Zinc in PDB 8drp: Focus/Local Refined Map in C4 of Signal Subtracted RYR1 Particles
Zinc Binding Sites:
The binding sites of Zinc atom in the Focus/Local Refined Map in C4 of Signal Subtracted RYR1 Particles
(pdb code 8drp). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Focus/Local Refined Map in C4 of Signal Subtracted RYR1 Particles, PDB code: 8drp:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 8drp
Go back to
Zinc Binding Sites List in 8drp
Zinc binding site 1 out
of 4 in the Focus/Local Refined Map in C4 of Signal Subtracted RYR1 Particles
![](/pictures/ZN/pdb/dr/8drp-ZN-sphere_01.jpg) Mono view
![](/pictures/ZN/pdb/dr/8drp-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 Focus/Local Refined Map in C4 of Signal Subtracted RYR1 Particles within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn5103
b:62.0
occ:1.00
|
NE2
|
A:HIS4978
|
2.0
|
59.5
|
1.0
|
ND1
|
A:HIS4983
|
2.0
|
49.1
|
1.0
|
SG
|
A:CYS4961
|
2.3
|
57.0
|
1.0
|
SG
|
A:CYS4958
|
2.3
|
58.4
|
1.0
|
CE1
|
A:HIS4978
|
2.7
|
56.0
|
1.0
|
CG
|
A:HIS4983
|
3.0
|
46.6
|
1.0
|
CE1
|
A:HIS4983
|
3.1
|
50.9
|
1.0
|
CD2
|
A:HIS4978
|
3.1
|
59.3
|
1.0
|
CB
|
A:HIS4983
|
3.3
|
43.2
|
1.0
|
N
|
A:CYS4961
|
3.6
|
55.6
|
1.0
|
CB
|
A:CYS4958
|
3.7
|
56.3
|
1.0
|
CB
|
A:CYS4961
|
3.8
|
58.2
|
1.0
|
ND1
|
A:HIS4978
|
3.9
|
56.1
|
1.0
|
CB
|
A:ILE4960
|
4.0
|
47.0
|
1.0
|
CG
|
A:HIS4978
|
4.1
|
57.5
|
1.0
|
CD2
|
A:HIS4983
|
4.1
|
46.1
|
1.0
|
NE2
|
A:HIS4983
|
4.1
|
47.4
|
1.0
|
CA
|
A:CYS4961
|
4.2
|
54.9
|
1.0
|
CG2
|
A:ILE4960
|
4.5
|
48.1
|
1.0
|
N
|
A:GLY4962
|
4.5
|
55.4
|
1.0
|
C
|
A:ILE4960
|
4.6
|
52.7
|
1.0
|
CA
|
A:ILE4960
|
4.6
|
47.6
|
1.0
|
N
|
A:ILE4960
|
4.6
|
51.0
|
1.0
|
CA
|
A:HIS4983
|
4.8
|
40.2
|
1.0
|
C
|
A:CYS4961
|
4.8
|
55.4
|
1.0
|
CG1
|
A:ILE4960
|
4.9
|
44.0
|
1.0
|
|
Zinc binding site 2 out
of 4 in 8drp
Go back to
Zinc Binding Sites List in 8drp
Zinc binding site 2 out
of 4 in the Focus/Local Refined Map in C4 of Signal Subtracted RYR1 Particles
![](/pictures/ZN/pdb/dr/8drp-ZN-sphere_02.jpg) Mono view
