Sodium in PDB 6lh7: Crystal Structure of Vibrio Cholerae Methionine Aminopeptidase with Partially Occupied Metals

All present enzymatic activity of Crystal Structure of Vibrio Cholerae Methionine Aminopeptidase with Partially Occupied Metals:
3.4.11.18;

The structure of Crystal Structure of Vibrio Cholerae Methionine Aminopeptidase with Partially Occupied Metals, PDB code: 6lh7 was solved by V.Pillalamarri, A.Addlagatta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.23 / 1.47
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.702, 50.293, 131.684, 90.00, 97.24, 90.00
R / Rfree (%)	15.2 / 17.7

The structure of Crystal Structure of Vibrio Cholerae Methionine Aminopeptidase with Partially Occupied Metals also contains other interesting chemical elements:

Nickel

(Ni)

4 atoms

The binding sites of Sodium atom in the Crystal Structure of Vibrio Cholerae Methionine Aminopeptidase with Partially Occupied Metals (pdb code 6lh7). 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 Vibrio Cholerae Methionine Aminopeptidase with Partially Occupied Metals, PDB code: 6lh7:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Vibrio Cholerae Methionine Aminopeptidase with Partially Occupied Metals


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 Vibrio Cholerae Methionine Aminopeptidase with Partially Occupied Metals within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:11.6 occ:1.00 O A:HOH532 2.1 13.9 1.0 O A:ILE76 2.2 10.6 1.0 O A:SER248 2.3 9.9 1.0 O A:ASN74 2.3 9.0 1.0 C A:ASN74 3.3 9.2 1.0 C A:SER248 3.3 7.9 1.0 C A:ILE76 3.4 9.3 1.0 O A:HOH647 3.5 12.8 1.0 N A:ASN74 3.6 9.6 1.0 N A:SER248 3.8 7.9 1.0 CA A:ASN74 3.9 9.9 1.0 CA A:SER248 3.9 8.3 1.0 C A:ILE73 3.9 9.7 1.0 CB A:SER248 3.9 9.0 1.0 N A:ILE76 4.0 9.1 1.0 O A:SER72 4.2 9.3 1.0 O A:ILE73 4.2 10.5 1.0 CA A:ILE76 4.2 10.0 1.0 N A:HIS75 4.3 9.7 1.0 N A:VAL77 4.3 9.2 1.0 O A:HOH533 4.4 11.3 1.0 N A:ALA249 4.4 7.9 1.0 C A:SER72 4.5 8.3 1.0 C A:HIS75 4.5 10.0 1.0 CA A:VAL77 4.5 8.7 1.0 OG A:SER248 4.7 9.9 1.0 CA A:HIS75 4.7 9.4 1.0 CA A:ILE73 4.7 9.3 1.0 N A:ILE73 4.7 9.0 1.0 CD1 A:ILE103 4.8 10.6 1.0 CB A:SER72 4.8 8.0 1.0 CA A:ALA249 4.8 8.5 1.0 CG1 A:ILE103 4.8 9.7 1.0 CB A:ILE76 4.9 10.4 1.0 O A:VAL77 5.0 10.1 1.0 C A:VAL77 5.0 8.9 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Vibrio Cholerae Methionine Aminopeptidase with Partially Occupied Metals


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 Vibrio Cholerae Methionine Aminopeptidase with Partially Occupied Metals within 5.0Å range: probe atom residue distance (Å) B Occ B:Na303 b:13.8 occ:1.00 O B:HOH538 2.1 14.3 1.0 O B:ILE76 2.3 12.6 1.0 O B:SER248 2.3 10.8 1.0 O B:ASN74 2.4 11.5 1.0 C B:ASN74 3.3 10.8 1.0 C B:SER248 3.4 10.4 1.0 C B:ILE76 3.4 10.4 1.0 O B:HOH605 3.5 14.3 1.0 N B:ASN74 3.6 11.8 1.0 N B:SER248 3.8 11.1 1.0 CB B:SER248 3.9 11.2 1.0 CA B:SER248 3.9 10.6 1.0 C B:ILE73 3.9 12.2 1.0 CA B:ASN74 3.9 11.3 1.0 N B:ILE76 4.0 11.1 1.0 O B:ILE73 4.2 11.7 1.0 O B:SER72 4.2 10.5 1.0 CA B:ILE76 4.2 11.2 1.0 N B:HIS75 4.4 11.1 1.0 N B:VAL77 4.4 10.1 1.0 O B:HOH516 4.4 13.0 1.0 C B:HIS75 4.4 10.9 1.0 N B:ALA249 4.4 10.4 1.0 C B:SER72 4.5 10.4 1.0 CA B:VAL77 4.5 12.0 1.0 OG B:SER248 4.6 12.8 1.0 N B:ILE73 4.7 10.2 1.0 CA B:HIS75 4.7 10.9 1.0 CA B:ILE73 4.7 10.7 1.0 CB B:SER72 4.8 9.7 1.0 CA B:ALA249 4.8 9.7 1.0 CG1 B:ILE103 4.8 11.7 1.0 CD1 B:ILE103 4.8 11.8 1.0 CB B:ILE76 4.9 11.2 1.0 O B:VAL77 4.9 11.4 1.0 C B:VAL77 5.0 11.4 1.0 CE B:MET122 5.0 11.5 1.0

V.Pillalamarri, C.G.Reddy, S.C.Bala, A.Jangam, V.V.Kutty, A.Addlagatta. Methionine Aminopeptidases with Short Sequence Inserts Within the Catalytic Domain Are Differentially Inhibited: Structural and Biochemical Studies of Three Proteins From Vibrio Spp. Eur.J.Med.Chem. V. 209 12883 2020.
ISSN: ISSN 0223-5234
PubMed: 33035924
DOI: 10.1016/J.EJMECH.2020.112883