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Zinc in PDB 2fze: Crystal Structure of the Binary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase with Adp-Ribose

Enzymatic activity of Crystal Structure of the Binary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase with Adp-Ribose

All present enzymatic activity of Crystal Structure of the Binary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase with Adp-Ribose:
1.1.1.1; 1.1.1.284;

Protein crystallography data

The structure of Crystal Structure of the Binary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase with Adp-Ribose, PDB code: 2fze 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) 29.60 / 1.90
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.234, 79.234, 310.964, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 20.9

Other elements in 2fze:

The structure of Crystal Structure of the Binary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase with Adp-Ribose also contains other interesting chemical elements:

Potassium (K) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Binary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase with Adp-Ribose (pdb code 2fze). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of the Binary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase with Adp-Ribose, PDB code: 2fze:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 2fze

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Zinc binding site 1 out of 6 in the Crystal Structure of the Binary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase with Adp-Ribose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Binary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase with Adp-Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn375

b:28.9
occ:1.00
 SG A:CYS110 2.4 17.0 1.0
SG A:CYS99 2.4 22.6 1.0
SG A:CYS102 2.4 21.1 1.0
SG A:CYS96 2.4 21.1 1.0
CB A:CYS110 3.2 18.4 1.0
CB A:CYS96 3.4 21.9 1.0
CB A:CYS99 3.4 24.0 1.0
CB A:CYS102 3.4 20.6 1.0
N A:CYS96 3.5 21.2 1.0
CA A:CYS110 3.7 19.2 1.0
N A:CYS99 3.8 25.6 1.0
N A:GLY97 3.8 21.6 1.0
CA A:CYS96 3.9 22.0 1.0
N A:CYS102 4.2 19.6 1.0
CA A:CYS99 4.2 24.7 1.0
N A:GLN111 4.3 20.0 1.0
C A:CYS96 4.3 22.2 1.0
C A:CYS110 4.4 20.0 1.0
N A:GLU98 4.4 25.2 1.0
CA A:CYS102 4.4 18.6 1.0
CB A:LYS112 4.4 26.0 1.0
C A:GLN95 4.5 19.3 1.0
N A:LYS112 4.5 23.8 1.0
CA A:GLN95 4.8 18.0 1.0
CA A:GLY97 4.8 22.3 1.0
C A:CYS99 4.9 23.6 1.0
N A:CYS110 4.9 18.7 1.0
O A:CYS99 4.9 22.7 1.0
C A:GLU98 5.0 27.7 1.0

Zinc binding site 2 out of 6 in 2fze

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Zinc binding site 2 out of 6 in the Crystal Structure of the Binary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase with Adp-Ribose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Binary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase with Adp-Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn376

b:31.6
occ:0.75
 ZN A:ZN376 0.0 31.6 0.8
ZN A:ZN376 2.1 28.2 0.2
NE2 A:HIS66 2.2 21.9 1.0
O A:HOH4014 2.2 30.1 1.0
SG A:CYS173 2.4 23.3 1.0
SG A:CYS44 2.6 23.9 1.0
CD2 A:HIS66 3.0 20.1 1.0
CE1 A:HIS66 3.3 21.5 1.0
OG1 A:THR46 3.5 23.2 1.0
CB A:CYS173 3.5 20.2 1.0
CB A:CYS44 3.7 21.6 1.0
CB A:THR46 3.9 22.0 1.0
O A:HOH4110 4.0 29.0 1.0
O A:HOH4097 4.1 27.7 1.0
O A:HOH4120 4.2 27.8 1.0
CG A:HIS66 4.2 18.4 1.0
ND1 A:HIS66 4.3 17.9 1.0
OE1 A:GLU67 4.5 26.2 1.0
O A:HOH4450 4.6 53.5 1.0
CG2 A:THR46 4.8 21.9 1.0
OH A:TYR92 4.9 22.7 1.0
CA A:CYS173 4.9 18.6 1.0
CE A:MET140 4.9 20.4 1.0
CE1 A:TYR92 4.9 20.7 1.0
N A:THR46 5.0 21.1 1.0

Zinc binding site 3 out of 6 in 2fze

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Zinc binding site 3 out of 6 in the Crystal Structure of the Binary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase with Adp-Ribose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Binary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase with Adp-Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn376

b:28.2
occ:0.25
 ZN A:ZN376 0.0 28.2 0.2
ZN A:ZN376 2.1 31.6 0.8
OE1 A:GLU67 2.5 26.2 1.0
CB A:CYS44 2.6 21.6 1.0
SG A:CYS44 2.6 23.9 1.0
NE2 A:HIS66 2.6 21.9 1.0
SG A:CYS173 2.7 23.3 1.0
CB A:CYS173 2.9 20.2 1.0
CD A:GLU67 3.1 23.6 1.0
CG A:GLU67 3.2 20.9 1.0
CD2 A:HIS66 3.3 20.1 1.0
CE1 A:HIS66 3.4 21.5 1.0
NH2 A:ARG368 3.7 20.6 1.0
CA A:CYS44 4.1 21.8 1.0
OE2 A:GLU67 4.1 24.2 1.0
N A:GLY174 4.1 18.3 1.0
O A:HOH4120 4.1 27.8 1.0
CA A:CYS173 4.3 18.6 1.0
O A:HOH4014 4.3 30.1 1.0
CG A:HIS66 4.3 18.4 1.0
ND1 A:HIS66 4.3 17.9 1.0
CB A:GLU67 4.6 17.9 1.0
C A:CYS173 4.7 19.4 1.0
O A:HOH4097 4.7 27.7 1.0
CZ A:ARG368 4.7 20.2 1.0
N A:CYS44 4.7 20.2 1.0
NE A:ARG368 4.9 19.1 1.0
O A:HOH4026 5.0 17.2 1.0
CA A:GLY174 5.0 17.4 1.0

