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Zinc in PDB 2fzw: Structure of the Binary Complex of the E67L Mutant of Human Glutathione-Dependent Formaldehyde Dehydrogenase with Nad(H)

Enzymatic activity of Structure of the Binary Complex of the E67L Mutant of Human Glutathione-Dependent Formaldehyde Dehydrogenase with Nad(H)

All present enzymatic activity of Structure of the Binary Complex of the E67L Mutant of Human Glutathione-Dependent Formaldehyde Dehydrogenase with Nad(H):
1.1.1.1; 1.1.1.284;

Protein crystallography data

The structure of Structure of the Binary Complex of the E67L Mutant of Human Glutathione-Dependent Formaldehyde Dehydrogenase with Nad(H), PDB code: 2fzw was solved by P.C.Sanghani, H.Robinson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.84
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.270, 79.270, 311.680, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 20.4

Other elements in 2fzw:

The structure of Structure of the Binary Complex of the E67L Mutant 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 Structure of the Binary Complex of the E67L Mutant of Human Glutathione-Dependent Formaldehyde Dehydrogenase with Nad(H) (pdb code 2fzw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of the Binary Complex of the E67L Mutant of Human Glutathione-Dependent Formaldehyde Dehydrogenase with Nad(H), PDB code: 2fzw:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2fzw

Go back to Zinc Binding Sites List in 2fzw
Zinc binding site 1 out of 4 in the Structure of the Binary Complex of the E67L Mutant 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 Structure of the Binary Complex of the E67L Mutant of Human Glutathione-Dependent Formaldehyde Dehydrogenase with Nad(H) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn375

b:16.4
occ:1.00
SG A:CYS110 2.4 14.4 1.0
SG A:CYS102 2.4 14.4 1.0
SG A:CYS96 2.4 16.4 1.0
SG A:CYS99 2.4 15.7 1.0
CB A:CYS110 3.2 13.2 1.0
CB A:CYS102 3.4 15.1 1.0
CB A:CYS96 3.4 17.6 1.0
CB A:CYS99 3.5 19.4 1.0
N A:CYS96 3.5 16.4 1.0
CA A:CYS110 3.7 14.4 1.0
N A:CYS99 3.8 19.5 1.0
N A:GLY97 3.8 15.9 1.0
CA A:CYS96 3.9 16.6 1.0
N A:CYS102 4.2 15.5 1.0
CA A:CYS99 4.2 18.6 1.0
N A:GLN111 4.3 16.0 1.0
C A:CYS96 4.3 16.9 1.0
CA A:CYS102 4.4 15.1 1.0
N A:GLU98 4.4 20.2 1.0
C A:CYS110 4.4 15.0 1.0
CB A:LYS112 4.4 21.2 1.0
C A:GLN95 4.6 14.1 1.0
N A:LYS112 4.6 19.3 1.0
CA A:GLY97 4.8 18.5 1.0
CA A:GLN95 4.8 13.1 1.0
C A:CYS99 4.9 18.5 1.0
N A:CYS110 4.9 14.2 1.0
C A:GLU98 5.0 21.8 1.0
O A:CYS99 5.0 17.4 1.0

Zinc binding site 2 out of 4 in 2fzw

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Zinc binding site 2 out of 4 in the Structure of the Binary Complex of the E67L Mutant 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 Structure of the Binary Complex of the E67L Mutant of Human Glutathione-Dependent Formaldehyde Dehydrogenase with Nad(H) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn376

b:23.0
occ:1.00
NE2 A:HIS66 2.2 17.5 1.0
O A:HOH1805 2.3 29.6 1.0
SG A:CYS173 2.4 14.5 0.8
SG A:CYS44 2.5 25.1 1.0
SG A:CYS173 3.0 23.4 0.2
CD2 A:HIS66 3.0 17.5 1.0
CE1 A:HIS66 3.3 19.2 1.0
CB A:CYS44 3.3 24.2 1.0
CB A:CYS173 3.4 16.9 0.8
CB A:CYS173 3.5 20.4 0.2
OG1 A:THR46 3.9 25.9 1.0
O A:HOH2095 4.0 42.6 1.0
CD1 A:LEU67 4.0 14.4 0.5
C5N A:NAD1377 4.2 32.9 1.0
CB A:THR46 4.2 24.9 1.0
CG A:HIS66 4.2 14.8 1.0
ND1 A:HIS66 4.3 17.0 1.0
O A:HOH1992 4.4 47.7 1.0
O A:HOH1806 4.6 27.7 1.0
C6N A:NAD1377 4.6 32.1 1.0
CA A:CYS44 4.8 24.6 1.0
C4N A:NAD1377 4.8 32.8 1.0
CA A:CYS173 4.9 17.2 0.8
OH A:TYR92 4.9 20.8 1.0
CA A:CYS173 4.9 19.2 0.2
CE1 A:TYR92 5.0 19.1 1.0
N A:GLY174 5.0 18.6 1.0

