Zinc in PDB 6khy: The Crystal Structure of Asfvap:Ag

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

Resolution Low / High (Å)	29.93 / 3.01
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	110.512, 148.504, 178.058, 90.00, 90.00, 90.00
R / Rfree (%)	21.1 / 24.9

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the The Crystal Structure of Asfvap:Ag (pdb code 6khy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the The Crystal Structure of Asfvap:Ag, PDB code: 6khy:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in the The Crystal Structure of Asfvap:Ag


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:Ag within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:31.6 occ:1.00 OE1 A:GLU142 1.9 40.2 1.0 NE2 A:HIS78 2.0 26.4 1.0 O1S A:MES304 2.0 57.4 1.0 NE2 A:HIS115 2.2 46.7 1.0 CD A:GLU142 2.6 35.2 1.0 CE1 A:HIS115 2.8 47.9 1.0 OE2 A:GLU142 2.8 39.1 1.0 CE1 A:HIS78 2.9 22.4 1.0 CD2 A:HIS78 3.1 29.0 1.0 CD2 A:HIS115 3.1 39.6 1.0 S A:MES304 3.1 51.9 1.0 O3S A:MES304 3.1 36.5 1.0 ND1 A:HIS115 3.8 41.2 1.0 CG A:HIS115 3.9 36.9 1.0 ZN A:ZN302 4.0 39.8 1.0 CG A:GLU142 4.0 25.5 1.0 ND1 A:HIS78 4.0 22.5 1.0 CG A:HIS78 4.1 27.1 1.0 O2S A:MES304 4.2 50.9 1.0 C8 A:MES304 4.2 72.4 1.0 OE1 A:GLU271 4.4 67.8 1.0 CE1 A:HIS182 4.5 42.2 1.0 CB A:GLU142 4.5 21.1 1.0 CE1 A:HIS218 4.7 31.0 1.0 CG1 A:VAL113 4.7 22.4 1.0 ND1 A:HIS218 4.9 33.8 1.0

Zinc binding site 2 out of 12 in the The Crystal Structure of Asfvap:Ag


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:Ag within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:39.8 occ:1.00 OE2 A:GLU271 1.9 63.6 1.0 OD2 A:ASP179 1.9 34.9 1.0 OE2 A:GLU142 2.0 39.1 1.0 O3S A:MES304 2.1 36.5 1.0 ND1 A:HIS218 2.1 33.8 1.0 CD A:GLU271 2.8 50.3 1.0 CG A:ASP179 3.0 34.6 1.0 CE1 A:HIS218 3.0 31.0 1.0 CG A:HIS218 3.1 32.9 1.0 OE1 A:GLU271 3.2 67.8 1.0 CD A:GLU142 3.2 35.2 1.0 CB A:HIS218 3.4 30.8 1.0 S A:MES304 3.6 51.9 1.0 CB A:ASP179 3.6 31.8 1.0 OE1 A:GLU142 3.9 40.2 1.0 ND2 A:ASN220 4.0 34.0 1.0 OD1 A:ASP179 4.0 35.2 1.0 ZN A:ZN301 4.0 31.6 1.0 NE2 A:HIS182 4.1 39.5 1.0 NE2 A:HIS218 4.1 29.2 1.0 CD2 A:HIS218 4.2 31.2 1.0 CG A:GLU271 4.2 40.7 1.0 CG A:GLU142 4.2 25.5 1.0 O1S A:MES304 4.2 57.4 1.0 CE1 A:HIS182 4.2 42.2 1.0 O2S A:MES304 4.3 50.9 1.0 ZN A:ZN303 4.3 41.0 1.0 C8 A:MES304 4.5 72.4 1.0 CE1 A:HIS233 4.6 34.0 1.0 CA A:ASP179 4.7 18.4 1.0 CD2 A:HIS182 4.7 31.6 1.0 ND1 A:HIS182 4.8 34.1 1.0 CB A:GLU271 4.8 42.7 1.0 NE2 A:HIS233 4.9 28.5 1.0 CA A:HIS218 5.0 18.0 1.0

