Zinc in PDB 8z3p: The Structure of Type III Crispr-Associated Deaminase in Complex CA6 and Atp, Fully Activated

The structure of The Structure of Type III Crispr-Associated Deaminase in Complex CA6 and Atp, Fully Activated also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the The Structure of Type III Crispr-Associated Deaminase in Complex CA6 and Atp, Fully Activated (pdb code 8z3p). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the The Structure of Type III Crispr-Associated Deaminase in Complex CA6 and Atp, Fully Activated, PDB code: 8z3p:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the The Structure of Type III Crispr-Associated Deaminase in Complex CA6 and Atp, Fully Activated


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Structure of Type III Crispr-Associated Deaminase in Complex CA6 and Atp, Fully Activated within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn702 b:212.3 occ:1.00 NE2 A:HIS266 2.0 175.1 1.0 NE2 A:HIS264 2.3 163.8 1.0 NE2 A:HIS471 2.3 174.4 1.0 CD2 A:HIS471 2.5 166.2 1.0 CE1 A:HIS266 2.6 168.6 1.0 CE1 A:HIS264 2.8 159.3 1.0 CD2 A:HIS266 3.3 167.1 1.0 CD2 A:HIS264 3.5 154.3 1.0 CE1 A:HIS471 3.6 169.2 1.0 CG A:HIS471 3.8 158.1 1.0 ND1 A:HIS266 3.9 160.8 1.0 ND1 A:HIS264 4.0 150.5 1.0 C6 A:ATP701 4.2 189.9 1.0 CG A:HIS266 4.2 159.1 1.0 N6 A:ATP701 4.2 186.1 1.0 OD1 A:ASP569 4.3 171.5 1.0 ND1 A:HIS471 4.3 161.4 1.0 OD2 A:ASP440 4.4 138.1 1.0 CG A:HIS264 4.4 146.7 1.0 HN62 A:ATP701 4.4 183.1 1.0 C5 A:ATP701 4.4 194.2 1.0 HN61 A:ATP701 4.4 185.0 1.0 N1 A:ATP701 4.5 188.1 1.0 CG A:ASP569 4.6 167.8 1.0 OD2 A:ASP569 4.6 168.7 1.0 N7 A:ATP701 4.8 193.2 1.0 C4 A:ATP701 5.0 194.3 1.0 CD A:ARG354 5.0 132.7 1.0 CB A:HIS471 5.0 151.5 1.0

Zinc binding site 2 out of 6 in the The Structure of Type III Crispr-Associated Deaminase in Complex CA6 and Atp, Fully Activated


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Structure of Type III Crispr-Associated Deaminase in Complex CA6 and Atp, Fully Activated within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn702 b:172.8 occ:1.00 NE2 B:HIS266 2.3 127.6 1.0 NE2 B:HIS264 2.3 115.8 1.0 CE1 B:HIS264 2.8 113.9 1.0 CE1 B:HIS471 3.1 133.8 1.0 CD2 B:HIS266 3.2 118.5 1.0 CE1 B:HIS266 3.3 131.2 1.0 CD2 B:HIS264 3.3 108.2 1.0 OD1 B:ASP569 3.6 128.2 1.0 OD2 B:ASP569 3.7 131.0 1.0 CG B:ASP569 3.8 124.5 1.0 ND1 B:HIS264 3.8 106.5 1.0 NE2 B:HIS471 3.9 136.7 1.0 NE2 B:HIS495 4.1 119.5 1.0 ND1 B:HIS471 4.1 125.8 1.0 C6 B:ATP701 4.1 156.4 1.0 CG B:HIS264 4.1 99.8 1.0 NH1 B:ARG354 4.1 118.9 1.0 N6 B:ATP701 4.2 146.6 1.0 C5 B:ATP701 4.2 160.7 1.0 HN61 B:ATP701 4.2 143.0 1.0 ND1 B:HIS266 4.3 127.8 1.0 CG B:HIS266 4.3 118.5 1.0 N7 B:ATP701 4.4 156.9 1.0 HN62 B:ATP701 4.5 143.2 1.0 N1 B:ATP701 4.6 156.7 1.0 CD2 B:HIS495 4.8 115.3 1.0 CB B:ASP569 4.8 110.5 1.0 C4 B:ATP701 4.8 163.2 1.0 CA B:ASP569 4.8 102.2 1.0 CE1 B:HIS495 4.9 112.6 1.0 CZ B:ARG354 5.0 116.3 1.0

