Zinc in PDB 7l48: Cryo-Em Structure of A Crispr-CAS12F Binary Complex
Zinc Binding Sites:
The binding sites of Zinc atom in the Cryo-Em Structure of A Crispr-CAS12F Binary Complex
(pdb code 7l48). 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 A Crispr-CAS12F Binary Complex, PDB code: 7l48:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 7l48
Go back to
Zinc Binding Sites List in 7l48
Zinc binding site 1 out
of 4 in the Cryo-Em Structure of A Crispr-CAS12F Binary Complex
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 Crispr-CAS12F Binary Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn601
b:204.8
occ:1.00
|
SG
|
A:CYS500
|
2.3
|
168.3
|
1.0
|
OD1
|
A:ASN482
|
2.5
|
153.8
|
1.0
|
CB
|
A:CYS500
|
2.7
|
168.3
|
1.0
|
CB
|
A:CYS475
|
2.9
|
144.7
|
1.0
|
SG
|
A:CYS475
|
3.0
|
144.7
|
1.0
|
CB
|
A:HIS480
|
3.1
|
150.2
|
1.0
|
CG
|
A:ASN482
|
3.3
|
153.8
|
1.0
|
ND2
|
A:ASN482
|
3.4
|
153.8
|
1.0
|
CA
|
A:CYS500
|
3.6
|
168.3
|
1.0
|
O
|
A:CYS478
|
3.9
|
139.1
|
1.0
|
CG
|
A:HIS480
|
4.0
|
150.2
|
1.0
|
CA
|
A:HIS480
|
4.2
|
150.2
|
1.0
|
N
|
A:HIS480
|
4.2
|
150.2
|
1.0
|
N
|
A:GLU501
|
4.3
|
155.5
|
1.0
|
CA
|
A:CYS475
|
4.4
|
144.7
|
1.0
|
ND1
|
A:HIS480
|
4.4
|
150.2
|
1.0
|
C
|
A:CYS500
|
4.4
|
168.3
|
1.0
|
SG
|
A:CYS478
|
4.5
|
139.1
|
1.0
|
CZ
|
A:PHE498
|
4.6
|
154.4
|
1.0
|
N
|
A:CYS500
|
4.7
|
168.3
|
1.0
|
C
|
A:HIS480
|
4.7
|
150.2
|
1.0
|
CB
|
A:ASN482
|
4.7
|
153.8
|
1.0
|
CE2
|
A:PHE498
|
4.9
|
154.4
|
1.0
|
CB
|
A:CYS503
|
4.9
|
164.2
|
1.0
|
N
|
A:CYS475
|
4.9
|
144.7
|
1.0
|
N
|
A:LEU481
|
5.0
|
142.6
|
1.0
|
|
Zinc binding site 2 out
of 4 in 7l48
Go back to
Zinc Binding Sites List in 7l48
Zinc binding site 2 out
of 4 in the Cryo-Em Structure of A Crispr-CAS12F Binary Complex
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 Crispr-CAS12F Binary Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn602
b:170.2
occ:1.00
|
CE1
|
A:HIS53
|
1.9
|
132.1
|
1.0
|
ND1
|
A:HIS53
|
2.2
|
132.1
|
1.0
|
SG
|
A:CYS72
|
2.3
|
111.1
|
1.0
|
SG
|
A:CYS69
|
2.3
|
109.8
|
1.0
|
SG
|
A:CYS50
|
2.4
|
133.0
|
1.0
|
NE2
|
A:HIS53
|
2.7
|
132.1
|
1.0
|
CG
|
A:HIS53
|
3.1
|
132.1
|
1.0
|
CB
|
A:CYS69
|
3.3
|
109.8
|
1.0
|
CD2
|
A:HIS53
|
3.3
|
132.1
|
1.0
|
CB
|
A:CYS50
|
3.5
|
133.0
|
1.0
|
CB
|
A:CYS72
|
3.6
|
111.1
|
1.0
|
N
|
A:CYS72
|
3.6
|
111.1
|
1.0
|
CA
|
A:CYS72
|
4.2
|
111.1
|
1.0
|
CB
|
A:HIS53
|
4.2
|
132.1
|
1.0
|
N
|
A:CYS50
|
4.3
|
133.0
|
1.0
|
CB
|
A:PHE71
|
4.3
|
112.3
|
1.0
|
CA
|
A:CYS50
|
4.4
|
133.0
|
1.0
|
C
|
A:PHE71
|
4.6
|
112.3
|
1.0
|
N
|
A:PHE71
|
4.6
|
112.3
|
1.0
|
CA
|
A:CYS69
|
4.7
|
109.8
|
1.0
|
CA
|
A:PHE71
|
4.8
|
112.3
|
1.0
|
