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Zinc in PDB 1ma0: Ternary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase with Nad+ and Dodecanoic Acid

Enzymatic activity of Ternary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase with Nad+ and Dodecanoic Acid

All present enzymatic activity of Ternary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase with Nad+ and Dodecanoic Acid:
1.1.1.1;

Protein crystallography data

The structure of Ternary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase with Nad+ and Dodecanoic Acid, PDB code: 1ma0 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) 19.82 / 2.30
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.660, 78.660, 310.920, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 22.3

Other elements in 1ma0:

The structure of Ternary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase with Nad+ and Dodecanoic Acid also contains other interesting chemical elements:

Potassium (K) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Ternary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase with Nad+ and Dodecanoic Acid (pdb code 1ma0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Ternary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase with Nad+ and Dodecanoic Acid, PDB code: 1ma0:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1ma0

Go back to Zinc Binding Sites List in 1ma0
Zinc binding site 1 out of 4 in the Ternary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase with Nad+ and Dodecanoic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Ternary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase with Nad+ and Dodecanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn5375

b:32.3
occ:1.00
 SG A:CYS110 2.2 28.5 1.0
SG A:CYS96 2.3 28.9 1.0
SG A:CYS102 2.3 28.0 1.0
SG A:CYS99 2.4 28.0 1.0
CB A:CYS110 3.1 28.6 1.0
CB A:CYS96 3.3 27.6 1.0
CB A:CYS99 3.4 28.8 1.0
N A:CYS96 3.4 24.9 1.0
CB A:CYS102 3.5 28.8 1.0
CA A:CYS110 3.6 28.1 1.0
N A:GLY97 3.8 28.8 1.0
CA A:CYS96 3.8 26.1 1.0
N A:CYS99 3.9 33.1 1.0
N A:CYS102 4.2 28.4 1.0
CA A:CYS99 4.2 32.3 1.0
C A:CYS96 4.2 28.4 1.0
N A:GLN111 4.3 29.5 1.0
C A:CYS110 4.4 29.2 1.0
CA A:CYS102 4.4 28.6 1.0
N A:GLU98 4.4 33.8 1.0
C A:GLN95 4.5 24.3 1.0
CB A:LYS112 4.6 32.8 1.0
N A:LYS112 4.6 29.9 1.0
CA A:GLN95 4.8 24.0 1.0
CA A:GLY97 4.8 31.0 1.0
N A:CYS110 4.9 28.4 1.0
C A:CYS99 4.9 32.6 1.0
O A:CYS99 4.9 33.7 1.0

Zinc binding site 2 out of 4 in 1ma0

Go back to Zinc Binding Sites List in 1ma0
Zinc binding site 2 out of 4 in the Ternary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase with Nad+ and Dodecanoic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Ternary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase with Nad+ and Dodecanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn5376

b:50.6
occ:1.00
 NE2 A:HIS66 2.3 31.4 1.0
SG A:CYS44 2.4 36.6 1.0
OE2 A:GLU67 2.4 33.5 1.0
SG A:CYS173 2.5 39.0 1.0
C12 A:DAO5378 2.7 30.4 1.0
CB A:CYS44 3.1 34.6 1.0
CD2 A:HIS66 3.2 27.9 1.0
CE1 A:HIS66 3.2 29.9 1.0
CD A:GLU67 3.3 30.5 1.0
CB A:CYS173 3.3 31.6 1.0
CG A:GLU67 3.5 30.7 1.0
NH2 A:ARG368 3.5 28.0 1.0
O A:HOH6788 3.8 39.9 1.0
C11 A:DAO5378 4.1 32.4 1.0
ND1 A:HIS66 4.3 29.1 1.0
CG A:HIS66 4.3 27.4 1.0
OE1 A:GLU67 4.4 32.4 1.0
CA A:CYS44 4.4 37.1 1.0
CZ A:ARG368 4.4 27.3 1.0
N A:GLY174 4.6 25.1 1.0
NE A:ARG368 4.7 25.7 1.0
N A:CYS44 4.7 35.1 1.0
CA A:CYS173 4.7 28.9 1.0
CB A:GLU67 4.9 28.2 1.0

Zinc binding site 3 out of 4 in 1ma0

Go back to Zinc Binding Sites List in 1ma0
Zinc binding site 3 out of 4 in the Ternary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase with Nad+ and Dodecanoic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Ternary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase with Nad+ and Dodecanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn6375

b:28.8
occ:1.00
 SG B:CYS110 2.3 22.3 1.0
SG B:CYS102 2.3 23.6 1.0
SG B:CYS99 2.3 21.8 1.0
SG B:CYS96 2.3 25.9 1.0
CB B:CYS110 3.1 22.6 1.0
CB B:CYS99 3.3 23.8 1.0
CB B:CYS102 3.5 21.6 1.0
CB B:CYS96 3.5 23.5 1.0
N B:CYS96 3.5 21.9 1.0
CA B:CYS110 3.6 22.1 1.0
N B:CYS99 3.8 24.9 1.0
N B:GLY97 3.9 26.1 1.0
CA B:CYS96 3.9 24.8 1.0
CA B:CYS99 4.1 23.8 1.0
N B:GLN111 4.2 24.2 1.0
N B:CYS102 4.2 19.6 1.0
C B:CYS110 4.3 23.6 1.0
C B:CYS96 4.3 25.7 1.0
CB B:LYS112 4.4 31.0 1.0
CA B:CYS102 4.4 21.1 1.0
N B:GLU98 4.5 28.4 1.0
N B:LYS112 4.5 25.3 1.0
C B:GLN95 4.6 22.5 1.0
CA B:GLN95 4.8 22.5 1.0
C B:CYS99 4.8 24.0 1.0
CA B:GLY97 4.8 28.1 1.0
N B:CYS110 4.9 22.0 1.0
O B:CYS99 5.0 25.2 1.0
C B:GLU98 5.0 28.8 1.0

Zinc binding site 4 out of 4 in 1ma0

Go back to Zinc Binding Sites List in 1ma0
Zinc binding site 4 out of 4 in the Ternary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase with Nad+ and Dodecanoic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Ternary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase with Nad+ and Dodecanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn6376

b:52.6
occ:1.00
 OE2 B:GLU67 2.3 37.0 1.0
NE2 B:HIS66 2.3 27.1 1.0
C12 B:DAO6378 2.4 18.2 1.0
SG B:CYS44 2.4 33.2 1.0
CB B:CYS44 2.6 29.8 1.0
SG B:CYS173 2.6 30.6 1.0
CE1 B:HIS66 3.2 26.0 1.0
CB B:CYS173 3.3 25.5 1.0
CD2 B:HIS66 3.3 24.3 1.0
CD B:GLU67 3.4 33.4 1.0
CG B:GLU67 3.7 29.8 1.0
C11 B:DAO6378 3.8 29.5 1.0
NH2 B:ARG368 3.8 24.5 1.0
O B:HOH6673 3.9 32.3 1.0
CA B:CYS44 4.1 28.4 1.0
ND1 B:HIS66 4.3 26.5 1.0
CG B:HIS66 4.4 23.5 1.0
OE1 B:GLU67 4.5 32.5 1.0
N B:GLY174 4.6 25.0 1.0
C5N B:NAD6377 4.7 24.8 1.0
CA B:CYS173 4.7 24.2 1.0
N B:CYS44 4.8 27.6 1.0
CZ B:ARG368 4.8 26.4 1.0
C10 B:DAO6378 4.9 32.4 1.0
C B:CYS44 4.9 28.0 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 02:57:02 2020

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