Zinc binding site 4 out of 6 in 2fze

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Zinc binding site 4 out of 6 in the Crystal Structure of the Binary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase with Adp-Ribose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Binary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase with Adp-Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn375

b:25.5
occ:1.00
 SG B:CYS102 2.4 15.2 1.0
SG B:CYS110 2.4 16.3 1.0
SG B:CYS99 2.4 18.2 1.0
SG B:CYS96 2.4 17.3 1.0
CB B:CYS110 3.1 15.9 1.0
CB B:CYS102 3.4 14.5 1.0
CB B:CYS99 3.4 19.8 1.0
CB B:CYS96 3.5 16.2 1.0
N B:CYS96 3.5 15.9 1.0
CA B:CYS110 3.6 16.4 1.0
N B:CYS99 3.8 20.3 1.0
N B:GLY97 3.9 18.6 1.0
CA B:CYS96 3.9 18.6 1.0
CA B:CYS99 4.2 19.4 1.0
N B:GLN111 4.2 16.3 1.0
N B:CYS102 4.2 15.7 1.0
C B:CYS96 4.3 19.4 1.0
C B:CYS110 4.3 18.0 1.0
CB B:LYS112 4.4 21.5 1.0
CA B:CYS102 4.4 14.7 1.0
N B:GLU98 4.4 21.5 1.0
N B:LYS112 4.5 18.7 1.0
C B:GLN95 4.6 15.9 1.0
CA B:GLN95 4.8 15.9 1.0
CA B:GLY97 4.8 19.7 1.0
C B:CYS99 4.8 17.9 1.0
N B:CYS110 4.9 14.0 1.0
O B:CYS99 4.9 17.1 1.0
C B:GLU98 5.0 22.9 1.0

Zinc binding site 5 out of 6 in 2fze

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Zinc binding site 5 out of 6 in the Crystal Structure of the Binary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase with Adp-Ribose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Binary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase with Adp-Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn376

b:24.1
occ:0.75
 ZN B:ZN376 0.0 24.1 0.8
NE2 B:HIS66 2.2 17.5 1.0
ZN B:ZN376 2.2 30.9 0.2
O B:HOH4094 2.2 21.6 1.0
SG B:CYS173 2.4 21.2 1.0
SG B:CYS44 2.5 21.4 1.0
CD2 B:HIS66 3.0 16.2 1.0
CE1 B:HIS66 3.2 18.5 1.0
CB B:CYS173 3.5 19.7 1.0
CB B:CYS44 3.5 19.7 1.0
OG1 B:THR46 3.7 18.3 1.0
O B:HOH4346 4.0 27.2 1.0
CB B:THR46 4.0 17.5 1.0
O B:HOH4261 4.1 34.2 1.0
CG B:HIS66 4.2 14.0 1.0
ND1 B:HIS66 4.3 14.4 1.0
O B:HOH4070 4.3 25.3 1.0
OE1 B:GLU67 4.5 26.6 1.0
O B:HOH4028 4.5 43.1 1.0
OH B:TYR92 4.8 20.2 1.0
CA B:CYS173 4.9 17.4 1.0
N B:THR46 4.9 16.6 1.0
CA B:CYS44 5.0 20.8 1.0
CE1 B:TYR92 5.0 17.1 1.0
CG2 B:THR46 5.0 17.7 1.0
CE B:MET140 5.0 19.1 1.0

Zinc binding site 6 out of 6 in 2fze

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Zinc binding site 6 out of 6 in the Crystal Structure of the Binary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase with Adp-Ribose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the Binary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase with Adp-Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn376

b:30.9
occ:0.25
 ZN B:ZN376 0.0 30.9 0.2
ZN B:ZN376 2.2 24.1 0.8
OE1 B:GLU67 2.4 26.6 1.0
CB B:CYS44 2.5 19.7 1.0
SG B:CYS44 2.6 21.4 1.0
SG B:CYS173 2.9 21.2 1.0
NE2 B:HIS66 2.9 17.5 1.0
CB B:CYS173 2.9 19.7 1.0
CD B:GLU67 2.9 23.2 1.0
CG B:GLU67 3.2 19.8 1.0
CD2 B:HIS66 3.6 16.2 1.0
CE1 B:HIS66 3.6 18.5 1.0
NH2 B:ARG368 3.7 21.2 1.0
OE2 B:GLU67 3.9 22.9 1.0
CA B:CYS44 3.9 20.8 1.0
N B:GLY174 4.0 18.2 1.0
O B:HOH4070 4.2 25.3 1.0
CA B:CYS173 4.3 17.4 1.0
O B:HOH4094 4.4 21.6 1.0
CG B:HIS66 4.5 14.0 1.0
ND1 B:HIS66 4.5 14.4 1.0
CB B:GLU67 4.6 17.2 1.0
O B:HOH4346 4.6 27.2 1.0
N B:CYS44 4.6 18.9 1.0
C B:CYS173 4.6 18.3 1.0
CZ B:ARG368 4.7 22.0 1.0
NE B:ARG368 4.8 19.6 1.0
O B:HOH4018 4.8 14.0 1.0
CA B:GLY174 4.9 17.6 1.0
C B:CYS44 4.9 20.1 1.0
N B:CYS173 5.0 15.8 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 Oct 16 23:58:32 2024

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