Calcium in PDB 6e90: Ternary Complex of Human Glycerol 3-Phosphate Dehydrogenase

All present enzymatic activity of Ternary Complex of Human Glycerol 3-Phosphate Dehydrogenase:
1.1.1.8;

The structure of Ternary Complex of Human Glycerol 3-Phosphate Dehydrogenase, PDB code: 6e90 was solved by L.S.Mydy, A.M.Gulick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	71.11 / 2.05
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	58.940, 79.560, 85.060, 63.87, 86.60, 83.61
R / Rfree (%)	17.7 / 22.6

The binding sites of Calcium atom in the Ternary Complex of Human Glycerol 3-Phosphate Dehydrogenase (pdb code 6e90). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Ternary Complex of Human Glycerol 3-Phosphate Dehydrogenase, PDB code: 6e90:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Ternary Complex of Human Glycerol 3-Phosphate Dehydrogenase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Ternary Complex of Human Glycerol 3-Phosphate Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:31.9 occ:1.00 OD1 A:ASP123 2.3 34.3 1.0 OE2 A:GLU305 2.4 34.7 1.0 O A:HOH550 2.7 26.6 1.0 O A:VAL122 2.7 23.0 1.0 O A:HOH543 2.7 27.8 1.0 OE1 A:GLU305 2.7 23.6 1.0 CD A:GLU305 2.9 30.4 1.0 HA A:ASP123 3.2 20.5 1.0 CG A:ASP123 3.3 45.5 1.0 C A:VAL122 3.8 23.2 1.0 O A:HOH520 3.9 18.5 1.0 OD2 A:ASP123 4.0 41.4 1.0 CA A:ASP123 4.0 17.1 1.0 O A:HOH548 4.2 29.1 1.0 CB A:ASP123 4.3 28.0 1.0 CG A:GLU305 4.4 30.6 1.0 N A:ASP123 4.4 21.8 1.0 ND1 A:HIS95 4.4 21.4 1.0 HD11 A:ILE132 4.4 24.5 1.0 H A:VAL122 4.5 16.5 1.0 HB2 A:HIS95 4.6 25.5 1.0 HG2 A:GLU305 4.6 36.7 1.0 O A:HIS95 4.7 19.6 1.0 HG3 A:GLU305 4.7 36.7 1.0 CE1 A:HIS95 4.8 25.8 1.0 HB3 A:ASP123 4.9 33.5 1.0 HB2 A:ASP123 4.9 33.5 1.0 HE1 A:HIS95 4.9 30.9 1.0 HG23 A:VAL122 4.9 24.5 1.0 HA A:GLN96 5.0 30.8 1.0 N A:VAL122 5.0 13.8 1.0

Calcium binding site 2 out of 2 in the Ternary Complex of Human Glycerol 3-Phosphate Dehydrogenase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Ternary Complex of Human Glycerol 3-Phosphate Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca403 b:25.4 occ:1.00 OE1 B:GLU305 2.4 27.4 1.0 OE2 B:GLU305 2.5 19.6 1.0 O B:HOH568 2.5 19.6 1.0 O B:VAL122 2.6 16.2 1.0 O B:HOH657 2.6 37.4 1.0 OD1 B:ASP123 2.6 38.1 1.0 CD B:GLU305 2.8 24.4 1.0 HA B:ASP123 3.2 28.8 1.0 CG B:ASP123 3.4 37.5 1.0 C B:VAL122 3.7 22.8 1.0 CA B:ASP123 4.0 24.0 1.0 O B:HOH574 4.0 13.8 1.0 OD2 B:ASP123 4.0 38.8 1.0 CG B:GLU305 4.3 21.6 1.0 N B:ASP123 4.3 17.3 1.0 CB B:ASP123 4.3 19.3 1.0 H B:VAL122 4.4 17.7 1.0 HB2 B:HIS95 4.5 14.8 1.0 HD11 B:ILE132 4.5 24.2 1.0 ND1 B:HIS95 4.5 16.1 1.0 HG2 B:GLU305 4.6 25.8 1.0 O D:HOH510 4.6 35.7 1.0 HG3 B:GLU305 4.6 25.8 1.0 O B:HIS95 4.7 19.5 1.0 O B:HOH508 4.9 20.7 1.0 HG23 B:VAL122 4.9 22.6 1.0 HB3 B:ASP123 4.9 23.1 1.0 N B:VAL122 4.9 14.8 1.0 CA B:VAL122 5.0 13.2 1.0 HB2 B:ASP123 5.0 23.1 1.0

L.S.Mydy, J.R.Cristobal, R.D.Katigbak, P.Bauer, A.C.Reyes, S.C.L.Kamerlin, J.P.Richard, A.M.Gulick. Human Glycerol 3-Phosphate Dehydrogenase: X-Ray Crystal Structures That Guide the Interpretation of Mutagenesis Studies. Biochemistry V. 58 1061 2019.
ISSN: ISSN 1520-4995
PubMed: 30640445
DOI: 10.1021/ACS.BIOCHEM.8B01103