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

The structure of Crystal Structure of Human D-2-Hydroxyglutarate Dehydrogenase in Complex with L-2-Hydroxyglutarate (L-2-Hg), PDB code: 6lpu 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)	47.27 / 2.92
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	71.709, 94.53, 72.789, 90, 112.25, 90
R / Rfree (%)	22.4 / 25.5

The binding sites of Zinc atom in the Crystal Structure of Human D-2-Hydroxyglutarate Dehydrogenase in Complex with L-2-Hydroxyglutarate (L-2-Hg) (pdb code 6lpu). 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 L-2-Hydroxyglutarate (L-2-Hg), PDB code: 6lpu:
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 L-2-Hydroxyglutarate (L-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 L-2-Hydroxyglutarate (L-2-Hg) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:35.5 occ:1.00 NE2 A:HIS434 2.1 30.5 1.0 O2 A:S2G603 2.1 36.4 1.0 NE2 A:HIS441 2.2 30.1 1.0 O3 A:S2G603 2.4 42.6 1.0 OE2 A:GLU475 2.4 39.0 1.0 CE1 A:HIS441 2.9 33.5 1.0 CE1 A:HIS434 2.9 33.6 1.0 O4 A:FAD601 2.9 41.0 1.0 C1 A:S2G603 3.0 40.9 1.0 C2 A:S2G603 3.1 41.8 1.0 CD2 A:HIS434 3.2 34.5 1.0 C4 A:FAD601 3.3 42.9 1.0 CD2 A:HIS441 3.3 34.9 1.0 CD A:GLU475 3.4 41.9 1.0 OE1 A:GLU475 3.6 42.8 1.0 N3 A:FAD601 3.6 46.4 1.0 ND1 A:HIS441 4.1 37.1 1.0 ND1 A:HIS434 4.1 33.3 1.0 C4X A:FAD601 4.1 42.2 1.0 NH2 A:ARG386 4.1 31.2 1.0 O1 A:S2G603 4.2 44.2 1.0 CG A:HIS434 4.2 34.5 1.0 CG A:HIS441 4.3 41.0 1.0 NE2 A:HIS476 4.4 40.3 1.0 N5 A:FAD601 4.5 41.7 1.0 C3 A:S2G603 4.5 40.6 0.5 C2 A:FAD601 4.6 47.9 1.0 CG A:GLU475 4.7 40.2 1.0 OD1 A:ASN439 4.9 37.7 1.0 C10 A:FAD601 5.0 36.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Human D-2-Hydroxyglutarate Dehydrogenase in Complex with L-2-Hydroxyglutarate (L-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 L-2-Hydroxyglutarate (L-2-Hg) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn602 b:39.7 occ:1.00 OE1 B:GLU475 2.0 37.9 1.0 O1 B:S2G603 2.0 36.8 1.0 NE2 B:HIS441 2.1 41.8 1.0 NE2 B:HIS434 2.2 37.5 1.0 O3 B:S2G603 2.5 34.9 1.0 CE1 B:HIS441 2.8 31.7 1.0 CD B:GLU475 2.9 35.8 1.0 C1 B:S2G603 3.0 39.0 1.0 CE1 B:HIS434 3.0 40.5 1.0 C2 B:S2G603 3.1 36.2 1.0 CD2 B:HIS434 3.2 31.6 1.0 OE2 B:GLU475 3.2 42.9 1.0 O4 B:FAD601 3.2 41.1 1.0 CD2 B:HIS441 3.3 38.3 1.0 C4 B:FAD601 3.5 36.2 1.0 N3 B:FAD601 3.7 39.3 1.0 ND1 B:HIS441 3.9 34.3 1.0 NH2 B:ARG386 4.0 36.2 1.0 O2 B:S2G603 4.1 38.8 1.0 ND1 B:HIS434 4.1 34.0 1.0 CG B:HIS441 4.2 31.7 1.0 CG B:HIS434 4.3 38.1 1.0 C4X B:FAD601 4.3 36.3 1.0 CG B:GLU475 4.3 36.9 1.0 NE2 B:HIS476 4.4 33.4 1.0 NH1 B:ARG386 4.4 40.4 1.0 C3 B:S2G603 4.5 35.0 0.5 C2 B:FAD601 4.6 36.9 1.0 N5 B:FAD601 4.7 36.4 1.0 CZ B:ARG386 4.7 39.8 1.0

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