Chlorine in PDB 3cng: Crystal Structure of Nudix Hydrolase From Nitrosomonas Europaea
Protein crystallography data
The structure of Crystal Structure of Nudix Hydrolase From Nitrosomonas Europaea, PDB code: 3cng
was solved by
J.Osipiuk,
X.Xu,
H.Zheng,
A.Savchenko,
A.M.Edwards,
A.Joachimiak,
Midwestcenter For Structural Genomics (Mcsg),
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
37.20 /
2.00
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
174.781,
49.506,
110.190,
90.00,
106.28,
90.00
|
R / Rfree (%)
|
18.1 /
23.3
|
Other elements in 3cng:
The structure of Crystal Structure of Nudix Hydrolase From Nitrosomonas Europaea also contains other interesting chemical elements:
Chlorine Binding Sites:
The binding sites of Chlorine atom in the Crystal Structure of Nudix Hydrolase From Nitrosomonas Europaea
(pdb code 3cng). This binding sites where shown within
5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the
Crystal Structure of Nudix Hydrolase From Nitrosomonas Europaea, PDB code: 3cng:
Jump to Chlorine binding site number:
1;
2;
3;
4;
5;
6;
7;
Chlorine binding site 1 out
of 7 in 3cng
Go back to
Chlorine Binding Sites List in 3cng
Chlorine binding site 1 out
of 7 in the Crystal Structure of Nudix Hydrolase From Nitrosomonas Europaea
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 1 of Crystal Structure of Nudix Hydrolase From Nitrosomonas Europaea within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl518
b:38.1
occ:0.80
|
O
|
B:HOH523
|
3.0
|
32.6
|
1.0
|
N
|
A:VAL79
|
3.2
|
34.8
|
1.0
|
CG2
|
A:VAL79
|
3.4
|
33.1
|
1.0
|
CB
|
A:THR77
|
3.6
|
34.9
|
1.0
|
N
|
A:LEU78
|
3.6
|
35.2
|
1.0
|
CB
|
A:VAL79
|
3.7
|
36.4
|
1.0
|
OG1
|
A:THR77
|
3.8
|
34.2
|
1.0
|
OG
|
B:SER104
|
3.8
|
36.3
|
1.0
|
CB
|
A:LEU78
|
3.8
|
35.6
|
1.0
|
CD2
|
B:LEU171
|
4.0
|
50.7
|
1.0
|
CA
|
A:LEU78
|
4.0
|
35.4
|
1.0
|
CG1
|
B:ILE173
|
4.0
|
36.8
|
1.0
|
CA
|
A:VAL79
|
4.0
|
35.8
|
1.0
|
C
|
A:LEU78
|
4.1
|
34.8
|
1.0
|
CD1
|
B:ILE173
|
4.2
|
36.7
|
1.0
|
C
|
A:THR77
|
4.3
|
34.1
|
1.0
|
CB
|
B:SER104
|
4.3
|
33.4
|
1.0
|
CG
|
B:LEU171
|
4.4
|
47.7
|
1.0
|
O
|
A:HOH548
|
4.4
|
33.9
|
1.0
|
CA
|
A:THR77
|
4.5
|
34.1
|
1.0
|
CG2
|
A:THR77
|
4.6
|
31.4
|
1.0
|
O
|
B:GLY172
|
4.7
|
41.9
|
1.0
|
CG
|
A:LEU78