Zinc binding site 3 out of 12 in the The Crystal Structure of Asfvap:Ag


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:Ag within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:41.0 occ:1.00 OD2 A:ASP231 1.9 36.0 1.0 NE2 A:HIS233 2.0 28.5 1.0 O2S A:MES304 2.0 50.9 1.0 NE2 A:HIS182 2.1 39.5 1.0 CG A:ASP231 2.5 37.6 1.0 OD1 A:ASP231 2.5 29.9 1.0 CE1 A:HIS233 2.7 34.0 1.0 CD2 A:HIS182 3.0 31.6 1.0 CE1 A:HIS182 3.1 42.2 1.0 S A:MES304 3.2 51.9 1.0 CD2 A:HIS233 3.2 26.6 1.0 O3S A:MES304 3.2 36.5 1.0 OD2 A:ASP179 3.7 34.9 1.0 ND1 A:HIS233 3.9 33.1 1.0 CB A:ASP231 4.0 43.8 1.0 O1S A:MES304 4.1 57.4 1.0 CG A:HIS233 4.1 32.1 1.0 CG A:HIS182 4.2 31.2 1.0 O3' F:DG16 4.2 48.9 1.0 ND1 A:HIS182 4.2 34.1 1.0 C8 A:MES304 4.3 72.4 1.0 C4' F:DG16 4.3 50.5 1.0 ZN A:ZN302 4.3 39.8 1.0 CG A:ASP179 4.5 34.6 1.0 C3' F:DG16 4.7 60.5 1.0 OD1 A:ASP179 4.8 35.2 1.0 C2' F:DG16 4.9 50.1 1.0 OE2 A:GLU142 4.9 39.1 1.0 ND2 A:ASN220 5.0 34.0 1.0 CA A:ASP231 5.0 43.1 1.0 OE2 A:GLU271 5.0 63.6 1.0

Zinc binding site 4 out of 12 in the The Crystal Structure of Asfvap:Ag


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:Ag within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:35.0 occ:1.00 OD2 B:ASP231 1.9 49.2 1.0 O1S B:MES304 2.0 49.6 1.0 NE2 B:HIS233 2.0 33.5 1.0 NE2 B:HIS182 2.2 36.6 1.0 CE1 B:HIS233 2.5 42.0 1.0 CG B:ASP231 2.6 44.0 1.0 OD1 B:ASP231 2.6 30.4 1.0 O3S B:MES304 2.8 66.5 1.0 S B:MES304 2.9 71.9 1.0 CE1 B:HIS182 3.2 44.2 1.0 CD2 B:HIS182 3.2 25.2 1.0 CD2 B:HIS233 3.3 27.8 1.0 ND1 B:HIS233 3.7 28.3 1.0 O2S B:MES304 3.9 48.4 1.0 O3' G:DT17 4.0 85.9 1.0 CB B:ASP231 4.0 44.1 1.0 O3' H:DG17 4.0 83.7 0.5 C4' H:DG17 4.0 92.2 0.5 CG B:HIS233 4.1 28.0 1.0 C8 B:MES304 4.1 90.8 1.0 C4' G:DT17 4.1 92.1 1.0 OD2 B:ASP179 4.2 22.2 1.0 ZN B:ZN303 4.2 40.5 1.0 ND1 B:HIS182 4.3 35.4 1.0 CG B:HIS182 4.3 28.9 1.0 C3' H:DG17 4.6 94.9 0.5 C3' G:DT17 4.6 95.7 1.0 CG B:ASP179 4.7 29.6 1.0 OE1 B:GLU271 4.7 38.3 1.0 C5' H:DG17 4.8 0.4 0.5 OD1 B:ASP179 4.8 30.3 1.0 OE2 B:GLU142 4.8 39.1 1.0 C2' G:DT17 4.9 99.8 1.0 O4' H:DG17 4.9 96.8 0.5 C2' H:DG17 4.9 0.8 0.5 C5' G:DT17 4.9 0.6 1.0 O4' G:DT17 5.0 96.7 1.0

