Sodium in PDB 2gtx: Structural Basis of Catalysis By Mononuclear Methionine Aminopeptidase

All present enzymatic activity of Structural Basis of Catalysis By Mononuclear Methionine Aminopeptidase:
3.4.11.18;

The structure of Structural Basis of Catalysis By Mononuclear Methionine Aminopeptidase, PDB code: 2gtx 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)	14.97 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.809, 64.257, 76.172, 90.00, 108.09, 90.00
R / Rfree (%)	19.6 / 24.1

The structure of Structural Basis of Catalysis By Mononuclear Methionine Aminopeptidase also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Sodium atom in the Structural Basis of Catalysis By Mononuclear Methionine Aminopeptidase (pdb code 2gtx). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structural Basis of Catalysis By Mononuclear Methionine Aminopeptidase, PDB code: 2gtx:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structural Basis of Catalysis By Mononuclear Methionine Aminopeptidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structural Basis of Catalysis By Mononuclear Methionine Aminopeptidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na265 b:10.9 occ:1.00 O A:SER231 2.2 6.4 1.0 O A:ASN74 2.3 8.7 1.0 O A:HOH3830 2.3 12.9 1.0 O A:VAL76 2.4 15.9 1.0 C A:SER231 3.2 8.2 1.0 O A:HOH3809 3.3 12.0 1.0 C A:ASN74 3.3 8.8 1.0 C A:VAL76 3.5 12.5 1.0 N A:ASN74 3.7 10.0 1.0 N A:SER231 3.8 8.3 1.0 CA A:SER231 3.8 8.0 1.0 CB A:SER231 3.9 8.1 1.0 CA A:ASN74 3.9 9.1 1.0 N A:VAL76 4.0 10.7 1.0 C A:ILE73 4.0 8.6 1.0 O A:HOH3811 4.2 3.7 1.0 N A:ALA232 4.3 6.9 1.0 CA A:VAL76 4.3 11.4 1.0 O A:ILE73 4.3 9.7 1.0 CD1 A:ILE93 4.4 12.3 1.0 O A:SER72 4.4 10.3 1.0 N A:GLU75 4.4 8.2 1.0 C A:GLU75 4.4 10.1 1.0 N A:VAL77 4.5 12.5 1.0 CA A:VAL77 4.6 11.9 1.0 C A:SER72 4.6 10.2 1.0 CG1 A:ILE93 4.6 9.1 1.0 CA A:ALA232 4.7 7.0 1.0 CA A:ILE73 4.7 10.0 1.0 OG A:SER231 4.7 7.2 1.0 N A:ILE73 4.7 9.5 1.0 CB A:SER72 4.7 8.2 1.0 CA A:GLU75 4.8 9.1 1.0 CB A:VAL76 4.8 10.9 1.0 CE A:MET112 4.8 5.7 1.0 O A:VAL77 4.8 10.0 1.0 O A:ILE93 4.9 9.0 1.0 C A:VAL77 5.0 11.9 1.0

Sodium binding site 2 out of 2 in the Structural Basis of Catalysis By Mononuclear Methionine Aminopeptidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structural Basis of Catalysis By Mononuclear Methionine Aminopeptidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na265 b:14.7 occ:1.00 O B:HOH3818 2.2 6.5 1.0 O B:SER231 2.3 9.7 1.0 O B:ASN74 2.3 11.3 1.0 O B:VAL76 2.4 13.4 1.0 C B:ASN74 3.3 13.4 1.0 O B:HOH3812 3.3 13.3 1.0 C B:SER231 3.3 10.9 1.0 C B:VAL76 3.5 11.2 1.0 N B:ASN74 3.7 12.4 1.0 CA B:ASN74 3.8 12.7 1.0 N B:SER231 3.9 10.6 1.0 N B:VAL76 3.9 11.3 1.0 CA B:SER231 3.9 10.4 1.0 CB B:SER231 3.9 10.4 1.0 C B:ILE73 4.0 10.6 1.0 O B:ILE73 4.2 11.1 1.0 N B:GLU75 4.3 12.6 1.0 CA B:VAL76 4.3 10.5 1.0 C B:GLU75 4.3 12.4 1.0 O B:HOH3821 4.3 3.9 1.0 O B:SER72 4.4 8.3 1.0 N B:ALA232 4.4 10.5 1.0 CD1 B:ILE93 4.4 7.2 1.0 N B:VAL77 4.5 10.9 1.0 OG B:SER231 4.6 13.0 1.0 C B:SER72 4.6 9.5 1.0 CG1 B:ILE93 4.6 8.1 1.0 CA B:GLU75 4.6 13.8 1.0 CA B:VAL77 4.6 10.6 1.0 CA B:ILE73 4.7 10.4 1.0 N B:ILE73 4.7 8.8 1.0 CB B:SER72 4.7 9.7 1.0 CA B:ALA232 4.7 9.6 1.0 CB B:VAL76 4.8 8.4 1.0 O B:ILE93 4.8 12.2 1.0 CE B:MET112 4.8 8.0 1.0 O B:VAL77 4.9 12.2 1.0 O B:GLU75 4.9 11.9 1.0 C B:VAL77 5.0 12.3 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