|
4.8
|
35.9
|
1.0
|
CD1
|
A:LEU78
|
4.9
|
29.3
|
1.0
|
|
Chlorine binding site 2 out
of 7 in 3cng
Go back to
Chlorine Binding Sites List in 3cng
Chlorine binding site 2 out
of 7 in the Crystal Structure of Nudix Hydrolase From Nitrosomonas Europaea
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 2 of Crystal Structure of Nudix Hydrolase From Nitrosomonas Europaea within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl519
b:40.0
occ:0.80
|
O3
|
A:GOL501
|
2.9
|
41.4
|
0.8
|
N
|
A:VAL150
|
3.2
|
37.6
|
1.0
|
C3
|
A:GOL501
|
3.3
|
36.4
|
0.8
|
O
|
A:HOH528
|
3.4
|
43.6
|
1.0
|
N
|
A:ARG149
|
3.6
|
37.1
|
1.0
|
CB
|
A:VAL150
|
3.7
|
37.7
|
1.0
|
CG1
|
A:VAL150
|
3.7
|
32.4
|
1.0
|
CB
|
A:ARG149
|
3.9
|
38.0
|
1.0
|
CB
|
A:PHE148
|
3.9
|
40.5
|
1.0
|
CD2
|
A:LEU105
|
3.9
|
41.0
|
1.0
|
CA
|
A:ARG149
|
4.0
|
37.9
|
1.0
|
CA
|
A:VAL150
|
4.0
|
38.0
|
1.0
|
C
|
A:ARG149
|
4.1
|
37.3
|
1.0
|
C
|
A:PHE148
|
4.2
|
38.4
|
1.0
|
CA
|
A:PHE148
|
4.3
|
39.7
|
1.0
|
CG2
|
A:ILE174
|
4.3
|
24.9
|
1.0
|
CG
|
A:PHE148
|
4.7
|
42.0
|
1.0
|
CD1
|
A:ILE174
|
4.8
|
26.9
|
1.0
|
C2
|
A:GOL501
|
4.8
|
37.7
|
0.8
|
CD1
|
A:PHE148
|
4.9
|
44.5
|
1.0
|
|
Chlorine binding site 3 out
of 7 in 3cng
Go back to
Chlorine Binding Sites List in 3cng
Chlorine binding site 3 out
of 7 in the Crystal Structure of Nudix Hydrolase From Nitrosomonas Europaea
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 3 of Crystal Structure of Nudix Hydrolase From Nitrosomonas Europaea within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl520
b:47.9
occ:0.80
|
N
|
A:LEU99
|
3.2
|
36.4
|
1.0
|
CA
|
A:GLU98
|
3.6
|
38.7
|
1.0
|
O
|
B:HOH555
|
3.7
|
42.4
|
1.0
|
CE1
|
B:PHE169
|
3.9
|
56.1
|
1.0
|
C
|
A:GLU98
|
3.9
|
37.8
|
1.0
|
CB
|
A:GLU98
|
4.0
|
39.0
|
1.0
|
CB
|
A:LEU99
|
4.1
|
36.5
|
1.0
|
CB
|
B:LEU171
|
4.3
|
46.6
|
1.0
|
CA
|
A:LEU99
|
4.3
|
36.3
|
1.0
|
CD1
|
B:PHE169
|
4.4
|
57.0
|
1.0
|
CG
|
A:GLU98
|
4.4
|
43.8
|
1.0
|
CD2
|
B:LEU171
|
4.5
|
50.7
|
1.0
|
O
|
A:ARG97
|
4.6
|
38.5
|
1.0
|
N
|
A:GLU98
|
4.8
|
38.0
|
1.0
|
CG
|
B:LEU171
|
4.9
|
47.7
|
1.0
|
O
|
A:LEU99
|
4.9
|
36.9
|
1.0
|
CD1
|
B:LEU171
|
4.9
|
47.6
|
1.0
|
N
|
B:LEU171
|
4.9
|
45.8
|
1.0
|
CZ
|
B:PHE169
|
5.0
|
56.2
|
1.0
|
|
Chlorine binding site 4 out
