Zinc in PDB 4xxo: Crystal Structure of Human APOBEC3A

The structure of Crystal Structure of Human APOBEC3A, PDB code: 4xxo was solved by M.F.Bohn, S.M.D.Shandilya, C.A.Schiffer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.73 / 2.84
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	94.752, 94.752, 213.962, 90.00, 90.00, 120.00
R / Rfree (%)	21.5 / 25.3

The structure of Crystal Structure of Human APOBEC3A also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Human APOBEC3A (pdb code 4xxo). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Crystal Structure of Human APOBEC3A, PDB code: 4xxo:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in the Crystal Structure of Human APOBEC3A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Human APOBEC3A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:45.0 occ:1.00 O A:HOH321 2.2 35.9 1.0 ZN A:ZN202 3.2 58.7 1.0 OG1 A:THR31 3.7 43.8 1.0 O A:HOH306 4.0 33.8 1.0 ND1 A:HIS70 4.1 51.0 1.0 N A:CYS101 4.4 60.5 1.0 CB A:CYS101 4.5 66.8 1.0 O A:SER99 4.5 62.6 1.0 CE1 A:HIS70 4.5 50.2 1.0 SG A:CYS101 4.6 68.9 1.0 CG A:HIS70 4.6 40.7 1.0 CB A:THR31 4.6 42.6 1.0 CB A:TRP98 4.7 46.4 1.0 CD2 A:TYR130 4.8 63.0 1.0 CE2 A:TYR130 4.8 62.2 1.0 CA A:PRO100 4.8 55.9 1.0 CG2 A:THR31 4.9 42.2 1.0 CG A:TYR130 5.0 64.5 1.0 CZ A:TYR130 5.0 71.1 1.0 CB A:HIS70 5.0 40.1 1.0

Zinc binding site 2 out of 7 in the Crystal Structure of Human APOBEC3A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Human APOBEC3A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:58.7 occ:1.00 ND1 A:HIS70 2.3 51.0 1.0 SG A:CYS106 2.4 56.1 1.0 SG A:CYS101 2.4 68.9 1.0 CE1 A:HIS70 3.1 50.2 1.0 CB A:CYS106 3.2 69.6 1.0 ZN A:ZN201 3.2 45.0 1.0 CG A:HIS70 3.3 40.7 1.0 CB A:CYS101 3.5 66.8 1.0 N A:CYS101 3.7 60.5 1.0 CB A:HIS70 3.7 40.1 1.0 O A:HOH321 3.9 35.9 1.0 CA A:CYS101 4.1 64.0 1.0 NE2 A:HIS70 4.2 53.6 1.0 CD2 A:HIS70 4.3 45.6 1.0 CA A:CYS106 4.4 67.9 1.0 N A:CYS106 4.5 65.3 1.0 C A:CYS101 4.7 67.4 1.0 C A:PRO100 4.8 60.9 1.0 O A:CYS101 4.8 64.8 1.0 CB A:TRP104 4.8 70.9 1.0 CA A:PRO100 5.0 55.9 1.0

Zinc binding site 3 out of 7 in the Crystal Structure of Human APOBEC3A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Human APOBEC3A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:53.5 occ:1.00 NE2 A:HIS29 2.2 44.6 1.0 CL A:CL206 2.8 47.0 1.0 CD2 A:HIS29 3.2 47.6 1.0 CE1 A:HIS29 3.2 32.9 1.0 NZ A:LYS30 4.1 46.6 1.0 CE A:LYS30 4.2 63.6 1.0 ND1 A:HIS29 4.3 30.8 1.0 CG A:HIS29 4.3 39.2 1.0 O A:HOH324 4.5 57.2 1.0 CD A:LYS30 5.0 49.2 1.0

Zinc binding site 4 out of 7 in the Crystal Structure of Human APOBEC3A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Human APOBEC3A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn204 b:41.1 occ:1.00 O A:HOH301 2.0 41.7 1.0 O A:HOH314 2.1 26.9 1.0 NE2 B:HIS56 2.3 30.3 1.0 NE2 A:HIS11 2.6 33.4 1.0 CE1 B:HIS56 2.9 35.0 1.0 CL B:CL203 3.2 41.5 1.0 CE1 A:HIS11 3.4 34.1 1.0 CD2 B:HIS56 3.5 39.9 1.0 CD2 A:HIS11 3.6 38.0 1.0 O B:HOH329 3.8 50.8 1.0 O A:HOH307 3.8 32.2 1.0 ND1 B:HIS56 4.2 31.6 1.0 O A:LEU12 4.2 45.8 1.0 O B:HOH307 4.4 35.7 1.0 O B:HOH310 4.4 46.0 1.0 CG B:HIS56 4.5 34.7 1.0 ND1 A:HIS11 4.6 37.3 1.0 N A:ASP14 4.6 34.7 1.0 CG A:HIS11 4.7 37.5 1.0 OD2 A:ASP14 4.7 47.0 1.0 CA A:MET13 4.7 33.5 1.0 CG A:ASP14 4.8 44.0 1.0 CZ A:PHE54 4.9 39.0 1.0

