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Zinc in PDB 1m6h: Human Glutathione-Dependent Formaldehyde Dehydrogenase

Enzymatic activity of Human Glutathione-Dependent Formaldehyde Dehydrogenase

All present enzymatic activity of Human Glutathione-Dependent Formaldehyde Dehydrogenase:
1.1.1.1;

Protein crystallography data

The structure of Human Glutathione-Dependent Formaldehyde Dehydrogenase, PDB code: 1m6h was solved by P.C.Sanghani, H.Robinson, W.F.Bosron, T.D.Hurley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.00
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.620, 78.620, 309.659, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 21.8

Other elements in 1m6h:

The structure of Human Glutathione-Dependent Formaldehyde Dehydrogenase also contains other interesting chemical elements:

Potassium (K) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Human Glutathione-Dependent Formaldehyde Dehydrogenase (pdb code 1m6h). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Human Glutathione-Dependent Formaldehyde Dehydrogenase, PDB code: 1m6h:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1m6h

Go back to Zinc Binding Sites List in 1m6h
Zinc binding site 1 out of 4 in the Human Glutathione-Dependent Formaldehyde Dehydrogenase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Glutathione-Dependent Formaldehyde Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1375

b:20.0
occ:1.00
SG A:CYS96 2.3 20.0 1.0
SG A:CYS110 2.3 19.7 1.0
SG A:CYS102 2.3 20.0 1.0
SG A:CYS99 2.4 20.5 1.0
CB A:CYS110 3.1 22.2 1.0
CB A:CYS99 3.4 22.4 1.0
CB A:CYS102 3.4 22.4 1.0
CB A:CYS96 3.4 19.4 1.0
N A:CYS96 3.5 18.9 1.0
CA A:CYS110 3.6 20.8 1.0
N A:CYS99 3.8 25.4 1.0
N A:GLY97 3.9 21.2 1.0
CA A:CYS96 3.9 19.6 1.0
CA A:CYS99 4.2 23.8 1.0
N A:CYS102 4.2 21.8 1.0
N A:GLN111 4.3 21.3 1.0
C A:CYS96 4.3 20.5 1.0
C A:CYS110 4.3 21.4 1.0
CA A:CYS102 4.4 21.4 1.0
N A:GLU98 4.4 26.7 1.0
C A:GLN95 4.5 19.1 1.0
CB A:LYS112 4.5 27.8 1.0
N A:LYS112 4.6 24.4 1.0
CA A:GLN95 4.7 19.0 1.0
N A:CYS110 4.9 20.7 1.0
C A:CYS99 4.9 24.4 1.0
CA A:GLY97 4.9 21.9 1.0
O A:CYS99 5.0 23.4 1.0
C A:GLU98 5.0 27.7 1.0

Zinc binding site 2 out of 4 in 1m6h

Go back to Zinc Binding Sites List in 1m6h
Zinc binding site 2 out of 4 in the Human Glutathione-Dependent Formaldehyde Dehydrogenase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Glutathione-Dependent Formaldehyde Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1376

b:19.8
occ:1.00
O A:HOH3010 2.1 14.0 1.0
NE2 A:HIS66 2.1 17.2 1.0
SG A:CYS173 2.3 16.7 1.0
SG A:CYS44 2.3 20.9 1.0
CD2 A:HIS66 3.1 15.8 1.0
CE1 A:HIS66 3.2 17.8 1.0
O A:HOH3068 3.3 40.5 1.0
CB A:CYS44 3.3 19.6 1.0
CB A:CYS173 3.4 14.8 1.0
O A:HOH3381 3.4 46.0 1.0
O A:HOH3231 3.9 41.3 1.0
OG1 A:THR46 3.9 21.4 1.0
O A:HOH3213 4.0 46.3 1.0
CB A:THR46 4.1 21.3 1.0
CG A:HIS66 4.2 14.7 1.0
ND1 A:HIS66 4.2 15.9 1.0
CE1 A:HIS45 4.7 29.8 1.0
OH A:TYR92 4.7 17.3 1.0
OE2 A:GLU67 4.7 19.9 1.0
O A:HOH3385 4.7 49.4 1.0
CA A:CYS173 4.8 15.4 1.0
CA A:CYS44 4.8 19.3 1.0
N A:GLY174 4.8 14.0 1.0
N A:THR46 4.8 21.5 1.0
ND1 A:HIS45 5.0 29.8 1.0

