Calcium in PDB 5ujk: Malate Dehydrogenase From Methylobacterium Extorquens, Complexed with Nad

All present enzymatic activity of Malate Dehydrogenase From Methylobacterium Extorquens, Complexed with Nad:
1.1.1.37;

The structure of Malate Dehydrogenase From Methylobacterium Extorquens, Complexed with Nad, PDB code: 5ujk was solved by J.M.Gonzalez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	54.09 / 1.53
Space group	P 64 2 2
Cell size a, b, c (Å), α, β, γ (°)	108.189, 108.189, 104.321, 90.00, 90.00, 120.00
R / Rfree (%)	12.4 / 17.7

The structure of Malate Dehydrogenase From Methylobacterium Extorquens, Complexed with Nad also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Calcium atom in the Malate Dehydrogenase From Methylobacterium Extorquens, Complexed with Nad (pdb code 5ujk). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Malate Dehydrogenase From Methylobacterium Extorquens, Complexed with Nad, PDB code: 5ujk:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Malate Dehydrogenase From Methylobacterium Extorquens, Complexed with Nad


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Malate Dehydrogenase From Methylobacterium Extorquens, Complexed with Nad within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:17.2 occ:1.00 O A:HOH714 2.4 18.1 1.0 OE1 A:GLU287 2.5 16.3 1.0 O A:HOH705 2.5 21.3 1.0 OE2 A:GLU287 2.6 16.7 1.0 CD A:GLU287 2.9 17.0 1.0 CG A:GLU287 4.3 17.0 1.0 O A:HOH743 4.6 19.5 1.0 N A:TYR264 4.6 17.8 1.0 O A:GLY262 4.9 18.3 1.0 O A:HOH772 4.9 31.5 1.0

Calcium binding site 2 out of 3 in the Malate Dehydrogenase From Methylobacterium Extorquens, Complexed with Nad


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Malate Dehydrogenase From Methylobacterium Extorquens, Complexed with Nad within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:29.7 occ:0.50 CA A:CA403 0.0 29.7 0.5 CA A:CA403 1.6 32.4 0.5 O A:HOH663 2.2 39.5 1.0 OE2 A:GLU166 2.8 21.5 1.0 OE1 A:GLU166 3.4 37.2 1.0 CD A:GLU166 3.5 25.9 1.0 CG A:GLU166 4.8 19.5 1.0

Calcium binding site 3 out of 3 in the Malate Dehydrogenase From Methylobacterium Extorquens, Complexed with Nad


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Malate Dehydrogenase From Methylobacterium Extorquens, Complexed with Nad within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:32.4 occ:0.50 CA A:CA403 0.0 32.4 0.5 CA A:CA403 1.6 29.7 0.5 O A:HOH663 2.8 39.5 1.0 OE2 A:GLU166 4.4 21.5 1.0 OE1 A:GLU166 4.7 37.2 1.0 CD A:GLU166 5.0 25.9 1.0

J.M.Gonzalez, R.Marti-Arbona, J.C.H.Chen, B.Broom-Peltz, C.J.Unkefer. Conformational Changes on Substrate Binding Revealed By Structures of Methylobacterium Extorquens Malate Dehydrogenase. Acta Crystallogr F Struct V. 74 610 2018BIOL Commun.
ISSN: ESSN 2053-230X
PubMed: 30279311
DOI: 10.1107/S2053230X18011809