
C:CYS4958
|
4.5
|
64.1
|
1.0
|
CE2
|
C:PHE4968
|
4.8
|
67.7
|
1.0
|
CB
|
C:ILE4960
|
4.8
|
61.0
|
1.0
|
N
|
C:GLY4962
|
4.9
|
65.5
|
1.0
|
C
|
C:CYS4961
|
4.9
|
63.2
|
1.0
|
C
|
C:ILE4960
|
4.9
|
61.0
|
1.0
|
CA
|
C:HIS4983
|
4.9
|
61.8
|
1.0
|
N
|
C:ILE4960
|
5.0
|
61.0
|
1.0
|
C
|
C:CYS4958
|
5.0
|
64.1
|
1.0
|
|
Zinc binding site 4 out
of 4 in 8sev
Go back to
Zinc Binding Sites List in 8sev
Zinc binding site 4 out
of 4 in the Cryo-Em Structure of RYR1 + Atp-Gamma-S (Local Refinement of Tmd)
![](/pictures/ZN/pdb/se/8sev-ZN-sphere_04.jpg) Mono view
![](/pictures/ZN/pdb/se/8sev-ZN-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Cryo-Em Structure of RYR1 + Atp-Gamma-S (Local Refinement of Tmd) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn5102
b:73.7
occ:1.00
|
ND1
|
D:HIS4983
|
2.0
|
62.5
|
1.0
|
NE2
|
D:HIS4978
|
2.0
|
66.0
|
1.0
|
SG
|
D:CYS4961
|
2.3
|
63.2
|
1.0
|
SG
|
D:CYS4958
|
2.3
|
64.3
|
1.0
|
CE1
|
D:HIS4978
|
2.7
|
66.0
|
1.0
|
CE1
|
D:HIS4983
|
2.9
|
62.5
|
1.0
|
CG
|
D:HIS4983
|
3.0
|
62.5
|
1.0
|
CB
|
D:CYS4958
|
3.0
|
64.3
|
1.0
|
CD2
|
D:HIS4978
|
3.3
|
66.0
|
1.0
|
CB
|
D:CYS4961
|
3.3
|
63.2
|
1.0
|
CB
|
D:HIS4983
|
3.4
|
62.5
|
1.0
|
N
|
D:CYS4961
|
3.8
|
63.2
|
1.0
|
ND1
|
D:HIS4978
|
3.9
|
66.0
|
1.0
|
NE2
|
D:HIS4983
|
4.0
|
62.5
|
1.0
|
CD2
|
D:HIS4983
|
4.1
|
62.5
|
1.0
|
CA
|
D:CYS4961
|
4.1
|
63.2
|
1.0
|
CG
|
D:HIS4978
|
4.2
|
66.0
|
1.0
|
CZ
|
D:PHE4968
|
4.4
|
68.2
|
1.0
|
CA
|
D:CYS4958
|
4.5
|
64.3
|
1.0
|
CE2
|
D:PHE4968
|
4.8
|
68.2
|
1.0
|
CB
|
D:ILE4960
|
4.8
|
61.1
|
1.0
|
N
|
D:GLY4962
|
4.9
|
65.6
|
1.0
|
C
|
D:CYS4961
|
4.9
|
63.2
|
1.0
|
C
|
D:ILE4960
|
4.9
|
61.1
|
1.0
|
CA
|
D:HIS4983
|
4.9
|
62.5
|
1.0
|
N
|
D:ILE4960
|
5.0
|
61.1
|
1.0
|
C
|
D:CYS4958
|
5.0
|
64.3
|
1.0
|
|
Reference:
S.Cholak,
J.W.Saville,
X.Zhu,
A.M.Berezuk,
K.S.Tuttle,
O.Haji-Ghassemi,
F.J.Alvarado,
F.Van Petegem,
S.Subramaniam.
Allosteric Modulation of Ryanodine Receptor RYR1 By Nucleotide Derivatives Structure 2023.
ISSN: ISSN 0969-2126
DOI: 10.1016/J.STR.2023.04.009
Page generated: Fri Jul 28 07:24:52 2023
|