Zinc in PDB 7y81: Cryoem Structure of Type III-E Crispr Craspase Gramp-Crrna Complex Bound to Non-Self Rna Target
Other elements in 7y81:
The structure of Cryoem Structure of Type III-E Crispr Craspase Gramp-Crrna Complex Bound to Non-Self Rna Target also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Cryoem Structure of Type III-E Crispr Craspase Gramp-Crrna Complex Bound to Non-Self Rna Target
(pdb code 7y81). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Cryoem Structure of Type III-E Crispr Craspase Gramp-Crrna Complex Bound to Non-Self Rna Target, PDB code: 7y81:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 7y81
Go back to
Zinc Binding Sites List in 7y81
Zinc binding site 1 out
of 4 in the Cryoem Structure of Type III-E Crispr Craspase Gramp-Crrna Complex Bound to Non-Self Rna Target
![](/pictures/ZN/pdb/y8/7y81-ZN-sphere_01.jpg) Mono view
![](/pictures/ZN/pdb/y8/7y81-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 Cryoem Structure of Type III-E Crispr Craspase Gramp-Crrna Complex Bound to Non-Self Rna Target within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn1801
b:81.1
occ:1.00
|
ND1
|
A:HIS747
|
2.1
|
54.3
|
1.0
|
SG
|
A:CYS752
|
2.3
|
46.8
|
1.0
|
SG
|
A:CYS755
|
2.3
|
46.3
|
1.0
|
SG
|
A:CYS750
|
2.3
|
60.9
|
1.0
|
CE1
|
A:HIS747
|
2.6
|
50.8
|
1.0
|
CB
|
A:CYS755
|
3.0
|
33.0
|
1.0
|
CB
|
A:CYS752
|
3.1
|
39.5
|
1.0
|
CG
|
A:HIS747
|
3.3
|
52.6
|
1.0
|
CB
|
A:CYS750
|
3.4
|
47.5
|
1.0
|
NE2
|
A:HIS747
|
3.8
|
47.7
|
1.0
|
N
|
A:CYS755
|
4.0
|
40.6
|
1.0
|
CA
|
A:CYS755
|
4.0
|
34.0
|
1.0
|
CB
|
A:HIS747
|
4.0
|
51.4
|
1.0
|
N
|
A:CYS752
|
4.1
|
40.5
|
1.0
|
CA
|
A:CYS752
|
4.1
|
36.3
|
1.0
|
CD
|
A:LYS744
|
4.2
|
52.7
|
1.0
|
CD2
|
A:HIS747
|
4.2
|
49.3
|
1.0
|
CA
|
A:CYS750
|
4.6
|
50.7
|
1.0
|
CA
|
A:HIS747
|
4.7
|
50.8
|
1.0
|
C
|
A:CYS750
|
4.7
|
51.5
|
1.0
|
C
|
A:CYS752
|
4.8
|
42.3
|
1.0
|
CE
|
A:MET754
|
4.8
|
35.8
|
1.0
|
CE
|
A:LYS744
|
4.8
|
54.7
|
1.0
|
O
|
A:CYS750
|
4.8
|
51.6
|
1.0
|
O
|
A:CYS752
|
4.9
|
48.3
|
1.0
|
NZ
|
A:LYS744
|
5.0
|
53.2
|
1.0
|
|
Zinc binding site 2 out
of 4 in 7y81
Go back to
Zinc Binding Sites List in 7y81
Zinc binding site 2 out
of 4 in the Cryoem Structure of Type III-E Crispr Craspase Gramp-Crrna Complex Bound to Non-Self Rna Target
![](/pictures/ZN/pdb/y8/7y81-ZN-sphere_02.jpg) Mono view
![](/pictures/ZN/pdb/y8/7y81-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 Cryoem Structure of Type III-E Crispr Craspase Gramp-Crrna Complex Bound to Non-Self Rna Target within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn1802
b:91.6
occ:1.00
|
SG
|
A:CYS501
|
2.3
|
42.9
|
1.0
|
SG
|
A:CYS491
|
2.3
|
56.0
|
1.0
|
SG
|
A:CYS503
|
2.3
|
44.0
|
1.0
|
SG
|
A:CYS506
|
2.3
|
41.7
|
1.0
|
CB
|
A:CYS506
|
2.9
|
25.2
|
1.0
|
CB
|
A:CYS491
|
3.3
|
41.2
|
1.0
|
CB
|
A:CYS503
|
3.3
|
33.1
|
1.0
|
CB
|
A:CYS501
|
3.3
|
34.0
|
1.0
|
CA
|
A:CYS506
|
4.0
|
28.3
|
1.0
|
N
|
A:CYS506
|
4.0
|
37.5
|
1.0
|
CA
|
A:CYS503
|
4.3
|
30.6
|
1.0
|
N
|
A:CYS503
|
4.3
|
36.6
|
1.0
|
CA
|
A:CYS491
|
4.4
|
42.1
|
1.0
|
N
|
A:CYS491
|
4.4
|
39.6
|
1.0
|
NH1
|
A:ARG480
|
4.5
|
23.1
|
1.0
|
CA
|
A:CYS501
|
4.6
|
39.1
|
1.0
|
O
|
A:CYS503
|
4.7
|
38.1
|
1.0
|
C
|
A:CYS503
|
4.8
|
35.1
|
