Zinc in PDB 6dwv: Crystal Structure of the Ligj Hydratase in the Apo State
Enzymatic activity of Crystal Structure of the Ligj Hydratase in the Apo State
All present enzymatic activity of Crystal Structure of the Ligj Hydratase in the Apo State:
4.2.1.83;
Protein crystallography data
The structure of Crystal Structure of the Ligj Hydratase in the Apo State, PDB code: 6dwv
was solved by
M.F.Mabanglo,
F.M.Raushel,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
26.14 /
2.20
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
82.170,
78.220,
135.690,
90.00,
90.02,
90.00
|
R / Rfree (%)
|
20.4 /
27.8
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of the Ligj Hydratase in the Apo State
(pdb code 6dwv). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Crystal Structure of the Ligj Hydratase in the Apo State, PDB code: 6dwv:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 6dwv
Go back to
Zinc Binding Sites List in 6dwv
Zinc binding site 1 out
of 4 in the Crystal Structure of the Ligj Hydratase in the Apo State
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 Ligj Hydratase in the Apo State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn401
b:34.3
occ:1.00
|
O
|
B:HOH573
|
1.9
|
15.5
|
1.0
|
NE2
|
B:HIS178
|
2.4
|
26.2
|
1.0
|
NE2
|
B:HIS10
|
2.6
|
20.2
|
1.0
|
NE2
|
B:HIS8
|
2.7
|
18.4
|
1.0
|
CE1
|
B:HIS178
|
3.1
|
28.0
|
1.0
|
CD2
|
B:HIS10
|
3.2
|
18.6
|
1.0
|
CE1
|
B:HIS8
|
3.4
|
19.1
|
1.0
|
CG
|
B:GLU284
|
3.5
|
23.0
|
1.0
|
CD2
|
B:HIS178
|
3.5
|
26.4
|
1.0
|
CE1
|
B:HIS10
|
3.7
|
15.9
|
1.0
|
CD2
|
B:HIS8
|
3.8
|
15.4
|
1.0
|
CD
|
B:GLU284
|
3.9
|
25.1
|
1.0
|
NE2
|
B:HIS223
|
4.0
|
16.6
|
1.0
|
CB
|
B:ALA72
|
4.1
|
36.2
|
1.0
|
OE1
|
B:GLU284
|
4.3
|
25.8
|
1.0
|
ND1
|
B:HIS178
|
4.3
|
27.1
|
1.0
|
OE2
|
B:GLU284
|
4.4
|
15.9
|
1.0
|
CE2
|
B:TYR194
|
4.4
|
24.5
|
1.0
|
CG
|
B:HIS10
|
4.4
|
18.9
|
1.0
|
ND1
|
B:HIS8
|
4.5
|
18.8
|
1.0
|
CG
|
B:HIS178
|
4.6
|
23.9
|
1.0
|
ND1
|
B:HIS10
|
4.7
|
18.4
|
1.0
|
CG
|
B:HIS8
|
4.8
|
19.7
|
1.0
|
O
|
C:HOH566
|
4.8
|
24.4
|
1.0
|
CD2
|
B:TYR194
|
4.8
|
23.5
|
1.0
|
CE1
|
B:HIS223
|
4.8
|
15.4
|
1.0
|
CB
|
B:GLU284
|
4.8
|
15.3
|
1.0
|
|
Zinc binding site 2 out
of 4 in 6dwv
Go back to
Zinc Binding Sites List in 6dwv
Zinc binding site 2 out
of 4 in the Crystal Structure of the Ligj Hydratase in the Apo State
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 Ligj Hydratase in the Apo State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn401
b:33.8
occ:1.00
|
NE2
|
A:HIS10
|
1.9
|
36.5
|
1.0
|
NE2
|
A:HIS178
|
1.9
|
47.0
|
1.0
|
NE2
|
A:HIS8
|
2.2
|
31.2
|
1.0
|
CE1
|
A:HIS10
|
2.7
|
38.3
|
1.0
|
CE1
|
A:HIS178
|
2.9
|
48.8
|
1.0
|
O
|
A:HOH559
|
2.9
|
43.9
|
1.0
|
CD2
|
A:HIS178
|
2.9
|
46.7
|
1.0
|
CD2
|
A:HIS10
|
3.0
|
37.8
|
1.0
|
CE1
|
A:HIS8
|
3.1
|
33.0
|
1.0
|
CD2
|
A:HIS8
|
3.2
|
36.2
|
1.0
|
ND1
|
A:HIS10
|
3.8
|
39.1
|
1.0
|
ND1
|
A:HIS178
|
4.0
|
46.7
|
1.0
|
CG
|
A:HIS10
|
4.0
|
