Sodium in PDB 2gu7: E. Coli Methionine Aminopeptidase Unliganded, 1:0.5

All present enzymatic activity of E. Coli Methionine Aminopeptidase Unliganded, 1:0.5:
3.4.11.18;

The structure of E. Coli Methionine Aminopeptidase Unliganded, 1:0.5, PDB code: 2gu7 was solved by Q.Z.Ye, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	14.00 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.200, 61.980, 77.050, 90.00, 107.36, 90.00
R / Rfree (%)	20.8 / 24.4

The structure of E. Coli Methionine Aminopeptidase Unliganded, 1:0.5 also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Sodium atom in the E. Coli Methionine Aminopeptidase Unliganded, 1:0.5 (pdb code 2gu7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the E. Coli Methionine Aminopeptidase Unliganded, 1:0.5, PDB code: 2gu7:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the E. Coli Methionine Aminopeptidase Unliganded, 1:0.5


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of E. Coli Methionine Aminopeptidase Unliganded, 1:0.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1 b:16.8 occ:1.00 O A:SER231 2.2 14.5 1.0 O A:HOH282 2.2 19.4 1.0 O A:ASN74 2.3 16.6 1.0 O A:VAL76 2.4 16.7 1.0 C A:ASN74 3.3 18.4 1.0 C A:SER231 3.3 15.6 1.0 C A:VAL76 3.5 15.7 1.0 O A:HOH267 3.6 17.6 1.0 N A:ASN74 3.7 14.6 1.0 CA A:ASN74 3.8 16.5 1.0 N A:SER231 3.8 16.0 1.0 CA A:SER231 3.9 16.0 1.0 C A:ILE73 3.9 15.4 1.0 CB A:SER231 3.9 17.0 1.0 N A:VAL76 4.0 18.2 1.0 O A:ILE73 4.2 16.0 1.0 O A:HOH278 4.2 12.1 1.0 CA A:VAL76 4.3 16.8 1.0 N A:GLU75 4.3 18.9 1.0 C A:GLU75 4.3 18.6 1.0 N A:ALA232 4.3 15.0 1.0 N A:VAL77 4.4 15.5 1.0 O A:SER72 4.4 13.8 1.0 CA A:VAL77 4.6 14.7 1.0 CD1 A:ILE93 4.6 15.4 1.0 C A:SER72 4.6 15.7 1.0 CA A:ILE73 4.6 15.9 1.0 N A:ILE73 4.6 15.6 1.0 CA A:ALA232 4.7 14.4 1.0 OG A:SER231 4.7 13.5 1.0 CA A:GLU75 4.7 20.2 1.0 CG1 A:ILE93 4.7 16.1 1.0 CB A:SER72 4.7 13.6 1.0 CB A:VAL76 4.8 19.2 1.0 O A:VAL77 4.8 14.9 1.0 CE A:MET112 4.8 8.8 1.0 O A:GLU75 4.9 18.7 1.0 O A:ILE93 5.0 13.9 1.0 C A:VAL77 5.0 16.5 1.0

Sodium binding site 2 out of 2 in the E. Coli Methionine Aminopeptidase Unliganded, 1:0.5


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of E. Coli Methionine Aminopeptidase Unliganded, 1:0.5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1 b:16.6 occ:1.00 O B:HOH270 2.1 17.3 1.0 O B:ASN74 2.3 16.7 1.0 O B:SER231 2.3 14.0 1.0 O B:VAL76 2.4 14.4 1.0 C B:ASN74 3.3 17.9 1.0 C B:SER231 3.4 14.9 1.0 C B:VAL76 3.5 14.2 1.0 O B:HOH267 3.6 15.5 1.0 N B:ASN74 3.7 17.0 1.0 CA B:ASN74 3.8 17.0 1.0 C B:ILE73 3.8 17.1 1.0 N B:VAL76 4.0 16.0 1.0 N B:SER231 4.0 16.2 1.0 CA B:SER231 4.0 16.3 1.0 CB B:SER231 4.0 18.1 1.0 O B:ILE73 4.1 16.8 1.0 O B:SER72 4.2 17.9 1.0 CA B:VAL76 4.3 15.4 1.0 N B:GLU75 4.4 16.9 1.0 O B:HOH281 4.4 10.0 1.0 C B:GLU75 4.4 17.4 1.0 C B:SER72 4.4 17.6 1.0 N B:VAL77 4.5 14.2 1.0 N B:ALA232 4.5 15.3 1.0 CA B:ILE73 4.5 16.6 1.0 N B:ILE73 4.5 17.4 1.0 CA B:VAL77 4.6 14.0 1.0 CE B:MET112 4.7 12.0 1.0 CD1 B:ILE93 4.7 18.0 1.0 CB B:SER72 4.7 14.5 1.0 CA B:GLU75 4.7 18.1 1.0 CG1 B:ILE93 4.8 18.0 1.0 O B:ILE93 4.8 14.8 1.0 OG B:SER231 4.8 18.1 1.0 CB B:VAL76 4.8 15.1 1.0 CA B:ALA232 4.8 14.6 1.0

Q.Z.Ye, S.X.Xie, Z.Q.Ma, M.Huang, R.P.Hanzlik. Structural Basis of Catalysis By Monometalated Methionine Aminopeptidase. Proc.Natl.Acad.Sci.Usa V. 103 9470 2006.
ISSN: ISSN 0027-8424
PubMed: 16769889
DOI: 10.1073/PNAS.0602433103