Zinc in PDB 6ki3: The Crystal Structure of Asfvap:Df Commplex

The structure of The Crystal Structure of Asfvap:Df Commplex, PDB code: 6ki3 was solved by Y.Chen, J.Gan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.35 / 2.35
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.637, 84.698, 98.585, 90.00, 93.66, 90.00
R / Rfree (%)	20.8 / 24.4

The binding sites of Zinc atom in the The Crystal Structure of Asfvap:Df Commplex (pdb code 6ki3). 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 Crystal Structure of Asfvap:Df Commplex, PDB code: 6ki3:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the The Crystal Structure of Asfvap:Df Commplex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Crystal Structure of Asfvap:Df Commplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:26.0 occ:1.00 OD2 A:ASP231 2.0 30.0 1.0 NE2 A:HIS233 2.1 27.8 1.0 NE2 A:HIS182 2.1 27.8 1.0 OP3 D:3DR10 2.2 30.6 1.0 OP2 D:3DR10 2.5 28.1 1.0 P D:3DR10 2.7 26.9 1.0 CG A:ASP231 2.8 30.3 1.0 CE1 A:HIS233 2.8 27.6 1.0 OD1 A:ASP231 2.9 30.0 1.0 CE1 A:HIS182 3.0 26.8 1.0 CD2 A:HIS182 3.1 27.7 1.0 CD2 A:HIS233 3.2 28.6 1.0 O D:HOH102 3.5 34.8 1.0 O3' C:DC9 3.6 31.1 1.0 O5' D:3DR10 3.6 33.1 1.0 ND1 A:HIS233 3.9 29.8 1.0 OD2 A:ASP179 4.1 24.3 1.0 OP1 D:3DR10 4.1 29.1 1.0 CG A:HIS233 4.1 30.2 1.0 CB A:ASP231 4.2 29.4 1.0 ND1 A:HIS182 4.2 30.0 1.0 CG A:HIS182 4.2 27.9 1.0 ZN A:ZN302 4.4 28.1 1.0 CG A:ASP179 4.7 26.7 1.0 C3' C:DC9 4.7 37.4 1.0 C5' D:3DR10 4.8 27.9 1.0 C4' C:DC9 4.8 36.1 1.0 OD1 A:ASP179 4.8 28.4 1.0 CD2 A:HIS145 4.9 31.1 1.0 OE1 A:GLU142 5.0 25.9 1.0

Zinc binding site 2 out of 6 in the The Crystal Structure of Asfvap:Df Commplex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Crystal Structure of Asfvap:Df Commplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:28.1 occ:1.00 OP2 D:3DR10 2.1 28.1 1.0 OD2 A:ASP179 2.1 24.3 1.0 OE1 A:GLU142 2.1 25.9 1.0 OE2 A:GLU271 2.3 25.6 1.0 ND1 A:HIS218 2.3 25.2 1.0 CE1 A:HIS218 3.0 22.0 1.0 CD A:GLU271 3.0 27.7 1.0 OE1 A:GLU271 3.0 24.0 1.0 CD A:GLU142 3.1 26.7 1.0 ZN A:ZN303 3.2 26.0 1.0 P D:3DR10 3.3 26.9 1.0 CG A:ASP179 3.3 26.7 1.0 CG A:HIS218 3.4 24.9 1.0 OE2 A:GLU142 3.5 25.4 1.0 OP1 D:3DR10 3.6 29.1 1.0 O5' D:3DR10 3.8 33.1 1.0 CB A:HIS218 3.9 24.5 1.0 CE1 A:HIS182 4.0 26.8 1.0 CB A:ASP179 4.0 24.1 1.0 NE2 A:HIS218 4.1 22.0 1.0 ND2 A:ASN220 4.2 26.3 1.0 NE2 A:HIS182 4.2 27.8 1.0 OD1 A:ASP179 4.3 28.4 1.0 CD2 A:HIS218 4.3 21.0 1.0 CG A:GLU142 4.4 25.3 1.0 CE1 A:HIS233 4.4 27.6 1.0 ZN A:ZN301 4.4 26.0 1.0 CG A:GLU271 4.5 27.1 1.0 OP3 D:3DR10 4.6 30.6 1.0 ND1 A:HIS182 4.7 30.0 1.0 NE2 A:HIS78 4.8 27.6 1.0 NE2 A:HIS233 4.8 27.8 1.0 C5' D:3DR10 4.9 27.9 1.0