35.5
|
1.0
|
CG
|
A:HIS178
|
4.0
|
45.2
|
1.0
|
ND1
|
A:HIS8
|
4.2
|
34.1
|
1.0
|
CG
|
A:HIS8
|
4.3
|
36.6
|
1.0
|
CB
|
A:ALA72
|
4.3
|
44.3
|
1.0
|
CG
|
A:GLU284
|
4.4
|
38.1
|
1.0
|
SD
|
A:MET176
|
4.6
|
33.2
|
1.0
|
|
Zinc binding site 3 out
of 4 in 6dwv
Go back to
Zinc Binding Sites List in 6dwv
Zinc binding site 3 out
of 4 in the Crystal Structure of the Ligj Hydratase in the Apo State
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 Ligj Hydratase in the Apo State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn401
b:40.5
occ:1.00
|
NE2
|
C:HIS8
|
2.0
|
20.0
|
1.0
|
O
|
C:HOH565
|
2.0
|
30.1
|
1.0
|
NE2
|
C:HIS178
|
2.4
|
22.4
|
1.0
|
CE1
|
C:HIS8
|
2.6
|
16.5
|
1.0
|
NE2
|
C:HIS10
|
2.7
|
23.8
|
1.0
|
CD2
|
C:HIS8
|
3.2
|
16.8
|
1.0
|
CD2
|
C:HIS178
|
3.3
|
21.3
|
1.0
|
CE1
|
C:HIS178
|
3.4
|
20.1
|
1.0
|
CD2
|
C:HIS10
|
3.4
|
22.8
|
1.0
|
CG
|
C:GLU284
|
3.7
|
17.0
|
1.0
|
CE1
|
C:HIS10
|
3.7
|
19.3
|
1.0
|
ND1
|
C:HIS8
|
3.8
|
20.8
|
1.0
|
NE2
|
C:HIS223
|
4.0
|
16.4
|
1.0
|
CG
|
C:HIS8
|
4.1
|
16.5
|
1.0
|
CD
|
C:GLU284
|
4.2
|
46.7
|
1.0
|
CE1
|
C:HIS223
|
4.5
|
16.3
|
1.0
|
ND1
|
C:HIS178
|
4.5
|
21.1
|
1.0
|
CG
|
C:HIS178
|
4.5
|
23.2
|
1.0
|
O
|
C:HOH511
|
4.5
|
22.7
|
1.0
|
OE2
|
C:GLU284
|
4.6
|
48.9
|
1.0
|
OE1
|
C:GLU284
|
4.7
|
44.7
|
1.0
|
CG
|
C:HIS10
|
4.7
|
22.5
|
1.0
|
CE2
|
C:TYR194
|
4.7
|
22.5
|
1.0
|
CB
|
C:ALA72
|
4.7
|
40.5
|
1.0
|
ND1
|
C:HIS10
|
4.8
|
23.3
|
1.0
|
CB
|
C:GLU284
|
5.0
|
16.8
|
1.0
|
|
Zinc binding site 4 out
of 4 in 6dwv
Go back to
Zinc Binding Sites List in 6dwv
Zinc binding site 4 out
of 4 in the Crystal Structure of the Ligj Hydratase in the Apo State
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 Ligj Hydratase in the Apo State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn401
b:25.1
occ:1.00
|
NE2
|
D:HIS10
|
1.9
|
39.4
|
1.0
|
NE2
|
D:HIS8
|
2.0
|
37.9
|
1.0
|
NE2
|
D:HIS178
|
2.1
|
54.5
|
1.0
|
CE1
|
D:HIS8
|
2.8
|
39.0
|
1.0
|
CE1
|
D:HIS10
|
2.8
|
42.9
|
1.0
|
CD2
|
D:HIS178
|
3.0
|
59.0
|
1.0
|
CD2
|
D:HIS8
|
3.0
|
41.2
|
1.0
|
CD2
|
D:HIS10
|
3.0
|
43.1
|
1.0
|
CE1
|
D:HIS178
|
3.1
|
59.9
|
1.0
|
O
|
D:HOH568
|
3.5
|
35.0
|
1.0
|
ND1
|
D:HIS8
|
3.9
|
40.9
|
1.0
|
ND1
|
D:HIS10
|
4.0
|
41.8
|
1.0
|
CG
|
D:HIS8
|
4.0
|
40.3
|
1.0
|
CG
|
D:GLU284
|
4.0
|
47.1
|
1.0
|
CG
|
D:HIS10
|
4.1
|
41.1
|
1.0
|
CG
|
D:HIS178
|
4.1
|
52.8
|
1.0
|
ND1
|
D:HIS178
|
4.2
|
58.0
|
1.0
|
SD
|
D:MET176
|
4.4
|
32.5
|
1.0
|
CB
|
D:ALA72
|
4.7
|
50.4
|
1.0
|
CD
|
D:GLU284
|
4.7
|
42.9
|
1.0
|
NE2
|
D:HIS223
|
4.8
|
28.6
|
1.0
|
OE2
|
D:GLU284
|
4.9
|
37.0
|
1.0
|
|
Reference:
T.N.Hogancamp,
M.F.Mabanglo,
F.M.Raushel.
Structure and Reaction Mechanism of the Ligj Hydratase: An Enzyme Critical For the Bacterial Degradation of Lignin in the Protocatechuate 4,5-Cleavage Pathway. Biochemistry V. 57 5841 2018.
ISSN: ISSN 1520-4995
PubMed: 30207699
DOI: 10.1021/ACS.BIOCHEM.8B00713
Page generated: Mon Oct 28 19:52:12 2024
|