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

Enzymatic activity of 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;

Protein crystallography data

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

Calcium Binding Sites:

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 6e90

Go back to Calcium Binding Sites List in 6e90
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 6e90

Go back to Calcium Binding Sites List in 6e90
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

Reference:

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
Page generated: Sat Dec 12 06:04:25 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy