Zinc in PDB 9vkn: Crystal Structure of Dhdr in Complex with Inducer L2HG

The structure of Crystal Structure of Dhdr in Complex with Inducer L2HG, PDB code: 9vkn was solved by P.Sun, B.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.81 / 2.44
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	126.984, 126.984, 39.776, 90, 90, 90
R / Rfree (%)	19.8 / 24

The structure of Crystal Structure of Dhdr in Complex with Inducer L2HG also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Dhdr in Complex with Inducer L2HG (pdb code 9vkn). 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 Dhdr in Complex with Inducer L2HG, PDB code: 9vkn:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Dhdr in Complex with Inducer L2HG


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 Dhdr in Complex with Inducer L2HG within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:40.7 occ:1.00 NE2 A:HIS217 1.8 46.8 1.0 NE2 A:HIS147 2.1 45.2 1.0 NE2 A:HIS195 2.1 42.8 1.0 O3 A:S2G301 2.2 53.3 1.0 O2 A:S2G301 2.2 37.3 1.0 OD1 A:ASP143 2.3 45.3 1.0 CE1 A:HIS217 2.4 53.9 1.0 CE1 A:HIS195 2.9 45.0 1.0 C2 A:S2G301 3.0 43.7 1.0 CE1 A:HIS147 3.0 37.8 1.0 C1 A:S2G301 3.0 42.5 1.0 CD2 A:HIS217 3.0 45.8 1.0 CD2 A:HIS147 3.2 43.4 1.0 CG A:ASP143 3.2 39.4 1.0 OD2 A:ASP143 3.3 47.7 1.0 CD2 A:HIS195 3.3 41.8 1.0 ND1 A:HIS217 3.6 38.2 1.0 CG A:HIS217 3.9 44.8 1.0 ND1 A:HIS195 4.1 42.4 1.0 ND1 A:HIS147 4.1 43.0 1.0 O1 A:S2G301 4.2 46.0 1.0 CG A:HIS147 4.3 41.7 1.0 NH2 A:ARG99 4.3 39.0 1.0 CG A:HIS195 4.3 40.6 1.0 C3 A:S2G301 4.4 44.0 1.0 CB A:ASP143 4.6 40.7 1.0 O A:ASP143 4.8 37.3 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Dhdr in Complex with Inducer L2HG


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 Dhdr in Complex with Inducer L2HG within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:49.9 occ:1.00 O3 B:S2G301 2.1 52.0 1.0 NE2 B:HIS195 2.2 50.4 1.0 NE2 B:HIS147 2.2 44.9 1.0 O1 B:S2G301 2.2 46.7 1.0 NE2 B:HIS217 2.3 50.2 1.0 OD1 B:ASP143 2.3 49.6 1.0 C2 B:S2G301 2.8 51.3 1.0 C1 B:S2G301 2.9 50.4 1.0 CE1 B:HIS217 3.1 51.6 1.0 CG B:ASP143 3.1 51.8 1.0 CE1 B:HIS195 3.1 44.3 1.0 OD2 B:ASP143 3.1 49.6 1.0 CE1 B:HIS147 3.2 42.5 1.0 CD2 B:HIS195 3.2 47.0 1.0 CD2 B:HIS147 3.2 49.1 1.0 CD2 B:HIS217 3.4 47.5 1.0 O2 B:S2G301 4.1 50.5 1.0 C3 B:S2G301 4.2 52.8 1.0 ND1 B:HIS195 4.2 56.5 1.0 ND1 B:HIS217 4.3 54.1 1.0 ND1 B:HIS147 4.3 48.0 1.0 CG B:HIS195 4.3 48.7 1.0 NH2 B:ARG99 4.3 48.3 1.0 CG B:HIS147 4.3 47.7 1.0 CG B:HIS217 4.5 51.6 1.0 CB B:ASP143 4.6 48.2 1.0 C4 B:S2G301 4.8 56.0 1.0 O B:ASP143 4.9 46.3 1.0

P.Sun, B.Wang. Crystal Structure of Dhdr in Complex with Inducer L2HG To Be Published.