Zinc in PDB 7l49: Cryo-Em Structure of Crispr-CAS12F Ternary Complex

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo-Em Structure of Crispr-CAS12F Ternary Complex (pdb code 7l49). 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 Crispr-CAS12F Ternary Complex, PDB code: 7l49:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 7l49

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Zinc binding site 1 out of 4 in the Cryo-Em Structure of Crispr-CAS12F Ternary 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 Crispr-CAS12F Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:61.7
occ:1.00
SG A:CYS500 2.3 40.4 1.0
SG A:CYS478 2.3 37.6 1.0
CB A:CYS503 3.0 41.9 1.0
O A:CYS478 3.1 37.6 1.0
SG A:CYS475 3.5 32.2 1.0
CB A:CYS500 3.6 40.4 1.0
N A:CYS503 3.7 41.9 1.0
CG A:LYS502 3.8 40.4 1.0
CB A:CYS478 3.8 37.6 1.0
CB A:CYS475 3.9 32.2 1.0
CA A:CYS503 3.9 41.9 1.0
CB A:HIS480 4.0 38.5 1.0
C A:CYS478 4.1 37.6 1.0
SG A:CYS503 4.1 41.9 1.0
N A:CYS478 4.2 37.6 1.0
CA A:CYS478 4.2 37.6 1.0
C A:LYS502 4.3 40.4 1.0
CD A:LYS502 4.6 40.4 1.0
N A:LYS502 4.7 40.4 1.0
N A:HIS480 4.8 38.5 1.0
CG A:HIS480 4.9 38.5 1.0
CA A:LYS502 4.9 40.4 1.0
CB A:LYS502 4.9 40.4 1.0
O A:LYS502 4.9 40.4 1.0
CA A:CYS500 5.0 40.4 1.0

Zinc binding site 2 out of 4 in 7l49

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Zinc binding site 2 out of 4 in the Cryo-Em Structure of Crispr-CAS12F Ternary 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 Crispr-CAS12F Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn602

b:61.2
occ:1.00
SG A:CYS72 2.3 31.1 1.0
SG A:CYS69 2.3 31.6 1.0
SG A:CYS50 2.4 42.3 1.0
CG A:HIS53 2.4 47.5 1.0
ND1 A:HIS53 2.4 47.5 1.0
CD2 A:HIS53 2.5 47.5 1.0
CE1 A:HIS53 2.6 47.5 1.0
NE2 A:HIS53 2.6 47.5 1.0
CB A:HIS53 3.3 47.5 1.0
CB A:CYS72 3.3 31.1 1.0
CB A:CYS69 3.4 31.6 1.0
N A:CYS72 3.6 31.1 1.0
CB A:CYS50 3.7 42.3 1.0
CA A:CYS72 4.0 31.1 1.0
N A:CYS50 4.2 42.3 1.0
CA A:CYS50 4.5 42.3 1.0
C A:PHE71 4.5 32.7 1.0
CB A:PHE71 4.6 32.7 1.0
CA A:HIS53 4.7 47.5 1.0
CA A:CYS69 4.9 31.6 1.0
N A:PHE71 4.9 32.7 1.0
CD2 A:PHE71 4.9 32.7 1.0
CA A:PHE71 5.0 32.7 1.0
N A:HIS53 5.0 47.5 1.0

Zinc binding site 3 out of 4 in 7l49

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Zinc binding site 3 out of 4 in the Cryo-Em Structure of Crispr-CAS12F Ternary 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 Crispr-CAS12F Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn601

b:90.9
occ:1.00
SG B:CYS500 2.3 65.1 1.0
SG B:CYS478 2.3 58.6 1.0
CB B:CYS503 3.2 64.3 1.0
CB B:CYS478 3.5 58.6 1.0
CB B:CYS500 3.7 65.1 1.0
SG B:CYS475 3.8 48.9 1.0
N B:CYS478 3.8 58.6 1.0
CB B:CYS475 3.9 48.9 1.0
O B:CYS478 4.0 58.6 1.0
CA B:CYS478 4.1 58.6 1.0
SG B:CYS503 4.1 64.3 1.0
N B:CYS503 4.3 64.3 1.0
CA B:CYS503 4.4 64.3 1.0
C B:CYS478 4.5 58.6 1.0
C B:LYS477 4.6 53.6 1.0
CG B:LYS502 4.7 61.8 1.0
CB B:LYS477 4.8 53.6 1.0
CB B:HIS480 4.9 60.1 1.0
CA B:CYS500 5.0 65.1 1.0

Zinc binding site 4 out of 4 in 7l49

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Zinc binding site 4 out of 4 in the Cryo-Em Structure of Crispr-CAS12F Ternary 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 Crispr-CAS12F Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn602

b:80.1
occ:1.00
CG B:HIS53 2.6 64.4 1.0
CD2 B:HIS53 2.8 64.4 1.0
CB B:HIS53 2.8 64.4 1.0
SG B:CYS50 3.0 64.7 1.0
OE2 B:GLU35 3.2 61.4 1.0
ND1 B:HIS53 3.4 64.4 1.0
NE2 B:HIS53 3.6 64.4 1.0
CB B:CYS50 3.8 64.7 1.0
CE1 B:HIS53 3.9 64.4 1.0
CD B:GLU35 4.1 61.4 1.0
CB B:PHE71 4.3 64.6 1.0
CA B:HIS53 4.4 64.4 1.0
CD2 B:PHE71 4.4 64.6 1.0
CG B:PHE71 4.5 64.6 1.0
OE1 B:GLU35 4.6 61.4 1.0
N B:HIS53 5.0 64.4 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: Mon Jul 12 17:20:36 2021

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