of 7 in 3cng
Go back to
Chlorine Binding Sites List in 3cng
Chlorine binding site 4 out
of 7 in the Crystal Structure of Nudix Hydrolase From Nitrosomonas Europaea
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 4 of Crystal Structure of Nudix Hydrolase From Nitrosomonas Europaea within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl514
b:43.0
occ:0.80
|
N
|
B:LEU99
|
3.4
|
37.5
|
1.0
|
O
|
B:HOH557
|
3.5
|
41.4
|
1.0
|
O
|
A:HOH538
|
3.6
|
41.0
|
1.0
|
CA
|
B:GLU98
|
3.6
|
39.0
|
1.0
|
CE1
|
A:PHE169
|
3.8
|
61.1
|
1.0
|
C
|
B:GLU98
|
4.0
|
38.1
|
1.0
|
CB
|
B:GLU98
|
4.1
|
39.5
|
1.0
|
CB
|
B:LEU99
|
4.2
|
37.4
|
1.0
|
CD1
|
A:LEU171
|
4.4
|
47.1
|
1.0
|
CA
|
B:LEU99
|
4.4
|
36.4
|
1.0
|
CG
|
B:GLU98
|
4.5
|
43.3
|
1.0
|
CB
|
A:LEU171
|
4.5
|
43.9
|
1.0
|
CD1
|
A:PHE169
|
4.6
|
63.2
|
1.0
|
CZ
|
A:PHE169
|
4.6
|
64.0
|
1.0
|
O
|
B:ARG97
|
4.7
|
36.7
|
1.0
|
N
|
B:GLU98
|
4.8
|
38.3
|
1.0
|
N
|
A:LEU171
|
4.8
|
44.1
|
1.0
|
O
|
B:LEU99
|
4.9
|
35.7
|
1.0
|
CG
|
A:LEU171
|
5.0
|
45.1
|
1.0
|
|
Chlorine binding site 5 out
of 7 in 3cng
Go back to
Chlorine Binding Sites List in 3cng
Chlorine binding site 5 out
of 7 in the Crystal Structure of Nudix Hydrolase From Nitrosomonas Europaea
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 5 of Crystal Structure of Nudix Hydrolase From Nitrosomonas Europaea within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl517
b:35.4
occ:0.80
|
O
|
A:HOH526
|
3.0
|
33.1
|
1.0
|
O
|
A:HOH542
|
3.2
|
35.0
|
1.0
|
N
|
B:VAL79
|
3.2
|
34.1
|
1.0
|
CG1
|
B:VAL79
|
3.3
|
33.2
|
0.4
|
CD2
|
A:LEU171
|
3.4
|
46.6
|
1.0
|
CG2
|
B:VAL79
|
3.4
|
33.6
|
0.6
|
N
|
B:LEU78
|
3.4
|
32.8
|
1.0
|
CB
|
B:VAL79
|
3.5
|
34.4
|
0.6
|
CB
|
B:THR77
|
3.5
|
36.3
|
1.0
|
OG1
|
B:THR77
|
3.7
|
36.8
|
1.0
|
CG2
|
B:VAL79
|
3.7
|
33.2
|
0.4
|
CB
|
B:LEU78
|
3.8
|
32.5
|
1.0
|
OG
|
A:SER104
|
3.8
|
34.1
|
1.0
|
CB
|
B:VAL79
|
3.9
|
34.0
|
0.4
|
CA
|
B:LEU78
|
3.9
|
33.6
|
1.0
|
CA
|
B:VAL79
|
4.0
|
34.3
|
0.6
|
C
|
B:LEU78
|
4.1
|
33.4
|
1.0
|
CA
|
B:VAL79
|
4.1
|
34.0
|
0.4
|
CG1
|
A:ILE173
|
4.1
|
34.1
|
1.0
|
C
|
B:THR77
|
4.2
|
34.3
|
1.0
|
CD1
|
A:ILE173
|
4.4
|
32.5
|
1.0
|
CA
|
B:THR77
|
4.4
|
36.0
|
1.0
|
O
|
B:HOH553
|
4.5
|
42.7
|
1.0
|
O
|
A:HOH610
|
4.5
|
41.8
|
1.0
|
CG
|
