Zinc in PDB 1kol: Crystal Structure of Formaldehyde Dehydrogenase

All present enzymatic activity of Crystal Structure of Formaldehyde Dehydrogenase:
1.2.1.46;

The structure of Crystal Structure of Formaldehyde Dehydrogenase, PDB code: 1kol was solved by N.Tanaka, Y.Kusakabe, K.Ito, T.Yoshimoto, K.T.Nakamura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.65
Space group	P 31 1 2
Cell size a, b, c (Å), α, β, γ (°)	85.686, 85.686, 190.752, 90.00, 90.00, 120.00
R / Rfree (%)	17.1 / 20.6

The binding sites of Zinc atom in the Crystal Structure of Formaldehyde Dehydrogenase (pdb code 1kol). 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 Formaldehyde Dehydrogenase, PDB code: 1kol:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Formaldehyde 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 Formaldehyde Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:16.5 occ:1.00 OD1 A:ASP169 1.9 16.2 1.0 O A:HOH1404 2.0 30.5 1.0 NE2 A:HIS67 2.0 13.5 1.0 SG A:CYS46 2.3 10.4 1.0 CD2 A:HIS67 3.0 12.9 1.0 CE1 A:HIS67 3.0 14.2 1.0 CG A:ASP169 3.1 13.9 1.0 CB A:CYS46 3.2 13.2 1.0 OD2 A:ASP169 3.5 14.5 1.0 C5N A:NAD1403 3.5 12.6 1.0 OG A:SER48 3.9 16.8 1.0 C6N A:NAD1403 4.1 12.8 1.0 ND1 A:HIS67 4.1 13.3 1.0 CB A:SER48 4.1 15.3 1.0 CG A:HIS67 4.1 13.3 1.0 C4N A:NAD1403 4.1 11.9 1.0 CB A:ASP169 4.3 13.7 1.0 CD A:GLU68 4.5 14.3 1.0 CG A:GLU68 4.5 13.4 1.0 O A:HOH1862 4.5 33.1 1.0 OE1 A:GLU68 4.5 15.8 1.0 CA A:CYS46 4.7 14.6 1.0 N A:SER48 4.9 14.3 1.0 CE1 A:TYR125 4.9 24.5 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Formaldehyde 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 Formaldehyde Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:11.6 occ:1.00 SG A:CYS103 2.3 9.1 1.0 SG A:CYS111 2.3 9.7 1.0 SG A:CYS100 2.3 8.4 1.0 SG A:CYS97 2.3 9.8 1.0 CB A:CYS111 3.3 11.0 1.0 CB A:CYS103 3.3 9.5 1.0 N A:CYS97 3.4 11.6 1.0 CB A:CYS100 3.4 10.3 1.0 CB A:CYS97 3.4 9.8 1.0 CA A:CYS111 3.7 9.9 1.0 N A:GLY98 3.8 10.7 1.0 CA A:CYS97 3.8 10.3 1.0 N A:LEU112 3.9 10.7 1.0 N A:CYS100 4.0 10.1 1.0 N A:CYS103 4.2 9.7 1.0 OG1 A:THR113 4.2 13.7 1.0 CA A:CYS100 4.2 9.1 1.0 C A:CYS97 4.3 12.1 1.0 C A:CYS111 4.3 11.4 1.0 N A:ARG99 4.3 11.5 1.0 CA A:CYS103 4.4 10.6 1.0 C A:ALA96 4.5 11.4 1.0 N A:THR113 4.7 12.1 1.0 C A:ARG99 4.7 12.3 1.0 CA A:ALA96 4.8 10.8 1.0 C A:CYS100 4.8 10.2 1.0 CA A:GLY98 4.8 9.8 1.0 O A:CYS100 4.9 9.8 1.0 CG2 A:THR113 5.0 15.8 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Formaldehyde 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 Formaldehyde Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1003 b:15.7 occ:1.00 OD1 B:ASP169 1.9 14.4 1.0 O B:HOH2404 2.0 32.4 1.0 NE2 B:HIS67 2.1 13.1 1.0 SG B:CYS46 2.3 10.4 1.0 CD2 B:HIS67 3.0 12.7 1.0 CG B:ASP169 3.0 12.8 1.0 CE1 B:HIS67 3.1 13.3 1.0 CB B:CYS46 3.2 12.9 1.0 C5N B:NAD2403 3.5 14.2 1.0 OD2 B:ASP169 3.5 14.2 1.0 OG B:SER48 3.9 16.0 1.0 C6N B:NAD2403 4.1 13.4 1.0 C4N B:NAD2403 4.1 13.5 1.0 CG B:HIS67 4.1 11.4 1.0 ND1 B:HIS67 4.2 12.1 1.0 CB B:SER48 4.2 14.4 1.0 CB B:ASP169 4.3 11.3 1.0 CG B:GLU68 4.5 13.5 1.0 CD B:GLU68 4.5 15.2 1.0 OE1 B:GLU68 4.5 16.6 1.0 O B:HOH2721 4.6 27.1 1.0 CA B:CYS46 4.7 12.9 1.0 N B:SER48 4.9 12.9 1.0 O B:HOH2408 5.0 12.2 1.0 CE1 B:TYR125 5.0 21.1 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Formaldehyde 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 Formaldehyde Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1004 b:11.2 occ:1.00 SG B:CYS100 2.3 8.6 1.0 SG B:CYS97 2.3 9.3 1.0 SG B:CYS103 2.3 8.5 1.0 SG B:CYS111 2.4 9.4 1.0 CB B:CYS111 3.4 9.7 1.0 CB B:CYS100 3.4 9.0 1.0 CB B:CYS103 3.4 10.2 1.0 N B:CYS97 3.5 11.3 1.0 CB B:CYS97 3.5 10.2 1.0 CA B:CYS111 3.7 9.8 1.0 N B:GLY98 3.8 8.4 1.0 CA B:CYS97 3.9 10.3 1.0 N B:CYS100 3.9 10.0 1.0 N B:LEU112 3.9 9.4 1.0 CA B:CYS100 4.2 9.0 1.0 N B:CYS103 4.2 9.6 1.0 OG1 B:THR113 4.2 12.5 1.0 C B:CYS111 4.2 11.2 1.0 C B:CYS97 4.3 10.8 1.0 N B:ARG99 4.3 10.1 1.0 CA B:CYS103 4.4 9.5 1.0 C B:ALA96 4.6 11.9 1.0 N B:THR113 4.7 10.6 1.0 C B:ARG99 4.8 11.7 1.0 C B:CYS100 4.8 11.0 1.0 O B:CYS100 4.9 10.7 1.0 CA B:GLY98 4.9 9.2 1.0 CA B:ALA96 4.9 10.3 1.0

N.Tanaka, Y.Kusakabe, K.Ito, T.Yoshimoto, K.T.Nakamura. Crystal Structure of Formaldehyde Dehydrogenase From Pseudomonas Putida: the Structural Origin of the Tightly Bound Cofactor in Nicotinoprotein Dehydrogenases J.Mol.Biol. V. 324 519 2002.
ISSN: ISSN 0022-2836
PubMed: 12445786
DOI: 10.1016/S0022-2836(02)01066-5