Zinc binding site 5 out of 7 in the Crystal Structure of Human APOBEC3A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Human APOBEC3A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn205 b:47.9 occ:1.00 NE2 A:HIS56 2.2 36.0 1.0 NE2 B:HIS11 2.2 38.7 1.0 O A:HOH316 2.4 18.5 1.0 CL B:CL203 2.6 41.5 1.0 CD2 A:HIS56 2.8 35.5 1.0 CE1 B:HIS11 3.0 40.5 1.0 CD2 B:HIS11 3.2 37.4 1.0 CE1 A:HIS56 3.3 41.6 1.0 O A:HOH307 3.7 32.2 1.0 O B:HOH307 3.8 35.7 1.0 CG A:HIS56 4.1 35.1 1.0 ND1 B:HIS11 4.2 37.1 1.0 ND1 A:HIS56 4.3 33.7 1.0 CG B:HIS11 4.3 40.8 1.0 O A:HOH301 4.3 41.7 1.0 O B:LEU12 4.5 39.0 1.0 CD1 B:ILE17 4.7 52.0 1.0 O A:HOH309 4.9 37.1 1.0 CE2 A:PHE54 4.9 32.6 1.0 OD1 B:ASP14 5.0 41.8 1.0

Zinc binding site 6 out of 7 in the Crystal Structure of Human APOBEC3A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Human APOBEC3A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:52.0 occ:1.00 ND1 B:HIS70 2.1 46.2 1.0 SG B:CYS101 2.3 60.2 1.0 SG B:CYS106 2.4 45.1 1.0 CE1 B:HIS70 2.9 47.4 1.0 ZN B:ZN202 3.1 44.1 1.0 CB B:CYS106 3.2 51.9 1.0 CG B:HIS70 3.2 49.2 1.0 CB B:CYS101 3.5 63.4 1.0 N B:CYS101 3.7 49.4 1.0 CB B:HIS70 3.7 46.4 1.0 NE2 B:HIS70 4.1 53.7 1.0 CA B:CYS101 4.1 56.6 1.0 CD2 B:HIS70 4.2 54.2 1.0 O B:HOH320 4.3 39.9 1.0 CB B:TRP104 4.4 68.5 1.0 CA B:CYS106 4.5 50.8 1.0 O B:HOH318 4.6 53.0 1.0 N B:CYS106 4.7 49.9 1.0 C B:PRO100 4.8 47.8 1.0 C B:CYS101 4.8 61.2 1.0 O B:HOH315 4.9 42.2 1.0 CA B:PRO100 4.9 50.8 1.0 O B:CYS101 5.0 57.8 1.0

Zinc binding site 7 out of 7 in the Crystal Structure of Human APOBEC3A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Human APOBEC3A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:44.1 occ:1.00 O B:HOH318 2.1 53.0 1.0 ZN B:ZN201 3.1 52.0 1.0 O B:HOH315 3.3 42.2 1.0 O B:HOH320 3.5 39.9 1.0 OG1 B:THR31 3.6 41.9 1.0 ND1 B:HIS70 3.8 46.2 1.0 CE1 B:HIS70 4.2 47.4 1.0 CG B:HIS70 4.3 49.2 1.0 N B:CYS101 4.4 49.4 1.0 SG B:CYS101 4.5 60.2 1.0 CB B:CYS101 4.6 63.4 1.0 CB B:THR31 4.6 35.6 1.0 O B:SER99 4.7 53.2 1.0 CB B:HIS70 4.7 46.4 1.0 CG2 B:THR31 4.7 36.4 1.0 CB B:TRP98 4.8 47.0 1.0 SG B:CYS106 4.8 45.1 1.0 NE2 B:HIS70 4.9 53.7 1.0 CE1 B:TYR130 4.9 56.0 1.0 CA B:PRO100 4.9 50.8 1.0 CD2 B:HIS70 4.9 54.2 1.0 CD1 B:TYR130 4.9 56.9 1.0 CZ B:TYR130 4.9 56.8 1.0

M.F.Bohn, S.M.Shandilya, T.V.Silvas, E.A.Nalivaika, T.Kouno, B.A.Kelch, S.P.Ryder, N.Kurt-Yilmaz, M.Somasundaran, C.A.Schiffer. The Ssdna Mutator APOBEC3A Is Regulated By Cooperative Dimerization. Structure V. 23 903 2015.
ISSN: ISSN 0969-2126
PubMed: 25914058
DOI: 10.1016/J.STR.2015.03.016