A:LEU171
|
4.5
|
45.1
|
1.0
|
CB
|
A:SER104
|
4.5
|
33.7
|
1.0
|
CG2
|
B:THR77
|
4.6
|
34.7
|
1.0
|
O
|
A:GLY172
|
4.7
|
35.6
|
1.0
|
CG1
|
B:VAL79
|
4.8
|
34.9
|
0.6
|
CG
|
B:LEU78
|
4.8
|
31.6
|
1.0
|
O
|
A:HOH584
|
4.9
|
42.1
|
1.0
|
|
Chlorine binding site 6 out
of 7 in 3cng
Go back to
Chlorine Binding Sites List in 3cng
Chlorine binding site 6 out
of 7 in the Crystal Structure of Nudix Hydrolase From Nitrosomonas Europaea
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 6 of Crystal Structure of Nudix Hydrolase From Nitrosomonas Europaea within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cl516
b:37.6
occ:0.80
|
O
|
D:HOH556
|
2.8
|
38.0
|
1.0
|
O
|
D:HOH608
|
2.9
|
31.6
|
1.0
|
N
|
C:VAL79
|
3.4
|
35.9
|
1.0
|
CG2
|
C:VAL79
|
3.5
|
37.9
|
1.0
|
CB
|
C:THR77
|
3.6
|
35.7
|
1.0
|
OG
|
D:SER104
|
3.6
|
35.3
|
1.0
|
N
|
C:LEU78
|
3.7
|
33.3
|
1.0
|
CB
|
C:VAL79
|
3.7
|
36.8
|
1.0
|
OG1
|
C:THR77
|
3.8
|
34.0
|
1.0
|
CD2
|
D:LEU171
|
3.9
|
45.0
|
1.0
|
CB
|
C:LEU78
|
4.0
|
35.5
|
1.0
|
CG1
|
D:ILE173
|
4.0
|
37.5
|
1.0
|
CA
|
C:LEU78
|
4.2
|
35.5
|
1.0
|
CD1
|
D:ILE173
|
4.2
|
37.7
|
1.0
|
CA
|
C:VAL79
|
4.2
|
37.0
|
1.0
|
C
|
C:LEU78
|
4.3
|
34.9
|
1.0
|
CB
|
D:SER104
|
4.3
|
35.3
|
1.0
|
C
|
C:THR77
|
4.3
|
34.5
|
1.0
|
CA
|
C:THR77
|
4.5
|
35.2
|
1.0
|
CG2
|
C:THR77
|
4.5
|
35.1
|
1.0
|
CG
|
D:LEU171
|
4.6
|
44.2
|
1.0
|
O
|
D:HOH623
|
4.6
|
44.0
|
1.0
|
O
|
C:HOH542
|
4.6
|
36.1
|
1.0
|
O
|
D:HOH616
|
4.7
|
44.6
|
1.0
|
O
|
D:GLY172
|
4.7
|
37.9
|
1.0
|
CG
|
C:LEU78
|
5.0
|
37.1
|
1.0
|
|
Chlorine binding site 7 out
of 7 in 3cng
Go back to
Chlorine Binding Sites List in 3cng
Chlorine binding site 7 out
of 7 in the Crystal Structure of Nudix Hydrolase From Nitrosomonas Europaea
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 7 of Crystal Structure of Nudix Hydrolase From Nitrosomonas Europaea within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Cl515
b:33.0
occ:0.80
|
NE2
|
D:HIS164
|
3.0
|
55.6
|
1.0
|
CD2
|
D:HIS164
|
3.8
|
58.6
|
1.0
|
CE1
|
D:HIS164
|
4.0
|
59.9
|
1.0
|
|
Reference:
J.Osipiuk,
X.Xu,
H.Zheng,
A.Savchenko,
A.M.Edwards,
A.Joachimiak.
X-Ray Crystal Structure of Nudix Hydrolase From Nitrosomonas Europaea. To Be Published.
Page generated: Sat Jul 20 17:41:01 2024
|