Zinc binding site 5 out of 12 in the The Crystal Structure of Asfvap:Ag


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:Ag within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:39.7 occ:1.00 OE1 B:GLU142 1.8 51.4 1.0 NE2 B:HIS78 1.9 43.0 1.0 O2S B:MES304 2.0 48.4 1.0 NE2 B:HIS115 2.1 57.9 1.0 CE1 B:HIS115 2.5 53.1 1.0 CD B:GLU142 2.7 44.6 1.0 CE1 B:HIS78 2.9 38.0 1.0 CD2 B:HIS78 3.0 43.1 1.0 OE2 B:GLU142 3.0 39.1 1.0 CD2 B:HIS115 3.1 47.7 1.0 S B:MES304 3.3 71.9 1.0 ND1 B:HIS115 3.5 61.0 1.0 O3S B:MES304 3.5 66.5 1.0 CG B:HIS115 3.8 46.3 1.0 ZN B:ZN303 3.9 40.5 1.0 ND1 B:HIS78 4.0 33.6 1.0 CG B:GLU142 4.1 29.7 1.0 CG B:HIS78 4.1 31.5 1.0 C8 B:MES304 4.2 90.8 1.0 O1S B:MES304 4.3 49.6 1.0 CE1 B:HIS182 4.5 44.2 1.0 CB B:GLU142 4.5 27.9 1.0 CE1 B:HIS218 4.6 35.7 1.0 OE2 B:GLU271 4.6 40.3 1.0 ND1 B:HIS218 4.9 29.6 1.0 CG1 B:VAL113 4.9 24.8 1.0

Zinc binding site 6 out of 12 in the The Crystal Structure of Asfvap:Ag


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:Ag within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:40.5 occ:1.00 OD2 B:ASP179 1.8 22.2 1.0 OE2 B:GLU142 1.9 39.1 1.0 O3S B:MES304 2.0 66.5 1.0 OE1 B:GLU271 2.0 38.3 1.0 ND1 B:HIS218 2.2 29.6 1.0 CD B:GLU271 2.9 37.5 1.0 CG B:ASP179 3.0 29.6 1.0 CD B:GLU142 3.1 44.6 1.0 CE1 B:HIS218 3.1 35.7 1.0 CG B:HIS218 3.2 26.5 1.0 OE2 B:GLU271 3.2 40.3 1.0 S B:MES304 3.4 71.9 1.0 CB B:HIS218 3.5 22.9 1.0 CB B:ASP179 3.7 26.4 1.0 OE1 B:GLU142 3.7 51.4 1.0 O2S B:MES304 3.8 48.4 1.0 NE2 B:HIS182 3.9 36.6 1.0 ZN B:ZN302 3.9 39.7 1.0 ND2 B:ASN220 3.9 28.0 1.0 CE1 B:HIS182 4.0 44.2 1.0 OD1 B:ASP179 4.0 30.3 1.0 CG B:GLU142 4.2 29.7 1.0 NE2 B:HIS218 4.2 33.6 1.0 C8 B:MES304 4.2 90.8 1.0 ZN B:ZN301 4.2 35.0 1.0 CD2 B:HIS218 4.3 29.6 1.0 CG B:GLU271 4.3 30.5 1.0 O1S B:MES304 4.3 49.6 1.0 CE1 B:HIS233 4.4 42.0 1.0 CD2 B:HIS182 4.5 25.2 1.0 ND1 B:HIS182 4.6 35.4 1.0 NE2 B:HIS233 4.8 33.5 1.0 CA B:ASP179 4.8 19.3 1.0 CG B:HIS182 5.0 28.9 1.0

