Zinc in PDB 2ejv: Crystal Structure of Threonine 3-Dehydrogenase Complexed with Nad+

All present enzymatic activity of Crystal Structure of Threonine 3-Dehydrogenase Complexed with Nad+:
1.1.1.103;

The structure of Crystal Structure of Threonine 3-Dehydrogenase Complexed with Nad+, PDB code: 2ejv was solved by R.Omi, T.Yao, M.Goto, I.Miyahara, K.Hirotsu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.99 / 2.55
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	135.758, 135.758, 268.593, 90.00, 90.00, 120.00
R / Rfree (%)	20.7 / 23.6

The binding sites of Zinc atom in the Crystal Structure of Threonine 3-Dehydrogenase Complexed with Nad+ (pdb code 2ejv). 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 Complexed with Nad+, PDB code: 2ejv:
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 Complexed with Nad+


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 Complexed with Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:85.0 occ:1.00 OE2 A:GLU64 2.2 49.1 1.0 NE2 A:HIS63 2.3 51.3 1.0 SG A:CYS38 2.5 57.5 1.0 CD2 A:HIS63 2.9 47.8 1.0 CB A:CYS38 3.1 52.5 1.0 CD A:GLU64 3.1 45.4 1.0 CG A:GLU64 3.2 43.2 1.0 CE1 A:HIS63 3.4 50.1 1.0 OE1 A:GLU148 3.7 50.5 1.0 CG A:HIS63 4.2 47.5 1.0 OE1 A:GLU64 4.3 48.0 1.0 ND1 A:HIS63 4.3 49.6 1.0 CA A:CYS38 4.4 52.4 1.0 N A:CYS38 4.5 50.5 1.0 CD A:GLU148 4.6 50.2 1.0 CB A:GLU64 4.7 44.2 1.0 OE2 A:GLU148 4.7 49.9 1.0 CB A:PRO149 4.8 44.8 1.0 NZ A:LYS336 5.0 37.5 1.0 O A:HOH1432 5.0 43.4 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Threonine 3-Dehydrogenase Complexed with Nad+


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 Complexed with Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:61.9 occ:1.00 SG A:CYS99 2.4 60.4 1.0 SG A:CYS96 2.4 63.9 1.0 SG A:CYS93 2.5 63.1 1.0 SG A:CYS107 2.6 59.3 1.0 CB A:CYS107 3.2 55.8 1.0 CB A:CYS99 3.4 64.2 1.0 N A:HIS94 3.5 65.2 1.0 CB A:CYS96 3.5 66.0 1.0 N A:CYS93 3.6 61.2 1.0 CB A:CYS93 3.6 61.7 1.0 CA A:CYS107 3.7 54.8 1.0 N A:CYS96 3.9 67.0 1.0 CA A:CYS93 3.9 62.7 1.0 N A:ALA95 4.1 68.0 1.0 C A:CYS93 4.1 64.2 1.0 N A:LEU108 4.2 57.9 1.0 N A:CYS99 4.3 63.6 1.0 CA A:CYS96 4.3 66.0 1.0 C A:CYS107 4.3 56.1 1.0 CA A:HIS94 4.4 66.3 1.0 CA A:CYS99 4.4 64.5 1.0 C A:VAL92 4.5 59.2 1.0 CB A:VAL92 4.6 58.1 1.0 N A:ASN109 4.7 60.9 1.0 O A:CYS96 4.7 65.4 1.0 C A:ALA95 4.7 68.4 1.0 C A:HIS94 4.8 67.5 1.0 C A:CYS96 4.8 66.3 1.0 ND2 A:ASN109 4.8 60.6 1.0 CA A:VAL92 4.9 57.5 1.0 CA A:ALA95 5.0 68.3 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Threonine 3-Dehydrogenase Complexed with Nad+


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 Complexed with Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:90.1 occ:1.00 NE2 B:HIS63 2.3 45.6 1.0 SG B:CYS38 2.6 54.7 1.0 OE2 B:GLU64 2.6 48.0 1.0 CB B:CYS38 2.9 50.3 1.0 CE1 B:HIS63 3.0 43.2 1.0 CD2 B:HIS63 3.3 42.9 1.0 CD B:GLU64 3.4 45.2 1.0 CG B:GLU64 3.6 43.8 1.0 OE1 B:GLU148 3.8 47.5 1.0 ND1 B:HIS63 4.2 43.9 1.0 CA B:CYS38 4.3 49.9 1.0 CG B:HIS63 4.3 42.7 1.0 OE1 B:GLU64 4.6 45.0 1.0 O B:HOH2390 4.6 58.5 1.0 CD B:GLU148 4.7 47.0 1.0 OE2 B:GLU148 4.8 48.2 1.0 N B:CYS38 4.8 47.8 1.0 OG1 B:THR40 4.8 47.4 1.0 CB B:THR40 4.9 46.7 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Threonine 3-Dehydrogenase Complexed with Nad+


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 Complexed with Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:48.2 occ:1.00 SG B:CYS107 2.3 44.9 1.0 SG B:CYS93 2.4 51.3 1.0 SG B:CYS99 2.4 51.4 1.0 SG B:CYS96 2.5 50.0 1.0 CB B:CYS107 3.2 43.5 1.0 CB B:CYS96 3.3 52.8 1.0 CB B:CYS99 3.5 55.2 1.0 N B:CYS93 3.6 47.0 1.0 CB B:CYS93 3.6 50.6 1.0 CA B:CYS107 3.7 44.1 1.0 N B:HIS94 3.8 52.5 1.0 CA B:CYS93 3.9 49.4 1.0 N B:CYS96 4.0 54.0 1.0 N B:LEU108 4.1 46.8 1.0 C B:CYS93 4.2 51.1 1.0 C B:CYS107 4.2 45.2 1.0 CA B:CYS96 4.2 54.0 1.0 N B:ALA95 4.2 53.6 1.0 N B:CYS99 4.3 56.7 1.0 CA B:CYS99 4.5 56.3 1.0 N B:ASN109 4.5 46.4 1.0 ND2 B:ASN109 4.7 45.5 1.0 CA B:HIS94 4.7 53.6 1.0 C B:VAL92 4.7 45.3 1.0 C B:ALA95 4.7 54.5 1.0 CB B:VAL92 4.7 42.3 1.0 C B:CYS96 4.8 56.0 1.0 O B:CYS96 4.9 56.9 1.0 CA B:VAL92 4.9 42.6 1.0 C B:HIS94 5.0 54.4 1.0

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