Zinc in PDB 3ir2: Crystal Structure of the APOBEC3G Catalytic Domain

The structure of Crystal Structure of the APOBEC3G Catalytic Domain, PDB code: 3ir2 was solved by 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)	50.00 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	68.338, 72.532, 97.433, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 20.8

The structure of Crystal Structure of the APOBEC3G Catalytic Domain also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Zinc atom in the Crystal Structure of the APOBEC3G Catalytic Domain (pdb code 3ir2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the APOBEC3G Catalytic Domain, PDB code: 3ir2:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the APOBEC3G Catalytic Domain


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 the APOBEC3G Catalytic Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:37.4 occ:1.00 O A:HOH17 2.1 13.2 1.0 ND1 A:HIS257 2.1 20.4 1.0 SG A:CYS288 2.2 18.8 1.0 SG A:CYS291 2.3 21.1 1.0 CE1 A:HIS257 3.0 21.2 1.0 CB A:CYS291 3.1 20.1 1.0 CG A:HIS257 3.1 19.9 1.0 CB A:CYS288 3.4 18.6 1.0 CB A:HIS257 3.5 19.5 1.0 O A:HOH28 3.5 28.9 1.0 OE2 A:GLU259 3.9 22.1 1.0 N A:CYS288 4.0 17.9 1.0 N A:CYS291 4.0 20.5 1.0 CA A:CYS291 4.1 20.1 1.0 NE2 A:HIS257 4.1 20.5 1.0 O A:HOH66 4.2 40.2 1.0 CA A:CYS288 4.2 18.3 1.0 O A:HOH65 4.2 33.3 1.0 CD2 A:HIS257 4.2 20.1 1.0 CD A:GLU259 4.5 21.1 1.0 C A:CYS288 4.6 19.3 1.0 O A:CYS288 4.6 18.9 1.0 OG A:SER290 4.8 24.0 1.0 OE1 A:GLU259 4.8 23.9 1.0 CA A:HIS257 5.0 19.5 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the APOBEC3G Catalytic Domain


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 the APOBEC3G Catalytic Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1101 b:33.2 occ:1.00 ND1 A:HIS248 1.9 20.1 1.0 O A:HOH48 1.9 15.8 1.0 NE2 A:HIS250 1.9 18.6 1.0 CE1 A:HIS248 2.7 19.3 1.0 CD2 A:HIS250 2.9 19.7 1.0 CE1 A:HIS250 2.9 18.4 1.0 CG A:HIS248 3.1 20.0 1.0 CB A:HIS248 3.6 20.3 1.0 O A:HOH51 3.6 24.2 1.0 NE2 A:HIS248 3.9 17.7 1.0 ND1 A:HIS250 4.0 18.6 1.0 CG A:HIS250 4.1 20.4 1.0 CD2 A:HIS248 4.1 19.4 1.0 O A:HOH463 4.2 33.0 1.0 O A:HOH457 4.8 29.2 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the APOBEC3G Catalytic Domain


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 the APOBEC3G Catalytic Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:35.3 occ:1.00 ND1 B:HIS257 2.1 26.2 1.0 O B:HOH94 2.1 22.8 1.0 SG B:CYS288 2.3 24.0 1.0 SG B:CYS291 2.3 24.9 1.0 CE1 B:HIS257 3.0 25.3 1.0 CB B:CYS291 3.1 23.6 1.0 CG B:HIS257 3.1 24.9 1.0 CB B:CYS288 3.4 22.2 1.0 CB B:HIS257 3.5 24.0 1.0 O B:HOH96 3.7 34.0 1.0 O B:HOH116 3.7 29.1 1.0 N B:CYS288 3.9 22.6 1.0 OE2 B:GLU259 4.0 26.0 1.0 N B:CYS291 4.0 23.2 1.0 CA B:CYS291 4.1 24.0 1.0 NE2 B:HIS257 4.1 23.6 1.0 CA B:CYS288 4.2 22.2 1.0 CD2 B:HIS257 4.2 24.6 1.0 CD B:GLU259 4.5 26.4 1.0 C B:CYS288 4.6 22.3 1.0 O B:CYS288 4.6 22.6 1.0 OG B:SER290 4.7 24.1 1.0 OE1 B:GLU259 4.9 28.9 1.0 O B:HOH95 5.0 19.0 1.0 O B:HOH9 5.0 20.1 1.0 CA B:HIS257 5.0 24.2 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the APOBEC3G Catalytic Domain


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 the APOBEC3G Catalytic Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1101 b:34.1 occ:1.00 ND1 B:HIS248 2.0 25.0 1.0 NE2 B:HIS250 2.1 23.3 1.0 CE1 B:HIS248 2.9 23.9 1.0 CD2 B:HIS250 3.0 24.9 1.0 CE1 B:HIS250 3.1 24.7 1.0 CG B:HIS248 3.1 26.5 1.0 CB B:HIS248 3.6 27.1 1.0 O B:HOH470 4.0 33.9 1.0 NE2 B:HIS248 4.1 23.8 1.0 CG B:HIS250 4.1 25.8 1.0 ND1 B:HIS250 4.2 24.0 1.0 CD2 B:HIS248 4.2 25.4 1.0

S.M.Shandilya, M.N.Nalam, E.A.Nalivaika, P.J.Gross, J.C.Valesano, K.Shindo, M.Li, M.Munson, W.E.Royer, E.Harjes, T.Kono, H.Matsuo, R.S.Harris, M.Somasundaran, C.A.Schiffer. Crystal Structure of the APOBEC3G Catalytic Domain Reveals Potential Oligomerization Interfaces. Structure V. 18 28 2010.
ISSN: ISSN 0969-2126
PubMed: 20152150
DOI: 10.1016/J.STR.2009.10.016