Sodium in PDB 2gu4: E. Coli Methionine Aminopeptidase in Complex with Nlep, 1: 0.5, Di-Metalated

All present enzymatic activity of E. Coli Methionine Aminopeptidase in Complex with Nlep, 1: 0.5, Di-Metalated:
3.4.11.18;

The structure of E. Coli Methionine Aminopeptidase in Complex with Nlep, 1: 0.5, Di-Metalated, PDB code: 2gu4 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)	14.85 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.704, 64.034, 76.347, 90.00, 108.10, 90.00
R / Rfree (%)	19.5 / 22.7

The structure of E. Coli Methionine Aminopeptidase in Complex with Nlep, 1: 0.5, Di-Metalated also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Sodium atom in the E. Coli Methionine Aminopeptidase in Complex with Nlep, 1: 0.5, Di-Metalated (pdb code 2gu4). 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 in Complex with Nlep, 1: 0.5, Di-Metalated, PDB code: 2gu4:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the E. Coli Methionine Aminopeptidase in Complex with Nlep, 1: 0.5, Di-Metalated


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 in Complex with Nlep, 1: 0.5, Di-Metalated within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1 b:10.1 occ:1.00 O A:ASN74 2.3 9.5 1.0 O A:SER231 2.3 7.3 1.0 O A:VAL76 2.3 12.2 1.0 O A:HOH3834 2.3 12.1 1.0 C A:ASN74 3.3 9.5 1.0 C A:SER231 3.3 7.1 1.0 C A:VAL76 3.4 11.1 1.0 O A:HOH3813 3.5 11.5 1.0 N A:ASN74 3.7 8.6 1.0 CA A:ASN74 3.8 9.1 1.0 N A:SER231 3.8 7.7 1.0 CB A:SER231 3.8 8.2 1.0 CA A:SER231 3.9 7.4 1.0 N A:VAL76 3.9 11.0 1.0 C A:ILE73 3.9 9.1 1.0 O A:ILE73 4.2 9.2 1.0 CA A:VAL76 4.2 10.5 1.0 O A:HOH3957 4.3 11.3 1.0 C A:GLU75 4.3 10.8 1.0 N A:GLU75 4.3 9.6 1.0 O A:SER72 4.4 7.0 1.0 N A:VAL77 4.4 10.7 1.0 N A:ALA232 4.4 6.6 1.0 CD1 A:ILE93 4.5 9.1 1.0 CA A:VAL77 4.6 10.1 1.0 C A:SER72 4.6 8.3 1.0 CG1 A:ILE93 4.6 8.0 1.0 OG A:SER231 4.6 7.7 1.0 CA A:ILE73 4.6 9.6 1.0 CA A:GLU75 4.7 10.3 1.0 N A:ILE73 4.7 7.6 1.0 CB A:SER72 4.7 7.9 1.0 CB A:VAL76 4.7 10.4 1.0 CA A:ALA232 4.8 6.8 1.0 O A:ILE93 4.9 10.0 1.0 O A:VAL77 4.9 9.4 1.0 O A:GLU75 4.9 12.0 1.0 C A:VAL77 5.0 11.1 1.0

Sodium binding site 2 out of 2 in the E. Coli Methionine Aminopeptidase in Complex with Nlep, 1: 0.5, Di-Metalated


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 in Complex with Nlep, 1: 0.5, Di-Metalated within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1 b:13.3 occ:1.00 O B:HOH3949 2.2 9.6 1.0 O B:SER231 2.3 8.8 1.0 O B:ASN74 2.3 10.4 1.0 O B:VAL76 2.3 11.8 1.0 C B:ASN74 3.2 11.5 1.0 C B:SER231 3.4 10.1 1.0 O B:HOH3821 3.4 11.8 1.0 C B:VAL76 3.5 10.4 1.0 N B:ASN74 3.6 10.6 1.0 CA B:ASN74 3.8 11.8 1.0 C B:ILE73 3.9 11.0 1.0 N B:VAL76 3.9 11.1 1.0 N B:SER231 3.9 8.8 1.0 CB B:SER231 3.9 9.8 1.0 CA B:SER231 4.0 8.8 1.0 O B:ILE73 4.2 11.3 1.0 CA B:VAL76 4.3 10.0 1.0 N B:GLU75 4.3 11.1 1.0 C B:GLU75 4.3 11.8 1.0 O B:SER72 4.3 9.9 1.0 N B:ALA232 4.4 10.0 1.0 N B:VAL77 4.5 8.7 1.0 CD1 B:ILE93 4.5 8.1 1.0 O B:HOH3814 4.5 8.8 1.0 C B:SER72 4.5 9.3 1.0 CG1 B:ILE93 4.5 8.1 1.0 CA B:ILE73 4.6 10.1 1.0 N B:ILE73 4.6 9.6 1.0 CA B:VAL77 4.6 9.2 1.0 OG B:SER231 4.6 9.9 1.0 CA B:GLU75 4.7 12.6 1.0 CB B:SER72 4.7 10.3 1.0 CB B:VAL76 4.7 11.1 1.0 CA B:ALA232 4.7 9.8 1.0 O B:ILE93 4.8 11.5 1.0 O B:GLU75 4.9 11.5 1.0 CE B:MET112 4.9 7.5 1.0 O B:VAL77 5.0 10.1 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