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:
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
Go back to
Zinc Binding Sites List in 2fzw
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 Oct 16 23:59:17 2024
|