Zinc binding site 7 out of 12 in the The Crystal Structure of Asfvap:Ag


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of The Crystal Structure of Asfvap:Ag within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:39.3 occ:1.00 OD2 C:ASP231 1.9 53.9 1.0 NE2 C:HIS233 2.0 38.3 1.0 NE2 C:HIS182 2.1 39.5 1.0 O3S C:MES304 2.1 47.7 1.0 OD1 C:ASP231 2.3 34.9 1.0 CG C:ASP231 2.4 42.8 1.0 O3' E:DG18 2.7 80.0 1.0 CE1 C:HIS233 2.8 38.6 1.0 CD2 C:HIS182 2.9 37.4 1.0 CD2 C:HIS233 3.1 30.1 1.0 CE1 C:HIS182 3.1 36.6 1.0 S C:MES304 3.5 83.5 1.0 OD2 C:ASP179 3.8 27.9 1.0 CB C:ASP231 3.9 45.6 1.0 ND1 C:HIS233 3.9 29.0 1.0 C3' E:DG18 4.1 72.8 1.0 CG C:HIS233 4.1 27.9 1.0 CG C:HIS182 4.1 41.1 1.0 O1S C:MES304 4.1 71.5 1.0 ND1 C:HIS182 4.2 34.6 1.0 ZN C:ZN302 4.3 41.0 1.0 C8 C:MES304 4.4 62.1 1.0 O2S C:MES304 4.4 71.4 1.0 CG C:ASP179 4.6 32.2 1.0 C4' E:DG18 4.7 70.5 1.0 OE1 C:GLU271 4.7 37.6 1.0 CA C:ASP231 4.8 44.5 1.0 C2' E:DG18 4.9 78.3 1.0 OD1 C:ASP179 4.9 34.2 1.0 OE2 C:GLU142 5.0 32.9 1.0

Zinc binding site 8 out of 12 in the The Crystal Structure of Asfvap:Ag


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of The Crystal Structure of Asfvap:Ag within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn302 b:41.0 occ:1.00 OE2 C:GLU142 1.8 32.9 1.0 OD2 C:ASP179 2.0 27.9 1.0 OE1 C:GLU271 2.0 37.6 1.0 ND1 C:HIS218 2.2 40.8 1.0 O2S C:MES304 2.2 71.4 1.0 CD C:GLU271 2.9 39.9 1.0 CD C:GLU142 3.0 33.8 1.0 CE1 C:HIS218 3.0 34.4 1.0 OE2 C:GLU271 3.1 50.3 1.0 O3S C:MES304 3.1 47.7 1.0 CG C:ASP179 3.1 32.2 1.0 CG C:HIS218 3.2 41.1 1.0 S C:MES304 3.2 83.5 1.0 OE1 C:GLU142 3.5 37.7 1.0 ZN C:ZN303 3.5 49.1 1.0 CB C:HIS218 3.6 34.3 1.0 CB C:ASP179 3.8 25.8 1.0 NE2 C:HIS182 3.9 39.5 1.0 ND2 C:ASN220 4.0 24.4 1.0 OD1 C:ASP179 4.1 34.2 1.0 NE2 C:HIS218 4.1 37.1 1.0 CE1 C:HIS182 4.1 36.6 1.0 CG C:GLU142 4.2 35.1 1.0 CD2 C:HIS218 4.2 37.5 1.0 ZN C:ZN301 4.3 39.3 1.0 CG C:GLU271 4.3 32.1 1.0 O1S C:MES304 4.3 71.5 1.0 C8 C:MES304 4.3 62.1 1.0 CE1 C:HIS233 4.3 38.6 1.0 CD2 C:HIS182 4.5 37.4 1.0 NE2 C:HIS233 4.6 38.3 1.0 ND1 C:HIS182 4.7 34.6 1.0 CA C:ASP179 4.9 27.3 1.0 CG C:HIS182 5.0 41.1 1.0