![](/pictures/ZN/pdb/dr/8drp-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 Focus/Local Refined Map in C4 of Signal Subtracted RYR1 Particles within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn5103
b:62.0
occ:1.00
|
NE2
|
B:HIS4978
|
2.0
|
59.5
|
1.0
|
ND1
|
B:HIS4983
|
2.0
|
49.1
|
1.0
|
SG
|
B:CYS4961
|
2.3
|
57.0
|
1.0
|
SG
|
B:CYS4958
|
2.3
|
58.4
|
1.0
|
CE1
|
B:HIS4978
|
2.7
|
56.0
|
1.0
|
CG
|
B:HIS4983
|
3.0
|
46.6
|
1.0
|
CE1
|
B:HIS4983
|
3.1
|
50.9
|
1.0
|
CD2
|
B:HIS4978
|
3.1
|
59.3
|
1.0
|
CB
|
B:HIS4983
|
3.3
|
43.2
|
1.0
|
N
|
B:CYS4961
|
3.6
|
55.6
|
1.0
|
CB
|
B:CYS4958
|
3.7
|
56.3
|
1.0
|
CB
|
B:CYS4961
|
3.8
|
58.2
|
1.0
|
ND1
|
B:HIS4978
|
3.9
|
56.1
|
1.0
|
CB
|
B:ILE4960
|
4.0
|
47.0
|
1.0
|
CG
|
B:HIS4978
|
4.1
|
57.5
|
1.0
|
CD2
|
B:HIS4983
|
4.1
|
46.1
|
1.0
|
NE2
|
B:HIS4983
|
4.1
|
47.4
|
1.0
|
CA
|
B:CYS4961
|
4.2
|
54.9
|
1.0
|
CG2
|
B:ILE4960
|
4.5
|
48.1
|
1.0
|
N
|
B:GLY4962
|
4.5
|
55.4
|
1.0
|
C
|
B:ILE4960
|
4.6
|
52.7
|
1.0
|
CA
|
B:ILE4960
|
4.6
|
47.6
|
1.0
|
N
|
B:ILE4960
|
4.6
|
51.0
|
1.0
|
CA
|
B:HIS4983
|
4.8
|
40.2
|
1.0
|
C
|
B:CYS4961
|
4.8
|
55.4
|
1.0
|
CG1
|
B:ILE4960
|
4.9
|
44.0
|
1.0
|
|
Zinc binding site 3 out
of 4 in 8drp
Go back to
Zinc Binding Sites List in 8drp
Zinc binding site 3 out
of 4 in the Focus/Local Refined Map in C4 of Signal Subtracted RYR1 Particles
![](/pictures/ZN/pdb/dr/8drp-ZN-sphere_03.jpg) Mono view
![](/pictures/ZN/pdb/dr/8drp-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 Focus/Local Refined Map in C4 of Signal Subtracted RYR1 Particles within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn5103
b:62.0
occ:1.00
|
NE2
|
C:HIS4978
|
2.0
|
59.5
|
1.0
|
ND1
|
C:HIS4983
|
2.0
|
49.1
|
1.0
|
SG
|
C:CYS4961
|
2.3
|
57.0
|
1.0
|
SG
|
C:CYS4958
|
2.3
|
58.4
|
1.0
|
CE1
|
C:HIS4978
|
2.7
|
56.0
|
1.0
|
CG
|
C:HIS4983
|
3.0
|
46.6
|
1.0
|
CE1
|
C:HIS4983
|
3.1
|
50.9
|
1.0
|
CD2
|
C:HIS4978
|
3.1
|
59.3
|
1.0
|
CB
|
C:HIS4983
|
3.3
|
43.2
|
1.0
|
N
|
C:CYS4961
|
3.6
|
55.6
|
1.0
|
CB
|
C:CYS4958
|
3.7
|
56.3
|
1.0
|
CB
|
C:CYS4961
|
3.8
|
58.2
|
1.0
|
ND1
|
C:HIS4978
|
3.9
|
56.1
|
1.0
|
CB
|
C:ILE4960
|
4.0
|
47.0
|
1.0
|
CG
|
C:HIS4978
|
4.1
|
57.5
|
1.0
|
CD2
|