Zinc binding site 3 out of 4 in 2fzw

Go back to Zinc Binding Sites List in 2fzw
Zinc binding site 3 out of 4 in the Structure of the Binary Complex of the E67L Mutant 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 Structure of the Binary Complex of the E67L Mutant of Human Glutathione-Dependent Formaldehyde Dehydrogenase with Nad(H) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn375

b:14.6
occ:1.00
SG B:CYS102 2.4 13.7 1.0
SG B:CYS110 2.4 12.6 1.0
SG B:CYS96 2.4 14.7 1.0
SG B:CYS99 2.4 14.0 1.0
CB B:CYS110 3.2 12.5 1.0
CB B:CYS99 3.4 17.2 1.0
CB B:CYS102 3.4 13.2 1.0
CB B:CYS96 3.4 13.9 1.0
N B:CYS96 3.5 14.7 1.0
CA B:CYS110 3.6 13.0 1.0
N B:CYS99 3.8 16.6 1.0
N B:GLY97 3.9 15.5 1.0
CA B:CYS96 3.9 16.0 1.0
CA B:CYS99 4.2 15.8 1.0
N B:GLN111 4.2 13.8 0.5
N B:GLN111 4.2 13.6 0.5
N B:CYS102 4.2 13.3 1.0
C B:CYS96 4.3 17.3 1.0
CB B:LYS112 4.3 19.5 1.0
C B:CYS110 4.4 14.1 1.0
N B:GLU98 4.4 18.3 1.0
CA B:CYS102 4.4 13.4 1.0
N B:LYS112 4.4 15.5 1.0
C B:GLN95 4.6 14.1 1.0
CA B:GLY97 4.8 17.5 1.0
C B:CYS99 4.8 15.4 1.0
CA B:GLN95 4.8 13.9 1.0
N B:CYS110 4.9 12.9 1.0
O B:CYS99 5.0 14.1 1.0
C B:GLU98 5.0 19.6 1.0

Zinc binding site 4 out of 4 in 2fzw

Go back to Zinc Binding Sites List in 2fzw
Zinc binding site 4 out of 4 in the Structure of the Binary Complex of the E67L Mutant 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 Structure of the Binary Complex of the E67L Mutant of Human Glutathione-Dependent Formaldehyde Dehydrogenase with Nad(H) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn376

b:14.9
occ:1.00
NE2 B:HIS66 2.1 11.1 1.0
O B:HOH2463 2.2 17.8 1.0
SG B:CYS173 2.4 15.7 1.0
SG B:CYS44 2.4 14.9 1.0
CD2 B:HIS66 3.0 10.9 1.0
CE1 B:HIS66 3.1 11.1 1.0
CB B:CYS44 3.3 13.9 1.0
CB B:CYS173 3.5 16.8 1.0
OG1 B:THR46 3.9 12.8 1.0
CD1 B:LEU67 4.0 8.0 0.5
O B:HOH2638 4.1 34.0 1.0
CB B:THR46 4.1 13.5 1.0
ND1 B:HIS66 4.2 10.0 1.0
CG B:HIS66 4.2 10.3 1.0
O B:HOH2628 4.3 22.9 1.0
O B:HOH2540 4.5 22.5 1.0
O B:HOH2876 4.7 33.0 1.0
CA B:CYS44 4.8 13.3 1.0
OH B:TYR92 4.9 21.6 1.0
CA B:CYS173 4.9 16.6 1.0
N B:THR46 5.0 12.0 1.0
O B:HOH2819 5.0 37.7 1.0
CE1 B:TYR92 5.0 17.6 1.0

Reference:

P.C.Sanghani, W.I.Davis, L.Zhai, H.Robinson. Structure-Function Relationships in Human Glutathione-Dependent Formaldehyde Dehydrogenase. Role of Glu-67 and Arg-368 in the Catalytic Mechanism. Biochemistry V. 45 4819 2006.
ISSN: ISSN 0006-2960
PubMed: 16605250
DOI: 10.1021/BI052554Q
Page generated: Wed Dec 16 03:28:48 2020

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