Zinc binding site 3 out of 6 in the The Structure of Type III Crispr-Associated Deaminase in Complex CA6 and Atp, Fully Activated


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Structure of Type III Crispr-Associated Deaminase in Complex CA6 and Atp, Fully Activated within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn703 b:165.4 occ:1.00 NE2 C:HIS266 2.3 114.1 1.0 NE2 C:HIS471 2.3 121.6 1.0 NE2 C:HIS264 2.3 114.9 1.0 CE1 C:HIS264 2.5 114.5 1.0 CE1 C:HIS471 2.5 122.4 1.0 CE1 C:HIS266 3.1 115.6 1.0 CD2 C:HIS264 3.2 106.0 1.0 ND1 C:HIS264 3.4 103.7 1.0 CD2 C:HIS266 3.4 102.7 1.0 NH1 C:ARG354 3.5 105.5 1.0 CD2 C:HIS471 3.6 109.7 1.0 CG C:HIS264 3.8 97.4 1.0 ND1 C:HIS471 3.8 117.6 1.0 ND1 C:HIS266 4.3 110.8 1.0 CZ C:ARG354 4.3 100.2 1.0 CG C:HIS471 4.4 107.0 1.0 OD1 C:ASP569 4.4 108.8 1.0 CG C:HIS266 4.5 98.6 1.0 CE1 C:HIS495 4.5 107.2 1.0 CD C:ARG354 4.6 91.8 1.0 C5 C:ATP701 4.6 127.8 1.0 C6 C:ATP701 4.6 128.4 1.0 CG C:ASP569 4.7 106.7 1.0 HN62 C:ATP701 4.7 120.1 1.0 N6 C:ATP701 4.7 123.6 1.0 OD2 C:ASP569 4.7 111.7 1.0 OD2 C:ASP440 4.7 101.7 1.0 N7 C:ATP701 4.7 125.7 1.0 NE C:ARG354 4.7 96.2 1.0 HN61 C:ATP701 5.0 119.9 1.0

Zinc binding site 4 out of 6 in the The Structure of Type III Crispr-Associated Deaminase in Complex CA6 and Atp, Fully Activated


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Structure of Type III Crispr-Associated Deaminase in Complex CA6 and Atp, Fully Activated within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn703 b:160.6 occ:1.00 CE1 D:HIS471 2.2 118.3 1.0 NE2 D:HIS471 2.3 120.4 1.0 NE2 D:HIS266 2.3 110.3 1.0 NE2 D:HIS264 2.3 112.6 1.0 CE1 D:HIS264 2.8 110.2 1.0 CE1 D:HIS266 2.9 112.7 1.0 CD2 D:HIS264 3.3 104.7 1.0 CD2 D:HIS266 3.5 103.2 1.0 ND1 D:HIS471 3.5 107.2 1.0 CD2 D:HIS471 3.7 111.6 1.0 OD2 D:ASP569 3.9 113.3 1.0 ND1 D:HIS264 3.9 103.5 1.0 OD2 D:ASP440 4.0 108.8 1.0 NH1 D:ARG354 4.0 103.0 1.0 ND1 D:HIS266 4.1 106.8 1.0 CD D:ARG354 4.1 94.9 1.0 CZ D:ARG354 4.1 103.3 1.0 CG D:HIS264 4.2 98.0 1.0 NE D:ARG354 4.2 102.6 1.0 CG D:HIS471 4.3 103.0 1.0 CG D:HIS266 4.4 98.8 1.0 NH2 D:ARG354 4.8 99.9 1.0 CB D:ALA442 4.9 101.9 1.0 C5 D:ATP701 4.9 127.2 1.0 N7 D:ATP701 4.9 126.9 1.0 CG D:ASP569 4.9 112.2 1.0 CG D:ASP440 5.0 100.8 1.0

