Sodium in PDB 2gu5: E. Coli Methionine Aminopeptidase in Complex with Nlep, 1: 1, Di-Metalated

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

The structure of E. Coli Methionine Aminopeptidase in Complex with Nlep, 1: 1, Di-Metalated, PDB code: 2gu5 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)	14.19 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.790, 64.606, 76.354, 90.00, 107.77, 90.00
R / Rfree (%)	21.1 / 23.3

The structure of E. Coli Methionine Aminopeptidase in Complex with Nlep, 1: 1, 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: 1, Di-Metalated (pdb code 2gu5). 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: 1, Di-Metalated, PDB code: 2gu5:
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: 1, 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: 1, Di-Metalated within 5.0Å range: probe atom residue distance (Å) B Occ A:Na300 b:8.2 occ:1.00 O A:ASN74 2.2 8.3 1.0 O A:SER231 2.3 6.8 1.0 O A:HOH3829 2.3 10.5 1.0 O A:VAL76 2.3 11.7 1.0 C A:ASN74 3.2 8.3 1.0 C A:SER231 3.3 7.4 1.0 O A:HOH3809 3.4 8.3 1.0 C A:VAL76 3.5 9.5 1.0 N A:ASN74 3.6 9.7 1.0 CA A:ASN74 3.8 9.5 1.0 N A:SER231 3.8 8.1 1.0 CB A:SER231 3.9 8.4 1.0 CA A:SER231 3.9 8.5 1.0 N A:VAL76 3.9 8.2 1.0 C A:ILE73 3.9 9.4 1.0 O A:ILE73 4.2 7.9 1.0 CA A:VAL76 4.3 8.7 1.0 N A:GLU75 4.3 9.5 1.0 C A:GLU75 4.3 9.9 1.0 O A:HOH3810 4.4 7.3 1.0 O A:SER72 4.4 8.0 1.0 N A:ALA232 4.4 7.1 1.0 CD1 A:ILE93 4.4 12.2 1.0 N A:VAL77 4.4 8.9 1.0 CG1 A:ILE93 4.6 7.8 1.0 C A:SER72 4.6 7.9 1.0 CA A:VAL77 4.6 8.3 1.0 CA A:ILE73 4.6 9.4 1.0 OG A:SER231 4.6 8.5 1.0 CA A:GLU75 4.7 10.1 1.0 N A:ILE73 4.7 9.2 1.0 CA A:ALA232 4.7 7.2 1.0 CB A:VAL76 4.7 8.9 1.0 CB A:SER72 4.8 8.0 1.0 O A:ILE93 4.9 9.2 1.0 CE A:MET112 4.9 7.8 1.0 O A:GLU75 5.0 9.5 1.0

Sodium binding site 2 out of 2 in the E. Coli Methionine Aminopeptidase in Complex with Nlep, 1: 1, 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: 1, Di-Metalated within 5.0Å range: probe atom residue distance (Å) B Occ B:Na300 b:9.4 occ:1.00 O B:HOH3817 2.2 11.6 1.0 O B:ASN74 2.2 9.5 1.0 O B:SER231 2.3 7.9 1.0 O B:VAL76 2.3 10.7 1.0 C B:ASN74 3.2 10.4 1.0 C B:SER231 3.3 8.0 1.0 O B:HOH3809 3.4 9.9 1.0 C B:VAL76 3.5 10.4 1.0 N B:ASN74 3.7 10.0 1.0 CA B:ASN74 3.8 10.8 1.0 N B:SER231 3.8 7.5 1.0 CB B:SER231 3.9 7.6 1.0 CA B:SER231 3.9 7.9 1.0 N B:VAL76 3.9 9.2 1.0 C B:ILE73 3.9 10.4 1.0 O B:ILE73 4.2 9.3 1.0 CA B:VAL76 4.2 8.8 1.0 N B:GLU75 4.3 11.7 1.0 C B:GLU75 4.3 10.2 1.0 O B:HOH3810 4.4 8.6 1.0 CD1 B:ILE93 4.4 10.5 1.0 N B:ALA232 4.4 8.4 1.0 O B:SER72 4.4 8.4 1.0 N B:VAL77 4.5 9.4 1.0 CG1 B:ILE93 4.6 8.2 1.0 CA B:GLU75 4.6 11.5 1.0 C B:SER72 4.6 8.8 1.0 CA B:VAL77 4.6 10.7 1.0 CA B:ILE73 4.6 9.5 1.0 OG B:SER231 4.7 8.9 1.0 N B:ILE73 4.7 8.3 1.0 CB B:VAL76 4.7 8.6 1.0 CA B:ALA232 4.7 8.4 1.0 CB B:SER72 4.7 8.6 1.0 O B:GLU75 4.9 9.2 1.0 CE B:MET112 4.9 9.3 1.0 O B:ILE93 4.9 10.9 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