Atomistry » Zinc » PDB 1kjz-1kys » 1kol
Atomistry »
  Zinc »
    PDB 1kjz-1kys »
      1kol »

Zinc in PDB 1kol: Crystal Structure of Formaldehyde Dehydrogenase

Enzymatic activity of Crystal Structure of Formaldehyde Dehydrogenase

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

Protein crystallography data

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

Zinc Binding Sites:

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 1kol

Go back to Zinc Binding Sites List in 1kol
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 1kol

Go back to Zinc Binding Sites List in 1kol
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 1kol

Go back to Zinc Binding Sites List in 1kol
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 1kol

Go back to Zinc Binding Sites List in 1kol
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

Reference:

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
Page generated: Wed Dec 16 02:55:23 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy