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Zinc in PDB 1m6w: Binary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase and 12-Hydroxydodecanoic Acid

Enzymatic activity of Binary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase and 12-Hydroxydodecanoic Acid

All present enzymatic activity of Binary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase and 12-Hydroxydodecanoic Acid:
1.1.1.1;

Protein crystallography data

The structure of Binary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase and 12-Hydroxydodecanoic Acid, PDB code: 1m6w 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) 20.00 / 2.30
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.632, 78.632, 309.417, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 22.5

Other elements in 1m6w:

The structure of Binary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase and 12-Hydroxydodecanoic Acid also contains other interesting chemical elements:

Potassium (K) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Binary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase and 12-Hydroxydodecanoic Acid (pdb code 1m6w). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Binary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase and 12-Hydroxydodecanoic Acid, PDB code: 1m6w:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1m6w

Go back to Zinc Binding Sites List in 1m6w
Zinc binding site 1 out of 4 in the Binary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase and 12-Hydroxydodecanoic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Binary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase and 12-Hydroxydodecanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1375

b:28.6
occ:1.00
 SG A:CYS110 2.2 20.4 1.0
SG A:CYS102 2.3 22.9 1.0
SG A:CYS96 2.4 23.5 1.0
SG A:CYS99 2.5 23.8 1.0
CB A:CYS110 3.1 22.0 1.0
CB A:CYS102 3.3 24.0 1.0
CB A:CYS96 3.4 22.1 1.0
N A:CYS96 3.4 19.4 1.0
CB A:CYS99 3.6 23.0 1.0
CA A:CYS110 3.7 21.7 1.0
N A:GLY97 3.8 23.9 1.0
CA A:CYS96 3.8 20.3 1.0
N A:CYS99 3.9 27.8 1.0
N A:CYS102 4.1 24.0 1.0
C A:CYS96 4.3 22.8 1.0
CA A:CYS102 4.3 24.0 1.0
CA A:CYS99 4.3 26.6 1.0
N A:GLN111 4.4 21.1 1.0
C A:CYS110 4.4 21.7 1.0
N A:GLU98 4.4 29.6 1.0
C A:GLN95 4.4 19.4 1.0
CB A:LYS112 4.4 27.7 1.0
N A:LYS112 4.6 23.2 1.0
CA A:GLN95 4.7 18.8 1.0
CA A:GLY97 4.8 26.2 1.0
N A:CYS110 4.9 23.6 1.0
C A:CYS99 4.9 27.0 1.0
O A:CYS99 4.9 28.2 1.0

Zinc binding site 2 out of 4 in 1m6w

Go back to Zinc Binding Sites List in 1m6w
Zinc binding site 2 out of 4 in the Binary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase and 12-Hydroxydodecanoic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Binary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase and 12-Hydroxydodecanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1376

b:29.0
occ:1.00
 O13 A:12H4378 2.0 45.2 1.0
NE2 A:HIS66 2.1 20.8 1.0
SG A:CYS173 2.2 17.1 1.0
SG A:CYS44 2.4 24.1 1.0
C1 A:12H4378 2.5 47.6 1.0
CD2 A:HIS66 3.1 19.7 1.0
CE1 A:HIS66 3.1 21.0 1.0
CB A:CYS44 3.3 22.4 1.0
CB A:CYS173 3.4 17.8 1.0
C2 A:12H4378 3.7 51.6 1.0
OG1 A:THR46 3.8 22.4 1.0
O A:HOH4395 3.9 31.6 1.0
CB A:THR46 4.1 23.2 1.0
CG A:HIS66 4.2 19.8 1.0
ND1 A:HIS66 4.2 20.0 1.0
C3 A:12H4378 4.7 53.4 1.0
OH A:TYR92 4.7 20.5 1.0
CA A:CYS173 4.7 19.1 1.0
N A:GLY174 4.8 18.5 1.0
CA A:CYS44 4.8 22.3 1.0
CE1 A:TYR92 4.9 20.4 1.0
OE2 A:GLU67 4.9 23.8 1.0
CG2 A:THR46 5.0 22.1 1.0
CZ A:TYR92 5.0 20.9 1.0
N A:THR46 5.0 24.6 1.0

Zinc binding site 3 out of 4 in 1m6w

Go back to Zinc Binding Sites List in 1m6w
Zinc binding site 3 out of 4 in the Binary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase and 12-Hydroxydodecanoic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Binary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase and 12-Hydroxydodecanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1375

b:26.1
occ:1.00
 SG B:CYS102 2.3 19.8 1.0
SG B:CYS110 2.3 17.4 1.0
SG B:CYS99 2.3 21.8 1.0
SG B:CYS96 2.4 21.1 1.0
CB B:CYS110 3.1 17.2 1.0
CB B:CYS99 3.4 21.1 1.0
CB B:CYS96 3.4 21.0 1.0
CB B:CYS102 3.4 19.7 1.0
N B:CYS96 3.5 20.0 1.0
CA B:CYS110 3.6 17.0 1.0
N B:GLY97 3.8 23.2 1.0
N B:CYS99 3.8 21.3 1.0
CA B:CYS96 3.9 22.0 1.0
CA B:CYS99 4.2 22.0 1.0
N B:GLN111 4.2 19.2 1.0
N B:CYS102 4.2 18.4 1.0
C B:CYS96 4.3 22.6 1.0
C B:CYS110 4.3 18.1 1.0
CB B:LYS112 4.3 27.3 1.0
CA B:CYS102 4.4 20.0 1.0
N B:GLU98 4.5 23.9 1.0
N B:LYS112 4.5 24.4 1.0
C B:GLN95 4.5 19.4 1.0
CA B:GLN95 4.7 19.5 1.0
CA B:GLY97 4.8 23.3 1.0
C B:CYS99 4.9 21.6 1.0
N B:CYS110 4.9 17.7 1.0

Zinc binding site 4 out of 4 in 1m6w

Go back to Zinc Binding Sites List in 1m6w
Zinc binding site 4 out of 4 in the Binary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase and 12-Hydroxydodecanoic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Binary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase and 12-Hydroxydodecanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1376

b:26.5
occ:1.00
 O13 B:12H5378 2.0 49.0 1.0
NE2 B:HIS66 2.1 13.9 1.0
SG B:CYS173 2.3 15.7 1.0
SG B:CYS44 2.4 16.9 1.0
C1 B:12H5378 2.9 51.8 1.0
CD2 B:HIS66 3.0 15.9 1.0
CE1 B:HIS66 3.1 17.8 1.0
CB B:CYS44 3.3 18.0 1.0
CB B:CYS173 3.4 16.2 1.0
C2 B:12H5378 3.5 56.1 1.0
OG1 B:THR46 3.9 19.8 1.0
O B:HOH5746 4.0 42.0 1.0
CB B:THR46 4.1 18.5 1.0
CG B:HIS66 4.2 14.3 1.0
ND1 B:HIS66 4.2 15.4 1.0
C3 B:12H5378 4.5 58.4 1.0
OH B:TYR92 4.6 17.1 1.0
CA B:CYS44 4.8 17.6 1.0
CA B:CYS173 4.8 15.8 1.0
OE2 B:GLU67 4.8 24.7 1.0
CZ B:TYR92 4.9 16.6 1.0
O B:HOH5762 4.9 44.6 1.0
N B:THR46 4.9 17.4 1.0
CE1 B:TYR92 4.9 15.3 1.0
CG2 B:THR46 5.0 15.8 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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