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Zinc in PDB 1mc5: Ternary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase with S-(Hydroxymethyl)Glutathione and Nadh

Enzymatic activity of Ternary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase with S-(Hydroxymethyl)Glutathione and Nadh

All present enzymatic activity of Ternary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase with S-(Hydroxymethyl)Glutathione and Nadh:
1.1.1.1; 1.2.1.1;

Protein crystallography data

The structure of Ternary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase with S-(Hydroxymethyl)Glutathione and Nadh, PDB code: 1mc5 was solved by P.C.Sanghani, 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) 48.83 / 2.60
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.656, 78.656, 311.428, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 24.9

Other elements in 1mc5:

The structure of Ternary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase with S-(Hydroxymethyl)Glutathione and Nadh also contains other interesting chemical elements:

Potassium (K) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Ternary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase with S-(Hydroxymethyl)Glutathione and Nadh (pdb code 1mc5). 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 S-(Hydroxymethyl)Glutathione and Nadh, PDB code: 1mc5:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1mc5

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Zinc binding site 1 out of 4 in the Ternary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase with S-(Hydroxymethyl)Glutathione and Nadh


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 S-(Hydroxymethyl)Glutathione and Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn375

b:38.8
occ:1.00
 SG A:CYS96 2.1 38.9 1.0
SG A:CYS110 2.2 27.5 1.0
SG A:CYS102 2.3 31.5 1.0
SG A:CYS99 2.4 43.3 1.0
CB A:CYS110 3.2 32.7 1.0
CB A:CYS96 3.2 39.3 1.0
CB A:CYS99 3.2 44.5 1.0
CB A:CYS102 3.3 32.2 1.0
N A:CYS96 3.5 39.4 1.0
N A:CYS99 3.7 46.7 1.0
CA A:CYS110 3.7 34.2 1.0
CA A:CYS96 3.8 39.8 1.0
N A:GLY97 3.9 41.3 1.0
N A:CYS102 4.0 35.1 1.0
CA A:CYS99 4.0 45.6 1.0
CA A:CYS102 4.2 33.9 1.0
C A:CYS96 4.3 40.5 1.0
N A:GLU98 4.5 46.0 1.0
C A:GLN95 4.5 38.4 1.0
N A:GLN111 4.5 35.4 1.0
C A:CYS110 4.5 35.2 1.0
CB A:LYS112 4.6 36.0 1.0
C A:CYS99 4.7 46.0 1.0
CA A:GLN95 4.7 37.8 1.0
N A:LYS112 4.8 35.5 1.0
C A:GLU98 4.9 47.9 1.0
O A:CYS99 4.9 45.9 1.0
CA A:GLY97 4.9 43.4 1.0
N A:CYS110 4.9 33.4 1.0

Zinc binding site 2 out of 4 in 1mc5

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Zinc binding site 2 out of 4 in the Ternary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase with S-(Hydroxymethyl)Glutathione and Nadh


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 S-(Hydroxymethyl)Glutathione and Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn376

b:41.2
occ:1.00
 OE2 A:AHE404 2.1 54.8 1.0
NE2 A:HIS66 2.2 36.8 1.0
SG A:CYS173 2.3 30.1 1.0
SG A:CYS44 2.3 47.0 1.0
CD2 A:AHE404 2.9 55.9 1.0
CD2 A:HIS66 3.0 36.1 1.0
CB A:CYS44 3.2 42.2 1.0
CE1 A:HIS66 3.3 36.5 1.0
OG1 A:THR46 3.4 43.3 1.0
CB A:CYS173 3.5 30.6 1.0
C5N A:NAD500 3.5 38.8 1.0
CB A:THR46 3.8 45.7 1.0
C6N A:NAD500 4.0 41.9 1.0
C4N A:NAD500 4.1 40.3 1.0
CG A:HIS66 4.2 37.1 1.0
ND1 A:HIS66 4.3 36.9 1.0
SG2 A:AHE404 4.6 56.1 1.0
CA A:CYS44 4.7 43.3 1.0
N A:GLY174 4.7 29.4 1.0
CG2 A:THR46 4.7 45.7 1.0
OH A:TYR92 4.8 44.4 1.0
CA A:CYS173 4.8 30.5 1.0
OE2 A:GLU67 4.8 46.9 1.0
N A:THR46 4.8 47.7 1.0
CE1 A:TYR92 4.9 45.3 1.0
CA A:THR46 5.0 46.3 1.0
N1N A:NAD500 5.0 43.3 1.0

