Zinc in PDB 6lpp: Crystal Structure of Human D-2-Hydroxyglutarate Dehydrogenase in Complex with D-2-Hydroxyglutarate (D-2-Hg)

The structure of Crystal Structure of Human D-2-Hydroxyglutarate Dehydrogenase in Complex with D-2-Hydroxyglutarate (D-2-Hg), PDB code: 6lpp was solved by J.Yang, H.Zhu, J.Ding, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.78 / 2.65
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	72.275, 94.593, 73.399, 90, 111.9, 90
R / Rfree (%)	20.4 / 24.6

The binding sites of Zinc atom in the Crystal Structure of Human D-2-Hydroxyglutarate Dehydrogenase in Complex with D-2-Hydroxyglutarate (D-2-Hg) (pdb code 6lpp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Human D-2-Hydroxyglutarate Dehydrogenase in Complex with D-2-Hydroxyglutarate (D-2-Hg), PDB code: 6lpp:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Human D-2-Hydroxyglutarate Dehydrogenase in Complex with D-2-Hydroxyglutarate (D-2-Hg)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Human D-2-Hydroxyglutarate Dehydrogenase in Complex with D-2-Hydroxyglutarate (D-2-Hg) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:24.1 occ:1.00 OE1 A:GLU475 1.9 29.6 1.0 O3 A:2HG603 2.1 32.3 1.0 NE2 A:HIS434 2.2 22.0 1.0 NE2 A:HIS441 2.2 30.9 1.0 O1 A:2HG603 2.3 27.8 1.0 O4 A:FAD601 2.9 33.3 1.0 CD A:GLU475 3.0 30.1 1.0 CE1 A:HIS441 3.0 27.1 1.0 CE1 A:HIS434 3.1 26.9 1.0 C2 A:2HG603 3.1 31.2 1.0 C1 A:2HG603 3.1 30.9 1.0 C4 A:FAD601 3.2 31.0 1.0 CD2 A:HIS434 3.2 27.2 1.0 CD2 A:HIS441 3.3 27.8 1.0 OE2 A:GLU475 3.5 29.8 1.0 N3 A:FAD601 3.5 25.7 1.0 C4X A:FAD601 4.0 28.8 1.0 NH2 A:ARG386 4.1 26.2 1.0 ND1 A:HIS441 4.2 27.8 1.0 ND1 A:HIS434 4.2 23.6 1.0 O2 A:2HG603 4.2 32.6 1.0 C3 A:2HG603 4.3 27.5 0.5 CG A:GLU475 4.3 33.0 1.0 CG A:HIS434 4.3 24.8 1.0 CG A:HIS441 4.3 32.6 1.0 NE2 A:HIS476 4.4 33.9 1.0 N5 A:FAD601 4.4 33.0 1.0 C2 A:FAD601 4.5 32.2 1.0 C4 A:2HG603 4.5 25.4 0.5 OD1 A:ASN439 4.8 32.7 1.0 O A:HOH714 4.9 26.9 1.0 C10 A:FAD601 4.9 29.4 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Human D-2-Hydroxyglutarate Dehydrogenase in Complex with D-2-Hydroxyglutarate (D-2-Hg)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Human D-2-Hydroxyglutarate Dehydrogenase in Complex with D-2-Hydroxyglutarate (D-2-Hg) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn602 b:27.8 occ:1.00 OE1 B:GLU475 1.9 30.4 1.0 O1 B:2HG603 2.0 31.1 1.0 NE2 B:HIS441 2.1 28.4 1.0 NE2 B:HIS434 2.2 25.7 1.0 O3 B:2HG603 2.3 24.2 1.0 CE1 B:HIS441 2.7 31.1 1.0 C1 B:2HG603 2.9 31.7 1.0 C2 B:2HG603 3.1 26.9 1.0 O4 B:FAD601 3.1 33.7 1.0 CD B:GLU475 3.1 27.2 1.0 CD2 B:HIS434 3.1 25.4 1.0 CE1 B:HIS434 3.3 25.9 1.0 CD2 B:HIS441 3.3 28.0 1.0 C4 B:FAD601 3.3 26.7 1.0 N3 B:FAD601 3.6 26.3 1.0 OE2 B:GLU475 3.6 29.4 1.0 ND1 B:HIS441 3.9 30.2 1.0 O2 B:2HG603 4.1 30.9 1.0 C4X B:FAD601 4.1 29.8 1.0 CG B:HIS441 4.2 27.5 1.0 NH2 B:ARG386 4.2 28.4 1.0 CG B:HIS434 4.3 30.3 1.0 CG B:GLU475 4.3 27.2 1.0 ND1 B:HIS434 4.3 26.6 1.0 C3 B:2HG603 4.3 27.6 0.5 NE2 B:HIS476 4.4 28.1 1.0 O B:HOH708 4.5 26.7 1.0 N5 B:FAD601 4.5 30.3 1.0 OD1 B:ASN439 4.5 26.3 1.0 C2 B:FAD601 4.5 27.6 1.0 C4 B:2HG603 4.6 24.7 0.5 C10 B:FAD601 4.9 24.6 1.0

J.Yang, H.Zhu, J.Ding. Crystal Structure of Human D-2-Hydroxyglutarate Dehydrogenase in Complex with D-2-Hydroxyglutarate (D-2-Hg) To Be Published.