Zinc in PDB 6lpx: Crystal Structure of Human D-2-Hydroxyglutarate Dehydrogenase in Complex with 2-Oxoglutarate (2-Og)

The structure of Crystal Structure of Human D-2-Hydroxyglutarate Dehydrogenase in Complex with 2-Oxoglutarate (2-Og), PDB code: 6lpx 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)	36.27 / 2.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	72.169, 94.94, 73.219, 90, 112.3, 90
R / Rfree (%)	18.7 / 23.6

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


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 2-Oxoglutarate (2-Og) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:29.9 occ:1.00 O5 A:AKG603 2.1 32.8 1.0 NE2 A:HIS434 2.1 29.1 1.0 NE2 A:HIS441 2.2 28.1 1.0 OE1 A:GLU475 2.3 30.6 1.0 O2 A:AKG603 2.4 37.0 1.0 C2 A:AKG603 2.8 35.7 1.0 O4 A:FAD601 2.9 35.4 1.0 C1 A:AKG603 3.0 38.7 1.0 CE1 A:HIS434 3.0 27.4 1.0 CE1 A:HIS441 3.0 29.4 1.0 C4 A:FAD601 3.2 33.9 1.0 CD A:GLU475 3.2 33.6 1.0 CD2 A:HIS434 3.2 26.4 1.0 OE2 A:GLU475 3.3 38.5 1.0 CD2 A:HIS441 3.3 30.6 1.0 N3 A:FAD601 3.5 31.4 1.0 C4X A:FAD601 4.0 32.0 1.0 ND1 A:HIS434 4.2 25.7 1.0 ND1 A:HIS441 4.2 33.6 1.0 O1 A:AKG603 4.2 38.9 1.0 C3 A:AKG603 4.3 40.7 1.0 CG A:HIS434 4.3 28.9 1.0 NH2 A:ARG386 4.3 29.7 1.0 CG A:HIS441 4.3 34.0 1.0 NE2 A:HIS476 4.4 33.3 1.0 N5 A:FAD601 4.4 32.4 1.0 C2 A:FAD601 4.5 32.4 1.0 CG A:GLU475 4.6 33.3 1.0 ND2 A:ASN439 4.7 33.3 1.0 C10 A:FAD601 4.9 30.2 1.0 C4 A:AKG603 4.9 47.4 1.0

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


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 2-Oxoglutarate (2-Og) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn602 b:25.4 occ:1.00 OE1 B:GLU475 2.0 30.2 1.0 NE2 B:HIS434 2.1 27.1 1.0 NE2 B:HIS441 2.1 29.4 1.0 O1 B:AKG603 2.4 28.5 1.0 O5 B:AKG603 2.5 28.1 1.0 CE1 B:HIS441 2.9 29.7 1.0 CD2 B:HIS434 2.9 28.3 1.0 CD B:GLU475 3.0 29.1 1.0 O4 B:FAD601 3.1 32.4 1.0 C2 B:AKG603 3.1 30.3 1.0 C1 B:AKG603 3.1 33.3 1.0 CE1 B:HIS434 3.2 27.6 1.0 CD2 B:HIS441 3.3 31.4 1.0 C4 B:FAD601 3.4 29.6 1.0 OE2 B:GLU475 3.4 30.9 1.0 N3 B:FAD601 3.7 28.6 1.0 ND1 B:HIS441 4.1 31.2 1.0 CG B:HIS434 4.1 30.0 1.0 NH2 B:ARG386 4.1 31.2 1.0 C4X B:FAD601 4.2 29.9 1.0 ND1 B:HIS434 4.2 29.3 1.0 CG B:HIS441 4.3 29.9 1.0 CG B:GLU475 4.3 27.2 1.0 O2 B:AKG603 4.3 34.4 1.0 O B:HOH705 4.4 27.1 1.0 NE2 B:HIS476 4.4 30.3 1.0 OD1 B:ASN439 4.5 32.2 1.0 C3 B:AKG603 4.5 36.2 1.0 N5 B:FAD601 4.6 31.5 1.0 C2 B:FAD601 4.7 29.8 1.0

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