1.0
|
C
|
A:CYS501
|
4.8
|
41.1
|
1.0
|
C
|
A:CYS491
|
4.9
|
43.9
|
1.0
|
O
|
A:CYS491
|
4.9
|
47.2
|
1.0
|
O
|
A:CYS501
|
4.9
|
42.7
|
1.0
|
|
Zinc binding site 3 out
of 4 in 7y81
Go back to
Zinc Binding Sites List in 7y81
Zinc binding site 3 out
of 4 in the Cryoem Structure of Type III-E Crispr Craspase Gramp-Crrna Complex Bound to Non-Self Rna Target
![](/pictures/ZN/pdb/y8/7y81-ZN-sphere_03.jpg) Mono view
![](/pictures/ZN/pdb/y8/7y81-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 Cryoem Structure of Type III-E Crispr Craspase Gramp-Crrna Complex Bound to Non-Self Rna Target within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn1803
b:64.5
occ:1.00
|
SG
|
A:CYS1414
|
2.3
|
29.6
|
1.0
|
SG
|
A:CYS1018
|
2.3
|
37.9
|
1.0
|
SG
|
A:CYS1417
|
2.3
|
46.2
|
1.0
|
SG
|
A:CYS1406
|
2.3
|
27.1
|
1.0
|
CB
|
A:CYS1417
|
2.7
|
22.7
|
1.0
|
CB
|
A:CYS1414
|
3.2
|
25.9
|
1.0
|
CB
|
A:CYS1406
|
3.4
|
33.6
|
1.0
|
CB
|
A:CYS1018
|
3.4
|
34.5
|
1.0
|
N
|
A:CYS1406
|
3.8
|
34.8
|
1.0
|
CA
|
A:CYS1417
|
4.0
|
17.6
|
1.0
|
N
|
A:CYS1414
|
4.0
|
28.4
|
1.0
|
N
|
A:CYS1417
|
4.1
|
26.1
|
1.0
|
CA
|
A:CYS1414
|
4.2
|
29.7
|
1.0
|
CA
|
A:CYS1406
|
4.2
|
32.7
|
1.0
|
OE2
|
A:GLU1012
|
4.3
|
44.1
|
1.0
|
N
|
A:CYS1018
|
4.4
|
40.5
|
1.0
|
CA
|
A:CYS1018
|
4.4
|
35.5
|
1.0
|
CB
|
A:ALA1020
|
4.8
|
31.0
|
1.0
|
C
|
A:PRO1405
|
4.8
|
41.2
|
1.0
|
O
|
A:CYS1414
|
4.8
|
44.8
|
1.0
|
C
|
A:CYS1414
|
4.8
|
32.6
|
1.0
|
NH2
|
A:ARG935
|
4.8
|
30.6
|
1.0
|
CA
|
A:PRO1405
|
4.8
|
36.3
|
1.0
|
C
|
A:CYS1018
|
4.9
|
38.1
|
1.0
|
NH2
|
A:ARG1008
|
4.9
|
24.5
|
1.0
|
|
Zinc binding site 4 out
of 4 in 7y81
Go back to
Zinc Binding Sites List in 7y81
Zinc binding site 4 out
of 4 in the Cryoem Structure of Type III-E Crispr Craspase Gramp-Crrna Complex Bound to Non-Self Rna Target
![](/pictures/ZN/pdb/y8/7y81-ZN-sphere_04.jpg) Mono view
![](/pictures/ZN/pdb/y8/7y81-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 Cryoem Structure of Type III-E Crispr Craspase Gramp-Crrna Complex Bound to Non-Self Rna Target within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn1805
b:97.5
occ:1.00
|
SG
|
A:CYS130
|
2.3
|
59.9
|
1.0
|
SG
|
A:CYS127
|
2.3
|
56.0
|
1.0
|
SG
|
A:CYS121
|
2.3
|
73.5
|
1.0
|
SG
|
A:CYS88
|
2.3
|
58.7
|
1.0
|
CB
|
A:CYS130
|
3.2
|
48.8
|
1.0
|
CB
|
A:CYS121
|
3.3
|
70.9
|
1.0
|
CB
|
A:CYS88
|
3.4
|
54.9
|
1.0
|
CB
|
A:CYS127
|
3.5
|
51.9
|
1.0
|
N
|
A:CYS130
|
4.0
|
51.3
|
1.0
|
N
|
A:CYS127
|
4.1
|
55.9
|
1.0
|
N
|
A:CYS88
|
4.1
|
54.9
|
1.0
|
CA
|
A:CYS130
|
4.2
|
48.5
|
1.0
|
CA
|
A:CYS88
|
4.3
|
56.6
|
1.0
|
CA
|
A:CYS127
|
4.3
|
52.1
|
1.0
|
NH1
|
A:ARG135
|
4.6
|
47.3
|
1.0
|
N
|
A:GLY90
|
4.7
|
56.9
|
1.0
|
CA
|
A:CYS121
|
4.7
|
71.1
|
1.0
|
C
|
A:CYS88
|
4.7
|
56.5
|
1.0
|
O
|
A:CYS127
|
4.9
|
54.5
|
1.0
|
CA
|
A:GLY90
|
4.9
|
48.8
|
1.0
|
C
|
A:CYS127
|
4.9
|
53.0
|
1.0
|
|
Reference:
N.Cui,
J.T.Zhang,
Z.Li,
X.Y.Liu,
C.Wang,
H.Huang,
N.Jia.
Structural Basis For the Non-Self Rna-Activated Protease Activity of the Type III-E Crispr Nuclease-Protease Craspase Nat Commun V. 13 7549 2022.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-022-35275-5
Page generated: Sat Apr 8 06:14:08 2023
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