Zinc in PDB 6lpq: Crystal Structure of Human D-2-Hydroxyglutarate Dehydrogenase in Complex with D-Malate (D-Mal)

The structure of Crystal Structure of Human D-2-Hydroxyglutarate Dehydrogenase in Complex with D-Malate (D-Mal), PDB code: 6lpq 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)	41.14 / 2.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	72.615, 94.569, 73.673, 90, 111.55, 90
R / Rfree (%)	21.5 / 25.5

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


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-Malate (D-Mal) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:27.2 occ:1.00 OE1 A:GLU475 2.0 35.4 1.0 O2 A:MLT603 2.1 33.1 1.0 NE2 A:HIS434 2.2 24.7 1.0 O3 A:MLT603 2.3 31.1 1.0 NE2 A:HIS441 2.4 29.2 1.0 C1 A:MLT603 2.8 34.4 1.0 O4 A:FAD601 2.8 28.4 1.0 C2 A:MLT603 2.9 35.2 1.0 CD A:GLU475 2.9 33.6 1.0 CE1 A:HIS434 3.1 23.6 1.0 CE1 A:HIS441 3.1 28.7 1.0 C4 A:FAD601 3.2 28.6 1.0 OE2 A:GLU475 3.2 26.4 1.0 CD2 A:HIS434 3.2 25.5 1.0 N3 A:FAD601 3.5 31.7 1.0 CD2 A:HIS441 3.6 30.4 1.0 C4X A:FAD601 4.0 28.4 1.0 O1 A:MLT603 4.0 33.7 1.0 NH2 A:ARG386 4.1 24.8 1.0 ND1 A:HIS434 4.2 22.0 1.0 ND1 A:HIS441 4.3 33.0 1.0 C3 A:MLT603 4.3 33.9 1.0 CG A:GLU475 4.3 34.2 1.0 CG A:HIS434 4.3 24.5 1.0 N5 A:FAD601 4.4 34.7 1.0 O5 A:MLT603 4.5 41.2 1.0 C2 A:FAD601 4.5 30.6 1.0 CG A:HIS441 4.5 31.3 1.0 NE2 A:HIS476 4.6 32.9 1.0 OD1 A:ASN439 4.9 29.7 1.0 C10 A:FAD601 4.9 23.7 1.0 C4 A:MLT603 5.0 36.1 1.0

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


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-Malate (D-Mal) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn602 b:28.3 occ:1.00 OE1 B:GLU475 2.1 31.8 1.0 O1 B:MLT603 2.2 31.2 1.0 NE2 B:HIS441 2.2 25.2 1.0 NE2 B:HIS434 2.2 24.7 1.0 O3 B:MLT603 2.4 26.7 1.0 CE1 B:HIS441 2.8 28.7 1.0 C1 B:MLT603 2.9 31.2 1.0 CD2 B:HIS434 3.0 24.7 1.0 C2 B:MLT603 3.1 26.8 1.0 CD B:GLU475 3.1 29.7 1.0 O4 B:FAD601 3.2 33.5 1.0 CE1 B:HIS434 3.3 25.7 1.0 CD2 B:HIS441 3.4 26.4 1.0 C4 B:FAD601 3.4 32.4 1.0 OE2 B:GLU475 3.6 27.1 1.0 N3 B:FAD601 3.7 29.8 1.0 ND1 B:HIS441 4.0 31.2 1.0 NH2 B:ARG386 4.1 31.8 1.0 O2 B:MLT603 4.1 26.8 1.0 C4X B:FAD601 4.2 32.1 1.0 CG B:HIS434 4.2 26.2 1.0 ND1 B:HIS434 4.3 23.0 1.0 CG B:HIS441 4.3 24.0 1.0 CG B:GLU475 4.4 26.0 1.0 O5 B:MLT603 4.5 35.1 1.0 NE2 B:HIS476 4.5 24.3 1.0 C3 B:MLT603 4.5 31.0 1.0 N5 B:FAD601 4.6 32.1 1.0 OD1 B:ASN439 4.6 25.8 1.0 C2 B:FAD601 4.6 30.1 1.0 C10 B:FAD601 5.0 25.2 1.0

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