Zinc binding site 3 out of 6 in the The Crystal Structure of Asfvap:Df Commplex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Crystal Structure of Asfvap:Df Commplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:26.0 occ:1.00 OP1 D:3DR10 2.0 29.1 1.0 NE2 A:HIS115 2.1 30.9 1.0 OE2 A:GLU142 2.1 25.4 1.0 NE2 A:HIS78 2.2 27.6 1.0 CD A:GLU142 2.9 26.7 1.0 OE1 A:GLU142 3.0 25.9 1.0 CE1 A:HIS115 3.1 28.6 1.0 CD2 A:HIS78 3.1 27.2 1.0 CD2 A:HIS115 3.1 28.2 1.0 CE1 A:HIS78 3.2 26.1 1.0 P D:3DR10 3.2 26.9 1.0 ZN A:ZN302 3.2 28.1 1.0 OP2 D:3DR10 3.4 28.1 1.0 O5' D:3DR10 4.0 33.1 1.0 ND1 A:HIS115 4.2 26.1 1.0 CE1 A:HIS218 4.2 22.0 1.0 ND1 A:HIS78 4.3 28.0 1.0 CG A:HIS115 4.3 27.7 1.0 CG A:HIS78 4.3 27.2 1.0 CG A:GLU142 4.3 25.3 1.0 C5' D:3DR10 4.4 27.9 1.0 OE1 A:GLU271 4.4 24.0 1.0 OP3 D:3DR10 4.4 30.6 1.0 ND1 A:HIS218 4.5 25.2 1.0 CG1 A:VAL113 4.6 25.8 1.0 CE1 A:HIS182 4.6 26.8 1.0 CB A:GLU142 4.8 23.1 1.0

Zinc binding site 4 out of 6 in the The Crystal Structure of Asfvap:Df Commplex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Crystal Structure of Asfvap:Df Commplex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:21.1 occ:1.00 NE2 B:HIS182 2.0 21.8 1.0 OD2 B:ASP231 2.0 26.0 1.0 OP3 G:3DR10 2.0 30.0 1.0 NE2 B:HIS233 2.1 18.9 1.0 OP2 G:3DR10 2.7 19.7 1.0 CG B:ASP231 2.8 22.7 1.0 P G:3DR10 2.8 19.6 1.0 OD1 B:ASP231 2.8 22.3 1.0 CD2 B:HIS182 3.0 20.0 1.0 CE1 B:HIS182 3.0 22.7 1.0 CE1 B:HIS233 3.0 20.5 1.0 CD2 B:HIS233 3.1 21.1 1.0 O5' G:3DR10 3.8 25.7 1.0 O3' F:DC9 4.1 45.2 1.0 OP1 G:3DR10 4.1 23.5 1.0 ND1 B:HIS182 4.1 19.2 1.0 OD2 B:ASP179 4.1 15.6 1.0 CG B:HIS182 4.1 19.2 1.0 ND1 B:HIS233 4.2 21.5 1.0 CG B:HIS233 4.2 23.2 1.0 O G:HOH104 4.2 34.1 1.0 CB B:ASP231 4.2 23.1 1.0 ZN B:ZN302 4.4 21.7 1.0 CG B:ASP179 4.7 17.8 1.0 C5' G:3DR10 4.9 28.9 1.0 OD1 B:ASP179 4.9 22.1 1.0

