Zinc in PDB 5zn8: Crystal Structure of Nicotinamidase Pnca From Bacillus Subtilis
Protein crystallography data
The structure of Crystal Structure of Nicotinamidase Pnca From Bacillus Subtilis, PDB code: 5zn8
was solved by
F.Shang,
J.Chen,
L.Wang,
Y.Xu,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
28.91 /
2.00
|
Space group
|
P 62
|
Cell size a, b, c (Å), α, β, γ (°)
|
90.037,
90.037,
86.181,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
15.4 /
22.3
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of Nicotinamidase Pnca From Bacillus Subtilis
(pdb code 5zn8). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the
Crystal Structure of Nicotinamidase Pnca From Bacillus Subtilis, PDB code: 5zn8:
Jump to Zinc binding site number:
1;
2;
Zinc binding site 1 out
of 2 in 5zn8
Go back to
Zinc Binding Sites List in 5zn8
Zinc binding site 1 out
of 2 in the Crystal Structure of Nicotinamidase Pnca From Bacillus Subtilis
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 Nicotinamidase Pnca From Bacillus Subtilis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn201
b:52.5
occ:1.00
|
OE2
|
A:GLU64
|
1.8
|
55.0
|
1.0
|
NE2
|
A:HIS55
|
1.9
|
41.5
|
1.0
|
OD2
|
A:ASP53
|
2.2
|
57.9
|
1.0
|
NE2
|
A:HIS71
|
2.2
|
55.5
|
1.0
|
CD
|
A:GLU64
|
2.7
|
53.7
|
1.0
|
CD2
|
A:HIS55
|
2.7
|
54.1
|
1.0
|
HD2
|
A:HIS55
|
2.8
|
65.0
|
1.0
|
O
|
A:HOH381
|
3.0
|
58.7
|
1.0
|
OE1
|
A:GLU64
|
3.0
|
41.5
|
1.0
|
CE1
|
A:HIS55
|
3.1
|
50.1
|
1.0
|
CG
|
A:ASP53
|
3.1
|
45.0
|
1.0
|
CE1
|
A:HIS71
|
3.1
|
54.1
|
1.0
|
O
|
A:HOH375
|
3.2
|
46.7
|
1.0
|
HE1
|
A:HIS71
|
3.2
|
64.9
|
1.0
|
CD2
|
A:HIS71
|
3.3
|
54.0
|
1.0
|
HE1
|
A:HIS55
|
3.4
|
60.1
|
1.0
|
OD1
|
A:ASP53
|
3.5
|
45.2
|
1.0
|
HD2
|
A:HIS71
|
3.5
|
64.9
|
1.0
|
HG2
|
A:GLU64
|
3.9
|
67.2
|
1.0
|
CG
|
A:HIS55
|
3.9
|
59.1
|
1.0
|
CG
|
A:GLU64
|
4.0
|
56.0
|
1.0
|
ND1
|
A:HIS55
|
4.1
|
45.1
|
1.0
|
HZ
|
A:PHE14
|
4.1
|
58.5
|
1.0
|
ND1
|
A:HIS71
|
4.3
|
58.6
|
1.0
|
HB3
|
A:ASP53
|
4.3
|
46.4
|
1.0
|
CB
|
A:ASP53
|
4.3
|
38.7
|
1.0
|
CG
|
A:HIS71
|
4.4
|
60.1
|
1.0
|
HE1
|
A:TYR106
|
4.5
|
31.9
|
1.0
|
O
|
A:HOH320
|
4.5
|
55.2
|
1.0
|
HG3
|
A:GLU64
|
4.6
|
67.2
|
1.0
|
HE1
|
A:HIS62
|
4.6
|
54.5
|
1.0
|
HB2
|
A:ASP53