Zinc binding site 9 out of 12 in the The Crystal Structure of Asfvap:Ag


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of The Crystal Structure of Asfvap:Ag within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn303 b:49.1 occ:1.00 O2S C:MES304 2.0 71.4 1.0 OE1 C:GLU142 2.0 37.7 1.0 NE2 C:HIS115 2.0 48.9 1.0 NE2 C:HIS78 2.0 36.3 1.0 O1S C:MES304 2.1 71.5 1.0 S C:MES304 2.5 83.5 1.0 CD C:GLU142 2.8 33.8 1.0 CD2 C:HIS115 2.9 40.3 1.0 CE1 C:HIS78 3.0 44.6 1.0 CD2 C:HIS78 3.0 53.0 1.0 CE1 C:HIS115 3.1 51.9 1.0 OE2 C:GLU142 3.1 32.9 1.0 O3S C:MES304 3.5 47.7 1.0 ZN C:ZN302 3.5 41.0 1.0 C8 C:MES304 3.8 62.1 1.0 ND1 C:HIS78 4.1 41.2 1.0 CG C:HIS115 4.1 43.2 1.0 ND1 C:HIS115 4.1 49.9 1.0 CG C:HIS78 4.1 49.4 1.0 CG C:GLU142 4.2 35.1 1.0 CE1 C:HIS218 4.3 34.4 1.0 CE1 C:HIS182 4.3 36.6 1.0 OE2 C:GLU271 4.4 50.3 1.0 ND1 C:HIS218 4.5 40.8 1.0 CB C:GLU142 4.6 27.2 1.0 NE2 C:HIS182 4.9 39.5 1.0 OE1 C:GLU271 4.9 37.6 1.0 CG1 C:VAL113 4.9 33.8 1.0

Zinc binding site 10 out of 12 in the The Crystal Structure of Asfvap:Ag


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of The Crystal Structure of Asfvap:Ag within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:34.8 occ:1.00 OD2 D:ASP231 1.9 55.5 1.0 NE2 D:HIS233 2.0 35.6 1.0 NE2 D:HIS182 2.1 29.9 1.0 O3S D:MES304 2.4 82.6 1.0 OD1 D:ASP231 2.5 35.1 1.0 CG D:ASP231 2.5 50.2 1.0 CE1 D:HIS233 2.7 45.5 1.0 O2S D:MES304 2.9 33.5 1.0 CE1 D:HIS182 3.0 39.6 1.0 CD2 D:HIS182 3.0 24.3 1.0 S D:MES304 3.1 46.9 1.0 CD2 D:HIS233 3.2 30.8 1.0 ND1 D:HIS233 3.9 38.5 1.0 CB D:ASP231 4.0 51.1 1.0 C8 D:MES304 4.0 85.0 1.0 OD2 D:ASP179 4.1 20.8 1.0 O3' J:DC18 4.1 0.9 1.0 CG D:HIS233 4.1 30.2 1.0 ND1 D:HIS182 4.2 32.7 1.0 CG D:HIS182 4.2 25.4 1.0 O3' I:DC16 4.2 0.5 0.4 ZN D:ZN302 4.2 39.0 1.0 C4' J:DC18 4.3 0.8 1.0 C4' I:DC16 4.3 0.7 0.4 O1S D:MES304 4.4 50.5 1.0 C2' J:DC18 4.6 0.6 1.0 CG D:ASP179 4.6 28.2 1.0 C3' J:DC18 4.6 0.5 1.0 OE1 D:GLU271 4.7 47.8 1.0 OD1 D:ASP179 4.7 28.9 1.0 C3' I:DC16 4.7 0.8 0.4 C2' I:DC16 4.7 0.8 0.4 O4' J:DC18 4.7 0.2 1.0 O4' I:DC16 4.8 0.2 0.4 OE2 D:GLU142 4.9 45.5 1.0 CA D:ASP231 4.9 44.8 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