Zinc in PDB 6sj4: Amidohydrolase, Ahs with Substrate Analog
Protein crystallography data
The structure of Amidohydrolase, Ahs with Substrate Analog, PDB code: 6sj4
was solved by
J.H.Naismith,
H.Song,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
65.08 /
1.81
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
135.320,
54.337,
139.844,
90.00,
111.45,
90.00
|
R / Rfree (%)
|
18.2 /
21
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Amidohydrolase, Ahs with Substrate Analog
(pdb code 6sj4). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the
Amidohydrolase, Ahs with Substrate Analog, PDB code: 6sj4:
Jump to Zinc binding site number:
1;
2;
Zinc binding site 1 out
of 2 in 6sj4
Go back to
Zinc Binding Sites List in 6sj4
Zinc binding site 1 out
of 2 in the Amidohydrolase, Ahs with Substrate Analog
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Amidohydrolase, Ahs with Substrate Analog within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn503
b:34.0
occ:1.00
|
NE2
|
A:HIS77
|
2.0
|
34.4
|
1.0
|
NE2
|
A:HIS75
|
2.0
|
33.3
|
1.0
|
NE2
|
A:HIS253
|
2.0
|
38.4
|
1.0
|
OD1
|
A:ASP345
|
2.2
|
37.3
|
1.0
|
CE1
|
A:HIS253
|
2.9
|
39.5
|
1.0
|
CE1
|
A:HIS75
|
2.9
|
34.1
|
1.0
|
CD2
|
A:HIS77
|
3.0
|
33.5
|
1.0
|
CE1
|
A:HIS77
|
3.0
|
35.7
|
1.0
|
CD2
|
A:HIS75
|
3.0
|
33.9
|
1.0
|
CD2
|
A:HIS253
|
3.0
|
38.1
|
1.0
|
CG
|
A:ASP345
|
3.2
|
36.6
|
1.0
|
O8
|
A:LFK501
|
3.2
|
53.5
|
1.0
|
C7
|
A:LFK501
|
3.4
|
52.4
|
1.0
|
O3
|
A:LFK501
|
3.5
|
52.1
|
1.0
|
OD2
|
A:ASP345
|
3.6
|
36.7
|
1.0
|
ND1
|
A:HIS253
|
4.1
|
39.8
|
1.0
|
ND1
|
A:HIS75
|
4.1
|
33.3
|
1.0
|
ND1
|
A:HIS77
|
4.1
|
35.4
|
1.0
|
CG
|
A:HIS77
|
4.1
|
33.6
|
1.0
|
CG
|
A:HIS75
|
4.1
|
33.0
|
1.0
|
CG
|
A:HIS253
|
4.1
|
37.9
|
1.0
|
C3
|
A:LFK501
|
4.2
|
51.1
|
1.0
|
NE2
|
A:HIS290
|
4.3
|
37.6
|
1.0
|
CB
|
A:ASP345
|
4.3
|
35.3
|
1.0
|
C21
|
A:LFK501
|
4.4
|
52.5
|
1.0
|
CA
|
A:ASP345
|
4.4
|
34.9
|
1.0
|
C4
|
A:LFK501
|
4.5
|
52.2
|
1.0
|
O
|
A:HOH649
|
4.7
|
46.1
|
1.0
|
C
|
A:ASP345
|
4.9
|
36.0
|
1.0
|
N
|
A:ALA346
|
5.0
|
34.6
|
1.0
|
CE1
|
A:HIS290
|
5.0
|
38.3
|
1.0
|
|
Zinc binding site 2 out
of 2 in 6sj4
Go back to
Zinc Binding Sites List in 6sj4
Zinc binding site 2 out
of 2 in the Amidohydrolase, Ahs with Substrate Analog
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Amidohydrolase, Ahs with Substrate Analog within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn504
b:25.9
occ:1.00
|
NE2
|
B:HIS253
|
2.0
|
27.5
|
1.0
|
NE2
|
B:HIS75
|
2.0
|
25.7
|
1.0
|
OD1
|
B:ASP345
|
2.0
|
34.8
|
1.0
|
NE2
|
B:HIS77
|
2.1
|
25.6
|
1.0
|
O8
|
B:LFK501
|
2.7
|
43.6
|
1.0
|
CE1
|
B:HIS253
|
2.9
|
29.7
|
1.0
|
CE1
|
B:HIS75
|
2.9
|
27.9
|
1.0
|
CG
|
B:ASP345
|
3.0
|
33.3
|
1.0
|
CD2
|
B:HIS77
|
3.0
|
24.3
|
1.0
|
CD2
|
B:HIS253
|
3.1
|
26.2
|
1.0
|
CD2
|
B:HIS75
|
3.1
|
26.1
|
1.0
|
CE1
|
B:HIS77
|
3.1
|
26.6
|
1.0
|
C7
|
B:LFK501
|
3.3
|
42.8
|
1.0
|
OD2
|
B:ASP345
|
3.4
|
37.1
|
1.0
|
O3
|
B:LFK501
|
3.6
|
41.7
|
1.0
|
ND1
|
B:HIS253
|
4.0
|
29.8
|
1.0
|
ND1
|
B:HIS75
|
4.0
|
27.6
|
1.0
|
NE2
|
B:HIS290
|
4.1
|
27.7
|
1.0
|
CG
|
B:HIS253
|
4.1
|
26.3
|
1.0
|
CG
|
B:HIS75
|
4.2
|
24.4
|
1.0
|
CG
|
B:HIS77
|
4.2
|
24.3
|
1.0
|
ND1
|
B:HIS77
|
4.2
|
25.6
|
1.0
|
CB
|
B:ASP345
|
4.2
|
32.3
|
1.0
|
C3
|
B:LFK501
|
4.3
|
39.8
|
1.0
|
C21
|
B:LFK501
|
4.3
|
39.2
|
1.0
|
CA
|
B:ASP345
|
4.4
|
30.6
|
1.0
|
C4
|
B:LFK501
|
4.6
|
39.6
|
1.0
|
O
|
B:HOH759
|
4.6
|
37.0
|
1.0
|
CE1
|
B:HIS290
|
4.9
|
28.9
|
1.0
|
N
|
B:ALA346
|
4.9
|
32.4
|
1.0
|
CD2
|
B:HIS290
|
4.9
|
28.7
|
1.0
|
C31
|
B:LFK501
|
5.0
|
39.0
|
1.0
|
C
|
B:ASP345
|
5.0
|
31.7
|
1.0
|
|
Reference:
H.Song,
C.Rao,
Z.Deng,
Y.Yi,
J.H.Naismith.
The Biosynthetic Pathway of the Benzoxazole in Nataxazole Proceeds Via An Unstable Ester and Has Synthetic Utility. Angew.Chem.Int.Ed.Engl. 2020.
ISSN: ESSN 1521-3773
PubMed: 31903677
DOI: 10.1002/ANIE.201915685
Page generated: Wed Dec 16 12:48:43 2020
|