Zinc binding site 3 out of 4 in 1m6h

Go back to Zinc Binding Sites List in 1m6h
Zinc binding site 3 out of 4 in the Human Glutathione-Dependent Formaldehyde Dehydrogenase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human Glutathione-Dependent Formaldehyde Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1375

b:17.2
occ:1.00
SG B:CYS99 2.3 16.0 1.0
SG B:CYS102 2.3 16.8 1.0
SG B:CYS96 2.4 17.1 1.0
SG B:CYS110 2.4 14.8 1.0
CB B:CYS110 3.1 16.7 1.0
CB B:CYS102 3.3 17.2 1.0
CB B:CYS99 3.4 19.1 1.0
CB B:CYS96 3.5 16.4 1.0
N B:CYS96 3.5 15.6 1.0
CA B:CYS110 3.6 17.1 1.0
N B:CYS99 3.8 19.3 1.0
N B:GLY97 3.8 17.8 1.0
CA B:CYS96 3.9 17.4 1.0
CA B:CYS99 4.1 18.3 1.0
N B:CYS102 4.2 14.2 1.0
N B:GLN111 4.2 16.7 1.0
C B:CYS110 4.3 17.3 1.0
C B:CYS96 4.3 18.6 1.0
CA B:CYS102 4.3 15.3 1.0
N B:GLU98 4.4 21.7 1.0
CB B:LYS112 4.4 21.0 1.0
N B:LYS112 4.5 18.9 1.0
C B:GLN95 4.5 15.4 1.0
CA B:GLN95 4.8 15.8 1.0
CA B:GLY97 4.8 20.1 1.0
C B:CYS99 4.8 18.0 1.0
O B:CYS99 4.8 16.6 1.0
N B:CYS110 4.9 17.6 1.0
C B:GLU98 4.9 22.3 1.0

Zinc binding site 4 out of 4 in 1m6h

Go back to Zinc Binding Sites List in 1m6h
Zinc binding site 4 out of 4 in the Human Glutathione-Dependent Formaldehyde Dehydrogenase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human Glutathione-Dependent Formaldehyde Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1376

b:15.8
occ:1.00
NE2 B:HIS66 2.1 14.0 1.0
O B:HOH3254 2.2 11.6 1.0
SG B:CYS173 2.3 14.4 1.0
SG B:CYS44 2.3 15.6 1.0
CD2 B:HIS66 3.0 13.2 1.0
CE1 B:HIS66 3.1 14.8 1.0
CB B:CYS44 3.3 16.2 1.0
CB B:CYS173 3.4 12.0 1.0
O B:HOH3487 3.6 40.2 1.0
OG1 B:THR46 3.9 14.7 1.0
CB B:THR46 4.0 13.9 1.0
O B:HOH3366 4.1 33.1 1.0
O B:HOH3439 4.1 43.5 1.0
ND1 B:HIS66 4.2 12.2 1.0
CG B:HIS66 4.2 13.3 1.0
OH B:TYR92 4.7 15.3 1.0
CA B:CYS44 4.8 15.7 1.0
OE2 B:GLU67 4.8 17.5 1.0
CA B:CYS173 4.8 11.4 1.0
N B:THR46 4.8 14.0 1.0
CG2 B:THR46 4.9 13.3 1.0
CE1 B:HIS45 4.9 29.0 1.0
N B:GLY174 4.9 12.7 1.0
CE1 B:TYR92 5.0 12.7 1.0
CZ B:TYR92 5.0 13.5 1.0

Reference:

P.C.Sanghani, H.Robinson, W.F.Bosron, T.D.Hurley. Human Glutathione-Dependent Formaldehyde Dehydrogenase. Structures of Apo, Binary, and Inhibitory Ternary Complexes. Biochemistry V. 41 10778 2002.
ISSN: ISSN 0006-2960
PubMed: 12196016
DOI: 10.1021/BI0257639
Page generated: Wed Dec 16 02:56:58 2020

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