Zinc binding site 5 out of 6 in the The Structure of Type III Crispr-Associated Deaminase in Complex CA6 and Atp, Fully Activated


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Structure of Type III Crispr-Associated Deaminase in Complex CA6 and Atp, Fully Activated within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn702 b:167.6 occ:1.00 CE1 E:HIS264 2.1 118.3 1.0 NE2 E:HIS471 2.3 137.6 1.0 NE2 E:HIS264 2.3 117.2 1.0 NE2 E:HIS266 2.3 128.7 1.0 CE1 E:HIS266 2.6 130.6 1.0 CE1 E:HIS471 3.1 135.3 1.0 ND1 E:HIS264 3.2 110.7 1.0 NH1 E:ARG354 3.4 118.0 1.0 CD2 E:HIS471 3.4 126.2 1.0 CD2 E:HIS264 3.5 109.4 1.0 CD2 E:HIS266 3.6 118.1 1.0 ND1 E:HIS266 3.8 124.3 1.0 CG E:HIS264 3.9 101.9 1.0 CZ E:ARG354 4.2 115.1 1.0 CD E:ARG354 4.2 105.8 1.0 ND1 E:HIS471 4.3 129.7 1.0 OD2 E:ASP569 4.4 123.4 1.0 CG E:HIS266 4.4 114.8 1.0 CG E:HIS471 4.5 120.4 1.0 NE E:ARG354 4.6 111.7 1.0 C5 E:ATP701 4.6 148.7 1.0 OD2 E:ASP440 4.7 115.4 1.0 C6 E:ATP701 4.7 143.3 1.0 N7 E:ATP701 4.8 145.4 1.0 C4 E:ATP701 4.9 154.0 1.0

Zinc binding site 6 out of 6 in the The Structure of Type III Crispr-Associated Deaminase in Complex CA6 and Atp, Fully Activated


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The Structure of Type III Crispr-Associated Deaminase in Complex CA6 and Atp, Fully Activated within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn702 b:215.0 occ:1.00 CE1 F:HIS471 2.2 180.0 1.0 CE1 F:HIS266 2.2 163.6 1.0 NE2 F:HIS264 2.3 162.3 1.0 NE2 F:HIS471 2.3 173.1 1.0 NE2 F:HIS266 2.3 174.7 1.0 CE1 F:HIS264 2.3 159.6 1.0 ND1 F:HIS471 3.4 179.1 1.0 ND1 F:HIS264 3.5 150.2 1.0 ND1 F:HIS266 3.5 151.5 1.0 CD2 F:HIS264 3.5 152.0 1.0 CD2 F:HIS471 3.6 166.2 1.0 CD2 F:HIS266 3.7 168.2 1.0 CG F:HIS471 4.1 167.5 1.0 CG F:HIS264 4.1 143.8 1.0 CD F:ARG354 4.1 133.6 1.0 CG F:HIS266 4.2 155.4 1.0 OD1 F:ASP440 4.3 145.7 1.0 NE F:ARG354 4.4 141.8 1.0 N7 F:ATP701 4.6 195.4 1.0 CZ F:ARG354 4.7 145.0 1.0 C5 F:ATP701 4.7 197.3 1.0 NH1 F:ARG354 4.8 141.9 1.0 CE1 F:HIS495 4.8 158.3 1.0 C6 F:ATP701 4.9 192.2 1.0 HN62 F:ATP701 5.0 184.3 1.0

Y.Li, Z.Li, P.Yan, C.Hua, J.Kong, W.Wu, Y.Cui, Y.Duan, S.Li, G.Li, S.Ji, Y.Chen, Y.Zhao, P.Yang, C.Hu, M.Lu, M.Chen, Y.Xiao. Antiviral Signaling of A Type III Crispr-Associated Deaminase. Science R0393 2024.
ISSN: ESSN 1095-9203
PubMed: 39666823
DOI: 10.1126/SCIENCE.ADR0393