Sodium in PDB 3mx6: Crystal Structure of Methionine Aminopeptidase From Rickettsia Prowazekii Bound to Methionine

All present enzymatic activity of Crystal Structure of Methionine Aminopeptidase From Rickettsia Prowazekii Bound to Methionine:
3.4.11.18;

The structure of Crystal Structure of Methionine Aminopeptidase From Rickettsia Prowazekii Bound to Methionine, PDB code: 3mx6 was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.370, 67.550, 80.890, 90.00, 97.43, 90.00
R / Rfree (%)	16.8 / 20.7

The structure of Crystal Structure of Methionine Aminopeptidase From Rickettsia Prowazekii Bound to Methionine also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Sodium atom in the Crystal Structure of Methionine Aminopeptidase From Rickettsia Prowazekii Bound to Methionine (pdb code 3mx6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Methionine Aminopeptidase From Rickettsia Prowazekii Bound to Methionine, PDB code: 3mx6:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Methionine Aminopeptidase From Rickettsia Prowazekii Bound to Methionine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Methionine Aminopeptidase From Rickettsia Prowazekii Bound to Methionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na261 b:12.2 occ:1.00 O A:VAL74 2.2 8.4 1.0 O A:HOH269 2.3 17.0 1.0 O A:SER229 2.3 7.8 1.0 O A:ASN72 2.3 11.9 1.0 O A:HOH371 3.1 16.5 1.0 C A:ASN72 3.3 11.2 1.0 C A:SER229 3.3 7.2 1.0 C A:VAL74 3.4 8.7 1.0 N A:ASN72 3.8 10.4 1.0 CB A:SER229 3.9 8.0 1.0 N A:VAL74 3.9 9.1 1.0 N A:SER229 3.9 8.3 1.0 CA A:SER229 4.0 7.0 1.0 CA A:ASN72 4.0 11.3 1.0 C A:ILE71 4.1 10.7 1.0 O A:SER70 4.1 7.7 1.0 O A:HOH275 4.2 9.1 1.0 CA A:VAL74 4.2 8.4 1.0 O A:ILE71 4.3 11.7 1.0 N A:HIS73 4.3 11.8 1.0 C A:HIS73 4.4 10.4 1.0 N A:ALA230 4.4 7.6 1.0 N A:VAL75 4.4 8.3 1.0 C A:SER70 4.5 7.9 1.0 CA A:HIS73 4.6 10.6 1.0 CA A:VAL75 4.6 9.0 1.0 CA A:ALA230 4.6 7.5 1.0 OG A:SER229 4.7 6.8 1.0 CB A:SER70 4.8 5.8 1.0 CB A:VAL74 4.8 8.4 1.0 N A:ILE71 4.8 8.0 1.0 CA A:ILE71 4.8 10.4 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Methionine Aminopeptidase From Rickettsia Prowazekii Bound to Methionine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Methionine Aminopeptidase From Rickettsia Prowazekii Bound to Methionine within 5.0Å range: probe atom residue distance (Å) B Occ B:Na261 b:10.0 occ:1.00 O B:HOH270 2.2 14.3 1.0 O B:SER229 2.3 8.4 1.0 O B:ASN72 2.3 9.7 1.0 O B:VAL74 2.3 7.8 1.0 O B:HOH310 3.2 11.7 1.0 C B:ASN72 3.3 9.4 1.0 C B:SER229 3.3 6.8 1.0 C B:VAL74 3.5 8.0 1.0 N B:ASN72 3.7 8.8 1.0 CB B:SER229 3.9 7.0 1.0 N B:SER229 3.9 7.2 1.0 CA B:ASN72 3.9 8.8 1.0 N B:VAL74 3.9 8.2 1.0 CA B:SER229 3.9 6.4 1.0 C B:ILE71 4.0 9.3 1.0 O B:SER70 4.1 6.9 1.0 O B:HOH478 4.2 9.0 1.0 O B:ILE71 4.2 10.5 1.0 CA B:VAL74 4.3 7.6 1.0 N B:HIS73 4.3 9.0 1.0 N B:ALA230 4.4 5.7 1.0 C B:HIS73 4.4 8.8 1.0 N B:VAL75 4.5 7.8 1.0 C B:SER70 4.5 6.3 1.0 CA B:HIS73 4.6 9.7 1.0 OG B:SER229 4.7 7.0 1.0 CA B:ALA230 4.7 6.3 1.0 CA B:VAL75 4.7 7.4 1.0 CA B:ILE71 4.8 8.5 1.0 CD1 B:ILE90 4.8 10.8 1.0 N B:ILE71 4.8 6.6 1.0 CB B:VAL74 4.8 7.8 1.0 CB B:SER70 4.9 5.8 1.0 CG1 B:ILE90 4.9 8.7 1.0

T.R.Helgren, C.Chen, P.Wangtrakuldee, T.E.Edwards, B.L.Staker, J.Abendroth, B.Sankaran, N.A.Housley, P.J.Myler, J.P.Audia, J.R.Horn, T.J.Hagen. Rickettsia Prowazekii Methionine Aminopeptidase As A Promising Target For the Development of Antibacterial Agents. Bioorg.Med.Chem. V. 25 813 2017.
ISSN: ISSN 0968-0896
PubMed: 28089350
DOI: 10.1016/J.BMC.2016.11.013