Sodium in PDB 6zjd: Crystal Structure of Human Adenylate Kinase 3, AK3, in Complex with Inhibitor Atp

All present enzymatic activity of Crystal Structure of Human Adenylate Kinase 3, AK3, in Complex with Inhibitor Atp:
2.7.4.10;

The structure of Crystal Structure of Human Adenylate Kinase 3, AK3, in Complex with Inhibitor Atp, PDB code: 6zjd 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)	26.86 / 1.75
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	42.524, 62.518, 49.804, 90.00, 108.20, 90.00
R / Rfree (%)	15.7 / 22

The structure of Crystal Structure of Human Adenylate Kinase 3, AK3, in Complex with Inhibitor Atp also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	3 atoms

The binding sites of Sodium atom in the Crystal Structure of Human Adenylate Kinase 3, AK3, in Complex with Inhibitor Atp (pdb code 6zjd). 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 Human Adenylate Kinase 3, AK3, in Complex with Inhibitor Atp, PDB code: 6zjd:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Human Adenylate Kinase 3, AK3, in Complex with Inhibitor Atp


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 Human Adenylate Kinase 3, AK3, in Complex with Inhibitor Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:37.8 occ:1.00 O A:HOH432 2.2 30.1 1.0 OD1 A:ASP40 2.5 17.4 1.0 OD2 A:ASP40 2.9 21.6 1.0 CG A:ASP40 3.1 18.1 1.0 O A:HOH440 3.1 28.4 1.0 O A:HOH658 3.5 34.7 1.0 NH2 A:ARG43 4.2 16.4 1.0 O A:HOH499 4.2 27.2 1.0 OG A:SER37 4.3 13.4 1.0 CB A:ASP40 4.6 12.0 1.0 CB A:SER37 4.7 15.4 1.0 O A:HOH546 4.7 18.8 1.0 NA A:NA308 4.7 30.0 1.0 O A:HOH730 4.7 39.2 0.5 O A:HOH462 4.8 23.2 1.0 O A:HOH611 4.8 20.6 1.0 O A:HOH521 4.9 29.2 1.0 CE1 A:HIS35 4.9 16.8 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Human Adenylate Kinase 3, AK3, in Complex with Inhibitor Atp


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 Human Adenylate Kinase 3, AK3, in Complex with Inhibitor Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na308 b:30.0 occ:1.00 OD2 A:ASP40 2.1 21.6 1.0 O A:HOH748 2.5 30.0 1.0 O A:HOH521 2.5 29.2 1.0 O A:HOH534 2.6 19.8 1.0 CG A:ASP40 3.1 18.1 1.0 O A:HOH432 3.3 30.1 1.0 CB A:ASP40 3.4 12.0 1.0 O A:HIS35 4.1 10.4 1.0 O A:HOH762 4.2 32.0 1.0 ND1 A:HIS35 4.2 16.0 1.0 OD1 A:ASP40 4.2 17.4 1.0 CB A:SER37 4.2 15.4 1.0 NA A:NA304 4.7 37.8 1.0 CE1 A:HIS35 4.7 16.8 1.0 N A:SER37 4.7 10.8 1.0 CG A:HIS35 4.8 11.0 1.0 C A:HIS35 5.0 13.7 1.0 CA A:ASP40 5.0 13.8 1.0

P.Rogne, B.Dulko-Smith, J.Goodman, M.Rosselin, C.Grundstrom, C.Hedberg, K.Nam, A.E.Sauer-Eriksson, M.Wolf-Watz. Structural Basis For Gtp Versus Atp Selectivity in the Nmp Kinase AK3. Biochemistry V. 59 3570 2020.
ISSN: ISSN 0006-2960
PubMed: 32822537
DOI: 10.1021/ACS.BIOCHEM.0C00549