Sodium in PDB 4x8l: Crystal Structure of E. Coli Adenylate Kinase P177A Mutant in Complex with Inhibitor AP5A

All present enzymatic activity of Crystal Structure of E. Coli Adenylate Kinase P177A Mutant in Complex with Inhibitor AP5A:
2.7.4.3;

The structure of Crystal Structure of E. Coli Adenylate Kinase P177A Mutant in Complex with Inhibitor AP5A, PDB code: 4x8l was solved by A.E.Sauer-Eriksson, M.Kovermann, J.Aden, C.Grundstrom, M.Wolf-Watz, U.H.Sauer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.00 / 1.70
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	82.572, 72.665, 79.309, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 21.1

The structure of Crystal Structure of E. Coli Adenylate Kinase P177A Mutant in Complex with Inhibitor AP5A also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of E. Coli Adenylate Kinase P177A Mutant in Complex with Inhibitor AP5A (pdb code 4x8l). 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 E. Coli Adenylate Kinase P177A Mutant in Complex with Inhibitor AP5A, PDB code: 4x8l:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of E. Coli Adenylate Kinase P177A Mutant in Complex with Inhibitor AP5A


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 E. Coli Adenylate Kinase P177A Mutant in Complex with Inhibitor AP5A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:10.5 occ:1.00 O A:ASN190 2.4 8.9 1.0 O A:HOH485 2.4 11.9 1.0 O A:HOH466 2.4 12.2 1.0 O A:VAL103 2.4 7.9 1.0 HB3 A:ASN102 3.2 23.3 1.0 C A:ASN190 3.3 8.9 1.0 HA A:THR191 3.5 5.6 1.0 C A:VAL103 3.5 4.8 1.0 HA A:ASP104 3.5 7.2 1.0 O A:HOH543 3.7 11.4 1.0 H A:VAL103 3.7 8.2 1.0 HA A:ASN190 3.9 7.4 1.0 HB A:THR191 4.0 7.9 1.0 N A:VAL103 4.0 6.9 1.0 N A:THR191 4.1 6.7 1.0 CB A:ASN102 4.1 19.4 1.0 CA A:THR191 4.1 4.6 1.0 O A:HOH422 4.1 8.2 1.0 HB2 A:ASN102 4.2 23.3 1.0 CA A:ASN190 4.2 6.2 1.0 N A:ASP104 4.3 5.2 1.0 CA A:ASP104 4.3 6.0 1.0 CA A:VAL103 4.4 6.0 1.0 O A:HOH471 4.5 43.5 1.0 OD1 A:ASP104 4.5 10.8 1.0 CB A:THR191 4.5 6.5 1.0 HB3 A:ASN190 4.6 11.9 1.0 C A:ASN102 4.7 11.2 1.0 H A:THR191 4.8 8.0 1.0 HA A:VAL103 4.9 7.2 1.0 CA A:ASN102 4.9 17.7 1.0 HA A:ASN102 4.9 21.3 1.0 O A:HOH744 5.0 21.8 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of E. Coli Adenylate Kinase P177A Mutant in Complex with Inhibitor AP5A


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 E. Coli Adenylate Kinase P177A Mutant in Complex with Inhibitor AP5A within 5.0Å range: probe atom residue distance (Å) B Occ B:Na303 b:23.9 occ:1.00 O B:HOH453 2.5 18.4 1.0 O B:HOH419 2.5 14.9 1.0 O B:ASN190 2.6 11.1 1.0 HA B:ASN190 2.9 10.1 1.0 C B:ASN190 3.3 8.0 1.0 CA B:ASN190 3.6 8.4 1.0 O B:HOH415 3.7 17.7 1.0 HB2 B:ASN102 3.8 15.6 1.0 HD22 B:ASN102 3.9 31.1 1.0 HB3 B:ASN190 3.9 10.3 1.0 O B:HOH463 4.2 8.7 1.0 O B:HOH504 4.2 26.5 1.0 O B:GLY189 4.3 12.2 1.0 CB B:ASN190 4.3 8.6 1.0 O B:HOH670 4.4 29.9 1.0 N B:THR191 4.5 11.3 1.0 HA B:THR191 4.5 12.0 1.0 ND2 B:ASN102 4.5 25.9 1.0 CB B:ASN102 4.6 13.0 1.0 O B:VAL103 4.7 13.8 1.0 N B:ASN190 4.7 11.3 1.0 HB3 B:ASN102 4.8 15.6 1.0 OD1 B:ASN190 4.9 9.5 1.0 C B:GLY189 4.9 10.5 1.0

M.Kovermann, J.Aden, C.Grundstrom, A.Elisabeth Sauer-Eriksson, U.H.Sauer, M.Wolf-Watz. Structural Basis For Catalytically Restrictive Dynamics of A High-Energy Enzyme State. Nat Commun V. 6 7644 2015.
ISSN: ESSN 2041-1723
PubMed: 26138143
DOI: 10.1038/NCOMMS8644