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Zinc in PDB 1mp0: Binary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase with Nad(H)

Enzymatic activity of Binary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase with Nad(H)

All present enzymatic activity of Binary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase with Nad(H):
1.1.1.1; 1.2.1.1;

Protein crystallography data

The structure of Binary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase with Nad(H), PDB code: 1mp0 was solved by P.C.Sanghani, H.Robinson, T.D.Hurley, W.F.Bosron, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.90 / 2.20
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.033, 79.033, 311.755, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 21.8

Other elements in 1mp0:

The structure of Binary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase with Nad(H) 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 with Nad(H) (pdb code 1mp0). 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 with Nad(H), PDB code: 1mp0:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1mp0

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Zinc binding site 1 out of 4 in the Binary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase with Nad(H)


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 with Nad(H) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn375

b:37.6
occ:1.00
 SG A:CYS110 2.3 18.0 1.0
SG A:CYS102 2.4 20.7 1.0
SG A:CYS96 2.4 21.2 1.0
SG A:CYS99 2.4 21.8 1.0
CB A:CYS110 3.2 20.6 1.0
CB A:CYS102 3.4 21.9 1.0
CB A:CYS96 3.4 19.8 1.0
CB A:CYS99 3.4 25.5 1.0
N A:CYS96 3.5 19.0 1.0
CA A:CYS110 3.6 21.6 1.0
N A:CYS99 3.8 27.5 1.0
N A:GLY97 3.8 21.1 1.0
CA A:CYS96 3.9 20.3 1.0
N A:CYS102 4.2 22.4 1.0
CA A:CYS99 4.2 26.5 1.0
C A:CYS96 4.3 21.5 1.0
N A:GLN111 4.3 24.8 1.0
CA A:CYS102 4.3 21.6 1.0
N A:GLU98 4.4 26.2 1.0
C A:CYS110 4.4 22.5 1.0
CB A:LYS112 4.4 30.1 1.0
C A:GLN95 4.5 19.9 1.0
N A:LYS112 4.6 26.7 1.0
CA A:GLN95 4.8 19.1 1.0
CA A:GLY97 4.8 22.4 1.0
C A:CYS99 4.8 26.9 1.0
N A:CYS110 4.9 21.8 1.0
O A:CYS99 4.9 28.3 1.0
C A:GLU98 4.9 28.8 1.0

Zinc binding site 2 out of 4 in 1mp0

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Zinc binding site 2 out of 4 in the Binary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase with Nad(H)


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 with Nad(H) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn376

b:35.6
occ:1.00
 OE2 A:GLU67 2.1 16.7 1.0
NE2 A:HIS66 2.2 24.9 1.0
SG A:CYS44 2.3 21.4 1.0
SG A:CYS173 2.4 23.5 1.0
CD A:GLU67 3.1 17.2 1.0
CE1 A:HIS66 3.1 23.0 1.0
CD2 A:HIS66 3.2 22.5 1.0
CB A:CYS44 3.2 21.4 1.0
CB A:CYS173 3.2 17.2 1.0
CG A:GLU67 3.4 18.2 1.0
NH2 A:ARG368 3.6 17.4 1.0
O A:HOH815 3.7 31.2 1.0
NE A:ARG368 4.1 16.9 1.0
OE1 A:GLU67 4.2 16.2 1.0
OG1 A:THR46 4.2 23.2 1.0
ND1 A:HIS66 4.2 23.5 1.0
CG A:HIS66 4.2 21.4 1.0
CZ A:ARG368 4.3 19.4 1.0
CA A:CYS44 4.5 23.9 1.0
O A:HOH1108 4.6 41.2 1.0
CB A:THR46 4.6 23.7 1.0
N A:GLY174 4.7 20.3 1.0
CA A:CYS173 4.7 19.3 1.0
N A:CYS44 4.7 22.1 1.0
CB A:GLU67 4.8 19.4 1.0
O A:HOH824 5.0 10.8 1.0
O A:HOH817 5.0 17.8 1.0