C:HIS4983
|
4.1
|
46.1
|
1.0
|
NE2
|
C:HIS4983
|
4.1
|
47.4
|
1.0
|
CA
|
C:CYS4961
|
4.2
|
54.9
|
1.0
|
CG2
|
C:ILE4960
|
4.5
|
48.1
|
1.0
|
N
|
C:GLY4962
|
4.5
|
55.4
|
1.0
|
C
|
C:ILE4960
|
4.6
|
52.7
|
1.0
|
CA
|
C:ILE4960
|
4.6
|
47.6
|
1.0
|
N
|
C:ILE4960
|
4.6
|
51.0
|
1.0
|
CA
|
C:HIS4983
|
4.8
|
40.2
|
1.0
|
C
|
C:CYS4961
|
4.8
|
55.4
|
1.0
|
CG1
|
C:ILE4960
|
4.9
|
44.0
|
1.0
|
|
Zinc binding site 4 out
of 4 in 8drp
Go back to
Zinc Binding Sites List in 8drp
Zinc binding site 4 out
of 4 in the Focus/Local Refined Map in C4 of Signal Subtracted RYR1 Particles
![](/pictures/ZN/pdb/dr/8drp-ZN-sphere_04.jpg) Mono view
![](/pictures/ZN/pdb/dr/8drp-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 Focus/Local Refined Map in C4 of Signal Subtracted RYR1 Particles within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn5103
b:62.0
occ:1.00
|
NE2
|
D:HIS4978
|
2.0
|
59.5
|
1.0
|
ND1
|
D:HIS4983
|
2.0
|
49.1
|
1.0
|
SG
|
D:CYS4961
|
2.3
|
57.0
|
1.0
|
SG
|
D:CYS4958
|
2.3
|
58.4
|
1.0
|
CE1
|
D:HIS4978
|
2.7
|
56.0
|
1.0
|
CG
|
D:HIS4983
|
3.0
|
46.6
|
1.0
|
CE1
|
D:HIS4983
|
3.1
|
50.9
|
1.0
|
CD2
|
D:HIS4978
|
3.1
|
59.3
|
1.0
|
CB
|
D:HIS4983
|
3.3
|
43.2
|
1.0
|
N
|
D:CYS4961
|
3.6
|
55.6
|
1.0
|
CB
|
D:CYS4958
|
3.7
|
56.3
|
1.0
|
CB
|
D:CYS4961
|
3.8
|
58.2
|
1.0
|
ND1
|
D:HIS4978
|
3.9
|
56.1
|
1.0
|
CB
|
D:ILE4960
|
4.0
|
47.0
|
1.0
|
CG
|
D:HIS4978
|
4.1
|
57.5
|
1.0
|
CD2
|
D:HIS4983
|
4.1
|
46.1
|
1.0
|
NE2
|
D:HIS4983
|
4.1
|
47.4
|
1.0
|
CA
|
D:CYS4961
|
4.2
|
54.9
|
1.0
|
CG2
|
D:ILE4960
|
4.5
|
48.1
|
1.0
|
N
|
D:GLY4962
|
4.5
|
55.4
|
1.0
|
C
|
D:ILE4960
|
4.6
|
52.7
|
1.0
|
CA
|
D:ILE4960
|
4.6
|
47.6
|
1.0
|
N
|
D:ILE4960
|
4.6
|
51.0
|
1.0
|
CA
|
D:HIS4983
|
4.8
|
40.2
|
1.0
|
C
|
D:CYS4961
|
4.8
|
55.4
|
1.0
|
CG1
|
D:ILE4960
|
4.9
|
44.0
|
1.0
|
|
Reference:
O.Haji-Ghassemi,
S.Y.Chen,
G.B.Gurrola,
W.Cai,
C.R.Valdivia,
H.H.Valdivia,
F.Van Petegem.
Cryo-Em Analysis of Calcin Binding to Ryanodine Receptors Reveals A Subconductance State That Is Abolished By Pka Phosphorylation. Sci Adv 2023.
ISSN: ESSN 2375-2548
Page generated: Fri Jul 28 06:49:10 2023
|