Zinc in PDB 6lpt: Crystal Structure of Human D-2-Hydroxyglutarate Dehydrogenase in Complex with D-Lactate (D-Lac)

The structure of Crystal Structure of Human D-2-Hydroxyglutarate Dehydrogenase in Complex with D-Lactate (D-Lac), PDB code: 6lpt 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)	36.39 / 2.62
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	72.263, 94.411, 73.575, 90, 111.77, 90
R / Rfree (%)	19.1 / 23.1

The binding sites of Zinc atom in the Crystal Structure of Human D-2-Hydroxyglutarate Dehydrogenase in Complex with D-Lactate (D-Lac) (pdb code 6lpt). 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-Lactate (D-Lac), PDB code: 6lpt:
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-Lactate (D-Lac)


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-Lactate (D-Lac) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:23.0 occ:1.00 O1 A:LAC603 2.0 27.6 1.0 O2 A:LAC603 2.0 26.8 1.0 NE2 A:HIS434 2.1 25.7 1.0 NE2 A:HIS441 2.3 29.7 1.0 OE2 A:GLU475 2.4 26.7 1.0 C1 A:LAC603 2.8 32.4 1.0 C2 A:LAC603 2.9 30.6 1.0 CE1 A:HIS441 2.9 27.9 1.0 CE1 A:HIS434 3.0 25.8 1.0 O4 A:FAD601 3.0 31.2 1.0 CD2 A:HIS434 3.1 26.6 1.0 CD A:GLU475 3.3 29.2 1.0 C4 A:FAD601 3.3 27.9 1.0 CD2 A:HIS441 3.4 24.1 1.0 OE1 A:GLU475 3.4 34.9 1.0 N3 A:FAD601 3.5 28.8 1.0 C3 A:LAC603 3.9 27.1 1.0 OXT A:LAC603 4.0 32.0 1.0 C4X A:FAD601 4.1 25.5 1.0 ND1 A:HIS434 4.1 24.6 1.0 ND1 A:HIS441 4.2 28.9 1.0 NH2 A:ARG386 4.2 26.2 1.0 CG A:HIS434 4.2 28.7 1.0 CG A:HIS441 4.4 28.9 1.0 C2 A:FAD601 4.4 29.3 1.0 NE2 A:HIS476 4.5 27.3 1.0 N5 A:FAD601 4.5 30.0 1.0 OD1 A:ASN439 4.6 35.9 1.0 CG A:GLU475 4.7 31.3 1.0 O A:HOH736 4.8 22.2 1.0 C10 A:FAD601 4.9 29.2 1.0

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


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-Lactate (D-Lac) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn602 b:29.1 occ:1.00 OE1 B:GLU475 2.0 26.1 1.0 O1 B:LAC603 2.0 28.6 1.0 NE2 B:HIS441 2.1 26.2 1.0 O2 B:LAC603 2.2 24.6 1.0 NE2 B:HIS434 2.2 28.0 1.0 C1 B:LAC603 2.8 29.6 1.0 CE1 B:HIS441 2.8 27.3 1.0 C2 B:LAC603 3.0 27.0 1.0 CD B:GLU475 3.0 24.2 1.0 CD2 B:HIS434 3.0 27.2 1.0 O4 B:FAD601 3.2 32.4 1.0 CE1 B:HIS434 3.2 29.0 1.0 CD2 B:HIS441 3.3 24.5 1.0 C4 B:FAD601 3.4 27.1 1.0 OE2 B:GLU475 3.5 27.9 1.0 N3 B:FAD601 3.7 27.8 1.0 OXT B:LAC603 3.9 30.5 1.0 C3 B:LAC603 4.0 25.1 1.0 ND1 B:HIS441 4.0 28.4 1.0 NH2 B:ARG386 4.1 27.5 1.0 C4X B:FAD601 4.2 27.3 1.0 CG B:HIS434 4.2 31.7 1.0 ND1 B:HIS434 4.2 28.3 1.0 CG B:HIS441 4.3 25.9 1.0 CG B:GLU475 4.3 26.6 1.0 NE2 B:HIS476 4.4 29.1 1.0 OD1 B:ASN439 4.5 32.3 1.0 O B:HOH734 4.5 25.2 1.0 N5 B:FAD601 4.6 25.8 1.0 C2 B:FAD601 4.6 27.7 1.0

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