Calcium in PDB 5ulv: Malate Dehydrogenase From Methylobacterium Extorquens

All present enzymatic activity of Malate Dehydrogenase From Methylobacterium Extorquens:
1.1.1.37;

The structure of Malate Dehydrogenase From Methylobacterium Extorquens, PDB code: 5ulv 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)	37.75 / 1.66
Space group	P 64 2 2
Cell size a, b, c (Å), α, β, γ (°)	108.995, 108.995, 104.659, 90.00, 90.00, 120.00
R / Rfree (%)	14 / 16.8

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

Calcium binding site 1 out of 2 in the Malate Dehydrogenase From Methylobacterium Extorquens


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:13.4 occ:1.00 O A:HOH752 2.4 14.3 1.0 OE1 A:GLU287 2.5 13.4 1.0 OE2 A:GLU287 2.5 14.7 1.0 O A:HOH746 2.6 15.1 1.0 CD A:GLU287 2.8 12.8 1.0 O A:HOH795 4.2 17.1 1.0 CG A:GLU287 4.3 13.3 1.0 O A:HOH774 4.6 16.7 1.0 N A:TYR264 4.7 14.9 1.0 O A:GLY262 4.9 15.6 1.0 O A:HOH607 4.9 15.1 1.0 O A:HOH824 5.0 25.0 1.0 CB A:GLU287 5.0 12.8 1.0

Calcium binding site 2 out of 2 in the Malate Dehydrogenase From Methylobacterium Extorquens


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:44.3 occ:1.00 O A:HOH832 1.5 23.0 1.0 O A:HOH572 2.1 30.1 1.0 O A:HOH528 2.3 33.9 1.0 OE2 A:GLU166 2.7 13.1 0.5 OE2 A:GLU166 3.0 15.8 0.5 CD A:GLU166 3.4 15.0 0.5 OE1 A:GLU166 3.5 14.4 0.5 CD A:GLU166 3.6 15.6 0.5 OE1 A:GLU166 3.7 17.6 0.5 CG A:GLU166 4.7 14.8 0.5 CG A:GLU166 4.8 14.1 0.5

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