Zinc in PDB 2dfv: Hyperthermophilic Threonine Dehydrogenase From Pyrococcus Horikoshii

All present enzymatic activity of Hyperthermophilic Threonine Dehydrogenase From Pyrococcus Horikoshii:
1.1.1.103;

The structure of Hyperthermophilic Threonine Dehydrogenase From Pyrococcus Horikoshii, PDB code: 2dfv was solved by K.Ishikawa, N.Higashi, T.Nakamura, T.Matsuura, A.Nakagawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	N/A / 2.05
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	144.433, 144.433, 305.069, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 23.9

The binding sites of Zinc atom in the Hyperthermophilic Threonine Dehydrogenase From Pyrococcus Horikoshii (pdb code 2dfv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Hyperthermophilic Threonine Dehydrogenase From Pyrococcus Horikoshii, PDB code: 2dfv:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Hyperthermophilic Threonine Dehydrogenase From Pyrococcus Horikoshii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Hyperthermophilic Threonine Dehydrogenase From Pyrococcus Horikoshii within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:15.5 occ:1.00 SG A:CYS103 2.3 11.5 1.0 SG A:CYS111 2.3 14.3 1.0 SG A:CYS100 2.3 12.3 1.0 SG A:CYS97 2.4 16.6 1.0 CB A:CYS111 3.3 12.7 1.0 CB A:CYS103 3.4 10.6 1.0 CB A:CYS97 3.6 18.3 1.0 CB A:CYS100 3.6 13.4 1.0 N A:CYS97 3.6 17.4 1.0 N A:CYS100 3.7 17.1 1.0 N A:GLY98 3.7 19.8 1.0 CA A:CYS111 3.8 13.4 1.0 N A:GLN112 3.9 16.3 1.0 CA A:CYS97 4.0 18.8 1.0 N A:CYS103 4.2 9.8 1.0 N A:LYS99 4.2 20.1 1.0 CA A:CYS100 4.2 13.2 1.0 C A:CYS97 4.2 20.4 1.0 C A:CYS111 4.2 15.2 1.0 CA A:CYS103 4.4 10.0 1.0 N A:ASN113 4.5 20.5 1.0 OD1 A:ASN113 4.6 28.4 1.0 CA A:GLY98 4.7 20.4 1.0 C A:VAL96 4.7 16.9 1.0 CB A:VAL96 4.8 16.4 1.0 C A:LYS99 4.8 19.2 1.0 C A:GLY98 4.8 20.4 1.0 C A:CYS100 4.9 11.4 1.0 CB A:ASN113 4.9 22.1 1.0 O A:CYS100 5.0 10.1 1.0 CA A:GLN112 5.0 18.9 1.0

Zinc binding site 2 out of 3 in the Hyperthermophilic Threonine Dehydrogenase From Pyrococcus Horikoshii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Hyperthermophilic Threonine Dehydrogenase From Pyrococcus Horikoshii within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1002 b:22.1 occ:1.00 SG B:CYS103 2.3 17.7 1.0 SG B:CYS100 2.3 20.6 1.0 SG B:CYS111 2.4 21.0 1.0 SG B:CYS97 2.5 24.3 1.0 CB B:CYS111 3.3 21.2 1.0 CB B:CYS103 3.4 16.6 1.0 CB B:CYS100 3.5 19.9 1.0 N B:CYS97 3.6 24.2 1.0 CB B:CYS97 3.7 26.2 1.0 N B:CYS100 3.7 22.7 1.0 CA B:CYS111 3.7 20.1 1.0 N B:GLY98 3.8 26.6 1.0 N B:GLN112 4.0 23.4 1.0 CA B:CYS97 4.0 25.7 1.0 CA B:CYS100 4.2 20.1 1.0 N B:CYS103 4.2 15.7 1.0 C B:CYS111 4.2 22.1 1.0 N B:LYS99 4.3 26.9 1.0 C B:CYS97 4.3 26.5 1.0 CA B:CYS103 4.4 16.3 1.0 N B:ASN113 4.5 28.4 1.0 OD1 B:ASN113 4.5 37.7 1.0 C B:VAL96 4.7 22.6 1.0 CA B:GLY98 4.7 27.1 1.0 CB B:VAL96 4.8 21.0 1.0 C B:LYS99 4.9 25.5 1.0 C B:CYS100 4.9 17.9 1.0 CB B:ASN113 4.9 29.9 1.0 C B:GLY98 4.9 27.5 1.0 O B:CYS100 5.0 16.8 1.0

Zinc binding site 3 out of 3 in the Hyperthermophilic Threonine Dehydrogenase From Pyrococcus Horikoshii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Hyperthermophilic Threonine Dehydrogenase From Pyrococcus Horikoshii within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1003 b:21.1 occ:1.00 SG C:CYS103 2.3 15.8 1.0 SG C:CYS111 2.3 19.7 1.0 SG C:CYS100 2.3 17.8 1.0 SG C:CYS97 2.4 21.6 1.0 CB C:CYS111 3.2 19.0 1.0 CB C:CYS103 3.2 15.6 1.0 CB C:CYS100 3.5 20.0 1.0 CB C:CYS97 3.6 23.3 1.0 N C:CYS97 3.7 22.9 1.0 N C:GLY98 3.7 24.6 1.0 CA C:CYS111 3.7 19.8 1.0 N C:CYS100 3.7 23.6 1.0 N C:GLN112 4.0 22.6 1.0 CA C:CYS97 4.0 23.6 1.0 CA C:CYS100 4.2 19.9 1.0 N C:CYS103 4.2 15.6 1.0 C C:CYS111 4.2 21.2 1.0 C C:CYS97 4.2 25.0 1.0 CA C:CYS103 4.3 15.8 1.0 N C:LYS99 4.3 25.9 1.0 N C:ASN113 4.5 27.1 1.0 OD1 C:ASN113 4.7 34.0 1.0 CA C:GLY98 4.7 25.3 1.0 C C:VAL96 4.8 22.6 1.0 CB C:VAL96 4.8 22.2 1.0 C C:CYS100 4.8 18.0 1.0 C C:GLY98 4.9 25.6 1.0 O C:CYS100 4.9 16.4 1.0 C C:LYS99 4.9 25.7 1.0 CB C:ASN113 4.9 29.3 1.0

K.Ishikawa, N.Higashi, T.Nakamura, T.Matsuura, A.Nakagawa. The First Crystal Structure of L-Threonine Dehydrogenase. J.Mol.Biol. V. 366 857 2007.
ISSN: ISSN 0022-2836
PubMed: 17188300
DOI: 10.1016/J.JMB.2006.11.060