Zinc in PDB 2dq4: Crystal Structure of Threonine 3-Dehydrogenase

All present enzymatic activity of Crystal Structure of Threonine 3-Dehydrogenase:
1.1.1.103;

The structure of Crystal Structure of Threonine 3-Dehydrogenase, PDB code: 2dq4 was solved by R.Omi, T.Yao, M.Goto, I.Miyahara, K.Hirotsu, Riken Structuralgenomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.99 / 2.50
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	136.349, 136.349, 269.714, 90.00, 90.00, 120.00
R / Rfree (%)	20.7 / 23.7

The binding sites of Zinc atom in the Crystal Structure of Threonine 3-Dehydrogenase (pdb code 2dq4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Threonine 3-Dehydrogenase, PDB code: 2dq4:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Threonine 3-Dehydrogenase


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 Threonine 3-Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:71.8 occ:1.00 OE2 A:GLU64 2.3 38.9 1.0 NE2 A:HIS63 2.3 43.4 1.0 SG A:CYS38 2.4 51.2 1.0 CB A:CYS38 3.1 45.2 1.0 CD2 A:HIS63 3.1 39.2 1.0 CD A:GLU64 3.2 36.2 1.0 CE1 A:HIS63 3.4 42.6 1.0 CG A:GLU64 3.5 34.2 1.0 OE1 A:GLU148 3.8 43.0 1.0 CG A:HIS63 4.3 39.2 1.0 OE1 A:GLU64 4.3 36.2 1.0 CA A:CYS38 4.3 45.1 1.0 ND1 A:HIS63 4.4 42.3 1.0 N A:CYS38 4.5 42.1 1.0 CD A:GLU148 4.7 42.2 1.0 OE2 A:GLU148 4.7 45.8 1.0 CB A:PRO149 4.9 32.5 1.0 OG1 A:THR40 4.9 46.3 1.0 CB A:GLU64 4.9 34.2 1.0 OD1 A:ASP41 5.0 47.0 1.0 O A:HOH580 5.0 39.8 1.0 C A:CYS38 5.0 44.7 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Threonine 3-Dehydrogenase


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 Threonine 3-Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:50.5 occ:1.00 SG A:CYS99 2.3 48.3 1.0 SG A:CYS96 2.4 49.5 1.0 SG A:CYS107 2.5 45.2 1.0 SG A:CYS93 2.5 54.2 1.0 CB A:CYS107 3.1 44.5 1.0 CB A:CYS93 3.5 51.5 1.0 CB A:CYS96 3.6 53.0 1.0 N A:HIS94 3.6 55.4 1.0 N A:CYS93 3.6 50.6 1.0 CB A:CYS99 3.7 49.2 1.0 CA A:CYS107 3.7 44.0 1.0 CA A:CYS93 3.9 52.9 1.0 N A:ALA95 4.1 57.5 1.0 N A:CYS96 4.1 54.1 1.0 C A:CYS93 4.1 54.5 1.0 N A:CYS99 4.3 47.6 1.0 N A:LEU108 4.3 47.3 1.0 C A:CYS107 4.3 45.1 1.0 CA A:CYS96 4.4 52.6 1.0 N A:ASN109 4.5 50.2 1.0 CA A:HIS94 4.5 56.4 1.0 CA A:CYS99 4.5 49.6 1.0 C A:ALA95 4.6 56.6 1.0 C A:VAL92 4.6 49.3 1.0 ND2 A:ASN109 4.7 48.6 1.0 CB A:ASN109 4.7 51.3 1.0 CB A:VAL92 4.8 46.2 1.0 C A:HIS94 4.8 57.1 1.0 CA A:ALA95 5.0 57.1 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Threonine 3-Dehydrogenase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Threonine 3-Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn503 b:82.7 occ:1.00 NE2 B:HIS63 2.2 38.6 1.0 SG B:CYS38 2.5 53.2 1.0 OE2 B:GLU64 2.5 41.3 1.0 CE1 B:HIS63 3.0 37.9 1.0 CB B:CYS38 3.1 48.2 1.0 CD2 B:HIS63 3.2 35.0 1.0 CD B:GLU64 3.3 40.3 1.0 CG B:GLU64 3.4 37.7 1.0 OE1 B:GLU148 3.8 38.6 1.0 ND1 B:HIS63 4.2 38.5 1.0 CG B:HIS63 4.3 35.5 1.0 CA B:CYS38 4.4 47.3 1.0 OE1 B:GLU64 4.4 41.0 1.0 N B:CYS38 4.7 44.3 1.0 CD B:GLU148 4.7 39.3 1.0 CB B:PRO149 4.8 31.1 1.0 OE2 B:GLU148 4.9 40.5 1.0 CB B:GLU64 5.0 36.1 1.0 OG1 B:THR40 5.0 52.2 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Threonine 3-Dehydrogenase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Threonine 3-Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn504 b:38.1 occ:1.00 SG B:CYS107 2.3 35.0 1.0 SG B:CYS93 2.4 39.4 1.0 SG B:CYS96 2.5 39.0 1.0 SG B:CYS99 2.5 40.1 1.0 CB B:CYS107 3.2 34.0 1.0 CB B:CYS96 3.4 41.7 1.0 CB B:CYS99 3.5 40.2 1.0 CB B:CYS93 3.5 39.9 1.0 N B:CYS93 3.6 38.1 1.0 N B:HIS94 3.7 43.2 1.0 CA B:CYS107 3.8 34.3 1.0 CA B:CYS93 3.9 39.6 1.0 N B:CYS96 4.0 43.0 1.0 N B:LEU108 4.1 38.0 1.0 C B:CYS93 4.1 42.0 1.0 N B:CYS99 4.3 38.9 1.0 N B:ALA95 4.3 45.6 1.0 C B:CYS107 4.3 36.1 1.0 CA B:CYS96 4.3 43.0 1.0 CA B:CYS99 4.4 39.8 1.0 N B:ASN109 4.5 36.5 1.0 CA B:HIS94 4.6 45.0 1.0 C B:VAL92 4.7 36.2 1.0 C B:ALA95 4.8 44.7 1.0 CB B:VAL92 4.8 33.7 1.0 ND2 B:ASN109 4.9 37.3 1.0 C B:CYS96 4.9 44.0 1.0 C B:HIS94 4.9 45.4 1.0 CA B:VAL92 5.0 35.2 1.0 O B:CYS96 5.0 45.2 1.0

R.Omi, T.Yao, M.Goto, I.Miyahara, K.Hirotsu. Crystal Structure of Threonine 3-Dehydrogenase To Be Published.