|
4.7
|
46.4
|
1.0
|
HB3
|
A:GLU64
|
4.7
|
65.9
|
1.0
|
CB
|
A:GLU64
|
4.8
|
54.9
|
1.0
|
HB2
|
A:GLU64
|
4.8
|
65.9
|
1.0
|
HD22
|
A:ASN72
|
4.9
|
59.4
|
1.0
|
CZ
|
A:PHE14
|
5.0
|
48.7
|
1.0
|
|
Zinc binding site 2 out
of 2 in 5zn8
Go back to
Zinc Binding Sites List in 5zn8
Zinc binding site 2 out
of 2 in the Crystal Structure of Nicotinamidase Pnca From Bacillus Subtilis
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 Nicotinamidase Pnca From Bacillus Subtilis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn201
b:35.3
occ:1.00
|
O
|
B:HOH311
|
1.6
|
32.4
|
1.0
|
NE2
|
B:HIS55
|
2.0
|
29.5
|
1.0
|
OE1
|
B:GLU64
|
2.1
|
34.9
|
1.0
|
OD2
|
B:ASP53
|
2.2
|
35.6
|
1.0
|
NE2
|
B:HIS71
|
2.2
|
36.8
|
1.0
|
CD2
|
B:HIS55
|
2.8
|
32.8
|
1.0
|
CG
|
B:ASP53
|
2.9
|
30.9
|
1.0
|
OD1
|
B:ASP53
|
2.9
|
32.7
|
1.0
|
HD2
|
B:HIS55
|
2.9
|
39.4
|
1.0
|
CE1
|
B:HIS71
|
3.0
|
37.3
|
1.0
|
CE1
|
B:HIS55
|
3.1
|
38.5
|
1.0
|
HE1
|
B:HIS71
|
3.1
|
44.8
|
1.0
|
CD
|
B:GLU64
|
3.1
|
33.9
|
1.0
|
CD2
|
B:HIS71
|
3.2
|
35.8
|
1.0
|
HE1
|
B:HIS55
|
3.4
|
46.2
|
1.0
|
OE2
|
B:GLU64
|
3.4
|
33.3
|
1.0
|
HD2
|
B:HIS71
|
3.5
|
42.9
|
1.0
|
HZ
|
B:PHE14
|
3.9
|
51.8
|
1.0
|
ND1
|
B:HIS71
|
4.0
|
38.5
|
1.0
|
CG
|
B:HIS55
|
4.0
|
29.3
|
1.0
|
ND1
|
B:HIS55
|
4.1
|
34.8
|
1.0
|
CG
|
B:HIS71
|
4.2
|
39.1
|
1.0
|
HD22
|
B:ASN72
|
4.2
|
50.4
|
1.0
|
O
|
B:HOH360
|
4.2
|
32.7
|
1.0
|
HB2
|
B:ASN72
|
4.3
|
43.8
|
1.0
|
CB
|
B:ASP53
|
4.3
|
33.3
|
1.0
|
HB3
|
B:GLU64
|
4.4
|
43.7
|
1.0
|
CG
|
B:GLU64
|
4.5
|
34.8
|
1.0
|
O
|
B:HOH383
|
4.5
|
39.9
|
1.0
|
HB2
|
B:GLU64
|
4.5
|
43.7
|
1.0
|
HB3
|
B:ASP53
|
4.5
|
39.9
|
1.0
|
HB2
|
B:ASP53
|
4.6
|
39.9
|
1.0
|
CB
|
B:GLU64
|
4.7
|
36.5
|
1.0
|
CZ
|
B:PHE14
|
4.8
|
43.2
|
1.0
|
O
|
B:HOH368
|
4.8
|
35.5
|
1.0
|
HE1
|
B:HIS62
|
4.8
|
37.0
|
1.0
|
HG2
|
B:GLU64
|
4.9
|
41.8
|
1.0
|
O
|
B:HOH315
|
5.0
|
32.0
|
1.0
|
|
Reference:
F.Shang,
J.Chen,
L.Wang,
L.Jin,
L.Zou,
T.Bu,
Y.Dong,
N.C.Ha,
K.H.Nam,
C.Quan,
Y.Xu.
Crystal Structure of the Nicotinamidase/Pyrazinamidase Pnca From Bacillus Subtilis. Biochem.Biophys.Res.Commun. V. 503 2906 2018.
ISSN: ESSN 1090-2104
PubMed: 30107912
DOI: 10.1016/J.BBRC.2018.08.067
Page generated: Wed Dec 16 11:27:17 2020
|