Sodium in PDB 6rze: Crystal Structure of E. Coli Adenylate Kinase R119A Mutant

All present enzymatic activity of Crystal Structure of E. Coli Adenylate Kinase R119A Mutant:
2.7.4.3;

The structure of Crystal Structure of E. Coli Adenylate Kinase R119A Mutant, PDB code: 6rze was solved by C.Grundstrom, P.Rogne, M.Wolf-Watz, A.E.Sauer-Eriksson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.22 / 1.69
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	134.314, 31.503, 53.189, 90.00, 110.93, 90.00
R / Rfree (%)	18.2 / 23.5

The structure of Crystal Structure of E. Coli Adenylate Kinase R119A Mutant also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of E. Coli Adenylate Kinase R119A Mutant (pdb code 6rze). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of E. Coli Adenylate Kinase R119A Mutant, PDB code: 6rze:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of E. Coli Adenylate Kinase R119A Mutant


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 R119A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:30.5 occ:1.00 O A:HOH710 2.1 28.7 1.0 O A:HOH619 2.2 27.8 1.0 O A:HOH545 2.2 28.2 1.0 O A:HOH571 4.1 41.1 1.0 OE2 A:GLU161 4.2 24.4 1.0 O A:HOH684 4.2 31.2 1.0 CD A:GLU161 4.4 21.8 1.0 OE1 A:GLU161 4.4 29.5 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of E. Coli Adenylate Kinase R119A Mutant


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 R119A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:40.9 occ:1.00 O A:HOH555 2.3 31.3 1.0 O A:HOH739 2.4 34.6 1.0 O A:HOH628 2.7 36.1 1.0 O A:HOH621 3.5 35.6 1.0 OE2 A:GLU108 4.0 15.8 1.0 OD1 A:ASP110 4.1 22.7 1.0 O A:HOH451 4.1 27.4 1.0 O A:HOH566 4.3 21.6 1.0 OD2 A:ASP110 4.4 29.5 1.0 O A:HOH625 4.4 19.6 0.4 NZ A:LYS195 4.5 38.3 1.0 CE1 A:HIS172 4.5 15.6 1.0 CG A:ASP110 4.6 24.7 1.0 ND1 A:HIS172 4.6 19.7 1.0 O A:HOH515 4.7 27.8 1.0 O A:HOH625 4.7 22.5 0.6

Sodium binding site 3 out of 3 in the Crystal Structure of E. Coli Adenylate Kinase R119A Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of E. Coli Adenylate Kinase R119A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:39.4 occ:1.00 O A:HOH574 2.2 25.1 1.0 O A:HOH752 2.3 32.1 1.0 O A:HOH663 2.4 21.4 1.0 O A:HOH534 2.6 37.1 1.0 O A:HOH694 3.9 38.7 1.0 O A:GLN28 4.2 17.6 1.0 NH2 A:ARG71 4.4 19.6 1.0 O A:HOH434 4.4 40.9 1.0 OD2 A:ASP33 4.5 24.3 1.0 O A:HOH590 4.5 19.5 1.0 O A:HOH640 4.7 10.1 1.0 O A:HOH531 4.8 17.3 1.0

P.Rogne, D.Andersson, C.Grundstrom, E.Sauer-Eriksson, A.Linusson, M.Wolf-Watz. Nucleation of An Activating Conformational Change By A Cation-Pi Interaction. Biochemistry V. 58 3408 2019.
ISSN: ISSN 0006-2960
PubMed: 31339702
DOI: 10.1021/ACS.BIOCHEM.9B00538