Zinc binding site 3 out of 4 in 1mc5

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Zinc binding site 3 out of 4 in the Ternary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase with S-(Hydroxymethyl)Glutathione and Nadh


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 S-(Hydroxymethyl)Glutathione and Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn375

b:29.9
occ:1.00
 SG B:CYS96 2.3 25.5 1.0
SG B:CYS102 2.4 21.4 1.0
SG B:CYS110 2.4 26.3 1.0
SG B:CYS99 2.4 26.1 1.0
CB B:CYS99 3.1 28.2 1.0
CB B:CYS110 3.2 28.9 1.0
CB B:CYS102 3.4 25.3 1.0
CB B:CYS96 3.5 27.4 1.0
N B:CYS96 3.6 28.8 1.0
CA B:CYS110 3.6 30.3 1.0
N B:CYS99 3.8 30.5 1.0
N B:GLY97 4.0 30.5 1.0
CA B:CYS96 4.0 28.5 1.0
CA B:CYS99 4.0 28.4 1.0
N B:GLN111 4.1 32.6 1.0
N B:CYS102 4.1 25.8 1.0
C B:CYS110 4.3 31.4 1.0
CA B:CYS102 4.4 26.1 1.0
N B:LYS112 4.4 33.7 1.0
C B:CYS96 4.5 29.5 1.0
CB B:LYS112 4.5 37.1 1.0
N B:GLU98 4.6 33.6 1.0
C B:GLN95 4.6 29.4 1.0
C B:CYS99 4.7 27.6 1.0
CA B:GLN95 4.9 29.2 1.0
N B:CYS110 4.9 30.7 1.0
O B:CYS99 4.9 26.0 1.0

Zinc binding site 4 out of 4 in 1mc5

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Zinc binding site 4 out of 4 in the Ternary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase with S-(Hydroxymethyl)Glutathione and Nadh


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 S-(Hydroxymethyl)Glutathione and Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn376

b:59.3
occ:1.00
 NE2 B:HIS66 2.3 36.0 1.0
CB B:CYS44 2.5 42.9 1.0
SG B:CYS44 2.5 52.6 1.0
OE2 B:GLU67 2.6 37.0 1.0
SG B:CYS173 2.6 39.2 1.0
CE1 B:HIS66 2.9 35.5 1.0
O B:HOH667 3.0 6.6 1.0
CB B:CYS173 3.3 32.2 1.0
CD2 B:HIS66 3.4 34.2 1.0
CD B:GLU67 3.6 35.5 1.0
NH2 B:ARG368 3.8 27.7 1.0
CA B:CYS44 4.0 41.7 1.0
ND1 B:HIS66 4.0 34.1 1.0
CG B:GLU67 4.0 34.0 1.0
CG B:HIS66 4.3 33.9 1.0
OG1 B:THR46 4.4 35.3 1.0
CB B:THR46 4.5 35.7 1.0
N B:CYS44 4.6 38.5 1.0
OE1 B:GLU67 4.7 34.1 1.0
N B:GLY174 4.7 27.6 1.0
CZ B:ARG368 4.8 28.1 1.0
C B:CYS44 4.8 42.2 1.0
CA B:CYS173 4.8 31.0 1.0
C5N B:NAD501 4.9 39.5 1.0
NE B:ARG368 5.0 27.7 1.0

Reference:

P.C.Sanghani, W.F.Bosron, T.D.Hurley. Human Glutathione-Dependent Formaldehyde Dehydrogenase. Structural Changes Associated with Ternary Complex Formation Biochemistry V. 41 15189 2002.
ISSN: ISSN 0006-2960
PubMed: 12484756
DOI: 10.1021/BI026705Q
Page generated: Sun Oct 13 05:30:02 2024

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