Zinc binding site 3 out of 4 in 1mp0

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Zinc binding site 3 out of 4 in the Binary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase with Nad(H)


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 with Nad(H) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn375

b:33.3
occ:1.00
 SG B:CYS102 2.3 17.5 1.0
SG B:CYS110 2.4 15.2 1.0
SG B:CYS96 2.4 18.6 1.0
SG B:CYS99 2.4 18.9 1.0
CB B:CYS110 3.2 18.2 1.0
CB B:CYS102 3.4 18.2 1.0
N B:CYS96 3.4 15.7 1.0
CB B:CYS96 3.5 14.9 1.0
CB B:CYS99 3.5 21.2 1.0
CA B:CYS110 3.6 19.7 1.0
N B:CYS99 3.8 23.3 1.0
N B:GLY97 3.9 21.4 1.0
CA B:CYS96 3.9 19.0 1.0
N B:GLN111 4.2 22.5 1.0
CA B:CYS99 4.2 22.4 1.0
N B:CYS102 4.3 17.9 1.0
C B:CYS96 4.3 20.0 1.0
C B:CYS110 4.3 21.2 1.0
CA B:CYS102 4.4 17.7 1.0
CB B:LYS112 4.4 25.5 1.0
N B:GLU98 4.4 24.4 1.0
N B:LYS112 4.5 22.9 1.0
C B:GLN95 4.5 17.8 1.0
CA B:GLN95 4.8 17.4 1.0
CA B:GLY97 4.9 21.6 1.0
N B:CYS110 4.9 19.0 1.0
C B:CYS99 4.9 21.5 1.0
C B:GLU98 5.0 25.5 1.0

Zinc binding site 4 out of 4 in 1mp0

Go back to Zinc Binding Sites List in 1mp0
Zinc binding site 4 out of 4 in the Binary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase with Nad(H)


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 with Nad(H) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn376

b:64.9
occ:1.00
 SG B:CYS44 2.2 36.5 1.0
OE2 B:GLU67 2.2 30.7 1.0
NE2 B:HIS66 2.5 26.9 1.0
SG B:CYS173 2.8 32.2 1.0
O B:HOH804 2.9 15.0 1.0
CB B:CYS44 3.0 33.9 1.0
CD B:GLU67 3.2 27.3 1.0
CE1 B:HIS66 3.2 26.2 1.0
CB B:CYS173 3.2 22.2 1.0
CD2 B:HIS66 3.5 25.1 1.0
CG B:GLU67 3.6 26.5 1.0
NH2 B:ARG368 3.7 22.7 1.0
OE1 B:GLU67 4.2 27.9 1.0
ND1 B:HIS66 4.3 23.6 1.0
O B:HOH990 4.4 46.2 1.0
CA B:CYS44 4.4 34.0 1.0
OG1 B:THR46 4.4 32.1 1.0
CG B:HIS66 4.5 22.6 1.0
N B:GLY174 4.5 20.4 1.0
CZ B:ARG368 4.5 24.6 1.0
NE B:ARG368 4.6 22.1 1.0
CA B:CYS173 4.6 21.2 1.0
CB B:THR46 4.7 29.5 1.0
N B:CYS44 4.8 29.8 1.0
C5N B:NAD778 4.9 19.1 1.0
C B:CYS44 5.0 34.5 1.0
C B:CYS173 5.0 19.6 1.0
CB B:GLU67 5.0 23.2 1.0

Reference:

P.C.Sanghani, H.Robinson, R.Bennett-Lovsey, T.D.Hurley, W.F.Bosron. Structure-Function Relationships in Human Class III Alcohol Dehydrogenase (Formaldehyde Dehydrogenase) Chem.Biol.Interact. V. 143 195 2003.
ISSN: ISSN 0009-2797
PubMed: 12604204
DOI: 10.1016/S0009-2797(02)00203-X
Page generated: Wed Dec 16 02:57:18 2020

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