CD2
|
A:PHE71
|
5.0
|
112.3
|
1.0
|
|
Zinc binding site 3 out
of 4 in 7l48
Go back to
Zinc Binding Sites List in 7l48
Zinc binding site 3 out
of 4 in the Cryo-Em Structure of A Crispr-CAS12F Binary Complex
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 Crispr-CAS12F Binary Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn601
b:149.3
occ:1.00
|
SG
|
B:CYS478
|
2.3
|
129.7
|
1.0
|
SG
|
B:CYS475
|
2.3
|
129.5
|
1.0
|
N
|
B:CYS478
|
2.6
|
129.7
|
1.0
|
CB
|
B:CYS475
|
2.7
|
129.5
|
1.0
|
O
|
B:CYS478
|
3.0
|
129.7
|
1.0
|
SG
|
B:CYS500
|
3.1
|
129.6
|
1.0
|
CA
|
B:CYS478
|
3.3
|
129.7
|
1.0
|
CB
|
B:CYS478
|
3.3
|
129.7
|
1.0
|
CB
|
B:LYS477
|
3.4
|
132.2
|
1.0
|
C
|
B:LYS477
|
3.5
|
132.2
|
1.0
|
C
|
B:CYS478
|
3.5
|
129.7
|
1.0
|
CA
|
B:LYS477
|
3.8
|
132.2
|
1.0
|
N
|
B:LYS477
|
3.9
|
132.2
|
1.0
|
CB
|
B:CYS503
|
4.0
|
131.6
|
1.0
|
CA
|
B:CYS475
|
4.0
|
129.5
|
1.0
|
CB
|
B:CYS500
|
4.1
|
129.6
|
1.0
|
C
|
B:CYS475
|
4.2
|
129.5
|
1.0
|
O
|
B:CYS475
|
4.4
|
129.5
|
1.0
|
SG
|
B:CYS503
|
4.4
|
131.6
|
1.0
|
O
|
B:LYS477
|
4.6
|
132.2
|
1.0
|
CG
|
B:LYS477
|
4.7
|
132.2
|
1.0
|
N
|
B:SER476
|
4.7
|
128.0
|
1.0
|
C
|
B:SER476
|
4.8
|
128.0
|
1.0
|
N
|
B:CYS475
|
4.8
|
129.5
|
1.0
|
N
|
B:GLY479
|
4.9
|
120.6
|
1.0
|
|
Zinc binding site 4 out
of 4 in 7l48
Go back to
Zinc Binding Sites List in 7l48
Zinc binding site 4 out
of 4 in the Cryo-Em Structure of A Crispr-CAS12F Binary Complex
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 Crispr-CAS12F Binary Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn602
b:451.1
occ:1.00
|
SG
|
B:CYS50
|
2.3
|
448.6
|
1.0
|
CB
|
B:CYS69
|
2.8
|
428.9
|
1.0
|
O
|
B:CYS69
|
2.9
|
428.9
|
1.0
|
C
|
B:CYS69
|
3.0
|
428.9
|
1.0
|
N
|
B:PHE71
|
3.2
|
426.0
|
1.0
|
SG
|
B:CYS69
|
3.3
|
428.9
|
1.0
|
CB
|
B:CYS50
|
3.3
|
448.6
|
1.0
|
N
|
B:CYS72
|
3.4
|
431.4
|
1.0
|
CA
|
B:CYS69
|
3.4
|
428.9
|
1.0
|
N
|
B:LEU70
|
3.6
|
411.0
|
1.0
|
CB
|
B:PHE71
|
3.7
|
426.0
|
1.0
|
CA
|
B:PHE71
|
3.8
|
426.0
|
1.0
|
N
|
B:CYS69
|
3.9
|
428.9
|
1.0
|
C
|
B:PHE71
|
4.1
|
426.0
|
1.0
|
C
|
B:LEU70
|
4.1
|
411.0
|
1.0
|
CB
|
B:CYS72
|
4.2
|
431.4
|
1.0
|
CA
|
B:CYS50
|
4.2
|
448.6
|
1.0
|
SG
|
B:CYS72
|
4.3
|
431.4
|
1.0
|
CA
|
B:CYS72
|
4.4
|
431.4
|
1.0
|
CD1
|
B:PHE71
|
4.4
|
426.0
|
1.0
|
CA
|
B:LEU70
|
4.5
|
411.0
|
1.0
|
CG
|
B:PHE71
|
4.6
|
426.0
|
1.0
|
|
Reference:
R.Xiao,
Z.Li,
S.Wang,
R.Han,
L.Chang.
Structural Basis For Substrate Recognition and Cleavage By the Dimerization-Dependent Crispr-CAS12F Nuclease. Nucleic Acids Res. V. 49 4120 2021.
ISSN: ESSN 1362-4962
PubMed: 33764415
DOI: 10.1093/NAR/GKAB179
Page generated: Tue Oct 29 22:40:43 2024
|