Zinc binding site 5 out of 6 in the The Crystal Structure of Asfvap:Df Commplex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Crystal Structure of Asfvap:Df Commplex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:21.7 occ:1.00 OE1 B:GLU142 2.0 18.4 1.0 OP2 G:3DR10 2.0 19.7 1.0 OE2 B:GLU271 2.1 16.1 1.0 OD2 B:ASP179 2.2 15.6 1.0 ND1 B:HIS218 2.3 16.6 1.0 CD B:GLU271 3.0 20.2 1.0 CD B:GLU142 3.0 19.6 1.0 CE1 B:HIS218 3.0 16.4 1.0 OE1 B:GLU271 3.3 17.4 1.0 P G:3DR10 3.3 19.6 1.0 CG B:ASP179 3.3 17.8 1.0 CG B:HIS218 3.4 18.5 1.0 ZN B:ZN303 3.4 21.2 1.0 OE2 B:GLU142 3.4 20.1 1.0 OP1 G:3DR10 3.8 23.5 1.0 O5' G:3DR10 3.8 25.7 1.0 CB B:ASP179 3.8 17.7 1.0 CB B:HIS218 3.8 16.1 1.0 CE1 B:HIS182 3.9 22.7 1.0 NE2 B:HIS182 4.1 21.8 1.0 NE2 B:HIS218 4.1 17.3 1.0 CD2 B:HIS218 4.3 16.3 1.0 CG B:GLU142 4.4 21.4 1.0 OD1 B:ASP179 4.4 22.1 1.0 CG B:GLU271 4.4 22.2 1.0 ZN B:ZN301 4.4 21.1 1.0 ND2 B:ASN220 4.4 19.1 1.0 CE1 B:HIS233 4.5 20.5 1.0 OP3 G:3DR10 4.5 30.0 1.0 ND1 B:HIS182 4.6 19.2 1.0 NE2 B:HIS233 4.8 18.9 1.0 CD2 B:HIS182 4.9 20.0 1.0 NE2 B:HIS78 4.9 18.4 1.0

Zinc binding site 6 out of 6 in the The Crystal Structure of Asfvap:Df Commplex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The Crystal Structure of Asfvap:Df Commplex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:21.2 occ:1.00 OE2 B:GLU142 1.9 20.1 1.0 OP1 G:3DR10 2.1 23.5 1.0 NE2 B:HIS78 2.2 18.4 1.0 NE2 B:HIS115 2.2 19.7 1.0 CD B:GLU142 3.0 19.6 1.0 CE1 B:HIS78 3.1 22.0 1.0 CD2 B:HIS115 3.2 20.8 1.0 P G:3DR10 3.2 19.6 1.0 CE1 B:HIS115 3.2 21.5 1.0 CD2 B:HIS78 3.2 20.8 1.0 OP2 G:3DR10 3.3 19.7 1.0 OE1 B:GLU142 3.3 18.4 1.0 ZN B:ZN302 3.4 21.7 1.0 O5' G:3DR10 3.9 25.7 1.0 ND1 B:HIS78 4.2 23.5 1.0 ND1 B:HIS115 4.3 21.8 1.0 CG B:GLU142 4.3 21.4 1.0 CG B:HIS78 4.3 22.6 1.0 CG B:HIS115 4.3 21.6 1.0 OE1 B:GLU271 4.4 17.4 1.0 C5' G:3DR10 4.4 28.9 1.0 CE1 B:HIS218 4.4 16.4 1.0 O B:HOH441 4.4 18.5 1.0 OP3 G:3DR10 4.5 30.0 1.0 CG1 B:VAL113 4.5 17.3 1.0 CE1 B:HIS182 4.5 22.7 1.0 CB B:GLU142 4.7 20.1 1.0 ND1 B:HIS218 4.7 16.6 1.0 OE2 B:GLU271 4.8 16.1 1.0

Y.Chen, X.Chen, Q.Huang, Z.Shao, Y.Gao, Y.Li, C.Yang, H.Liu, J.Li, Q.Wang, J.Ma, Y.Z.Zhang, Y.Gu, J.Gan. A Unique Dna-Binding Mode of African Swine Fever Virus Ap Endonuclease. Cell Discov V. 6 13 2020.
ISSN: ESSN 2056-5968
PubMed: 32194979
DOI: 10.1038/S41421-020-0146-2