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

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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

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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

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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

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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: Mon Jul 12 17:20:31 2021

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