Magnesium 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:

Chlorine	(Cl)	2 atoms
Zinc	(Zn)	4 atoms

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

Magnesium binding site 1 out of 2 in the Crystal Structure of the APOBEC3G Catalytic Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the APOBEC3G Catalytic Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg385 b:40.4 occ:1.00 NE2 A:HIS367 2.1 18.9 1.0 O A:HOH481 2.2 22.5 1.0 O A:HOH480 2.2 17.4 1.0 O A:HOH482 2.2 23.0 1.0 OE1 A:GLU209 2.3 28.8 1.0 O A:HOH470 2.4 28.7 1.0 CE1 A:HIS367 2.9 17.9 1.0 CD2 A:HIS367 3.1 17.8 1.0 CD A:GLU209 3.3 28.1 1.0 OE2 A:GLU209 3.6 28.1 1.0 ND1 A:HIS367 4.1 18.3 1.0 CG A:HIS367 4.2 19.3 1.0 O A:HOH408 4.3 25.8 1.0 CD A:PRO210 4.4 25.8 1.0 O A:HOH432 4.4 40.2 1.0 CG A:GLU209 4.6 26.7 1.0 OE2 A:GLU366 4.8 35.1 1.0 CG A:PRO210 4.8 25.5 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the APOBEC3G Catalytic Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg385 b:32.8 occ:1.00 OG B:SER372 2.9 24.2 1.0 O B:HOH144 2.9 32.1 1.0 O B:HOH411 3.0 31.5 1.0 N B:ILE337 3.1 19.9 1.0 CA B:SER336 3.7 20.8 1.0 CG1 B:ILE337 3.8 18.5 1.0 CB B:ILE337 3.8 19.4 1.0 CB B:SER336 3.9 21.2 1.0 C B:SER336 3.9 20.1 1.0 CB B:SER372 4.1 21.1 1.0 CA B:ILE337 4.1 19.2 1.0 CD2 B:LEU375 4.2 15.7 1.0 CA B:SER372 4.3 20.9 1.0 O B:ILE337 4.4 19.4 1.0 C B:ILE337 4.8 19.6 1.0 O B:SER372 4.8 20.2 1.0 O B:HOH145 4.8 28.1 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