Sodium in PDB 6rl0: Recombinant Pseudomonas Stutzeri Nitrous Oxide Reductase, Form I
Enzymatic activity of Recombinant Pseudomonas Stutzeri Nitrous Oxide Reductase, Form I
All present enzymatic activity of Recombinant Pseudomonas Stutzeri Nitrous Oxide Reductase, Form I:
1.7.2.4;
Protein crystallography data
The structure of Recombinant Pseudomonas Stutzeri Nitrous Oxide Reductase, Form I, PDB code: 6rl0
was solved by
L.Zhang,
A.Wuest,
B.Prasser,
C.Mueller,
O.Einsle,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.91 /
1.78
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
108.916,
73.372,
136.342,
90.00,
95.07,
90.00
|
R / Rfree (%)
|
15.7 /
19.2
|
Other elements in 6rl0:
The structure of Recombinant Pseudomonas Stutzeri Nitrous Oxide Reductase, Form I also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the Recombinant Pseudomonas Stutzeri Nitrous Oxide Reductase, Form I
(pdb code 6rl0). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the
Recombinant Pseudomonas Stutzeri Nitrous Oxide Reductase, Form I, PDB code: 6rl0:
Jump to Sodium binding site number:
1;
2;
3;
4;
Sodium binding site 1 out
of 4 in 6rl0
Go back to
Sodium Binding Sites List in 6rl0
Sodium binding site 1 out
of 4 in the Recombinant Pseudomonas Stutzeri Nitrous Oxide Reductase, Form I
![](/pictures/NA/pdb/rl/6rl0-NA-sphere_01.jpg) Mono view
![](/pictures/NA/pdb/rl/6rl0-NA-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Recombinant Pseudomonas Stutzeri Nitrous Oxide Reductase, Form I within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na708
b:27.7
occ:0.95
|
O
|
A:MET168
|
2.3
|
16.4
|
1.0
|
O
|
A:HOH1085
|
2.3
|
24.0
|
1.0
|
O
|
A:HOH976
|
2.3
|
19.6
|
1.0
|
O
|
A:HOH1159
|
2.4
|
24.5
|
1.0
|
O
|
A:HOH1209
|
2.4
|
28.1
|
1.0
|
O
|
A:HOH981
|
2.5
|
24.1
|
1.0
|
C
|
A:MET168
|
3.5
|
16.8
|
1.0
|
O
|
A:ILE116
|
3.9
|
17.7
|
1.0
|
O
|
A:HOH1213
|
4.0
|
35.0
|
1.0
|
N
|
A:MET168
|
4.0
|
17.9
|
1.0
|
O
|
A:HOH1145
|
4.0
|
33.3
|
1.0
|
O
|
A:HOH975
|
4.2
|
31.2
|
1.0
|
CA
|
A:MET168
|
4.3
|
17.5
|
1.0
|
O
|
A:HOH1185
|
4.4
|
34.0
|
1.0
|
N
|
A:ILE169
|
4.4
|
16.2
|
1.0
|
CA
|
A:ILE169
|
4.5
|
17.2
|
1.0
|
O
|
A:HOH1088
|
4.6
|
22.3
|
1.0
|
O
|
A:HOH1148
|
4.7
|
31.4
|
1.0
|
CB
|
A:ILE169
|
4.9
|
18.3
|
1.0
|
O
|
A:MET227
|
5.0
|
21.2
|
1.0
|
CB
|
A:MET168
|
5.0
|
16.6
|
1.0
|
|
Sodium binding site 2 out
of 4 in 6rl0
Go back to
Sodium Binding Sites List in 6rl0
Sodium binding site 2 out
of 4 in the Recombinant Pseudomonas Stutzeri Nitrous Oxide Reductase, Form I
![](/pictures/NA/pdb/rl/6rl0-NA-sphere_02.jpg) Mono view
![](/pictures/NA/pdb/rl/6rl0-NA-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Recombinant Pseudomonas Stutzeri Nitrous Oxide Reductase, Form I within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na708
b:26.1
occ:1.00
|
O
|
B:HOH1186
|
2.3
|
29.0
|
1.0
|
O
|
B:HOH1064
|
2.3
|
25.3
|
1.0
|
O
|
B:HOH1130
|
2.3
|
26.6
|
1.0
|
O
|
B:MET168
|
2.4
|
17.6
|
1.0
|
O
|
B:HOH1005
|
2.4
|
24.7
|
1.0
|
O
|
B:HOH991
|
2.5
|
18.1
|
1.0
|
C
|
B:MET168
|
3.5
|
18.4
|
1.0
|
O
|
B:ILE116
|
4.0
|
20.1
|
1.0
|
N
|
B:MET168
|
4.1
|
18.4
|
1.0
|
O
|
B:HOH1051
|
4.1
|
31.8
|
1.0
|
O
|
B:HOH1191
|
4.1
|
39.7
|
1.0
|
O
|
B:HOH1105
|
4.2
|
32.2
|
1.0
|
O
|
B:HOH1097
|
4.3
|
35.0
|
1.0
|
O
|
B:HOH1171
|
4.4
|
38.7
|
1.0
|
CA
|
B:MET168
|
4.4
|
18.3
|
1.0
|
N
|
B:ILE169
|
4.4
|
18.4
|
1.0
|
O
|
B:HOH857
|
4.5
|
31.6
|
1.0
|
O
|
B:HOH1075
|
4.5
|
21.0
|
1.0
|
CA
|
B:ILE169
|
4.5
|
18.0
|
1.0
|
O
|
B:HOH1115
|
4.7
|
24.9
|
1.0
|
CB
|
B:ILE169
|
4.9
|
18.7
|
1.0
|
O
|
B:MET227
|
4.9
|
21.2
|
1.0
|
|
Sodium binding site 3 out
of 4 in 6rl0
Go back to
Sodium Binding Sites List in 6rl0
Sodium binding site 3 out
of 4 in the Recombinant Pseudomonas Stutzeri Nitrous Oxide Reductase, Form I
![](/pictures/NA/pdb/rl/6rl0-NA-sphere_03.jpg) Mono view
![](/pictures/NA/pdb/rl/6rl0-NA-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Recombinant Pseudomonas Stutzeri Nitrous Oxide Reductase, Form I within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na709
b:30.0
occ:0.97
|
O
|
C:HOH1112
|
2.3
|
29.2
|
1.0
|
O
|
C:HOH921
|
2.4
|
26.6
|
1.0
|
O
|
C:MET168
|
2.4
|
21.5
|
1.0
|
O
|
C:HOH1156
|
2.4
|
34.7
|
1.0
|
O
|
C:HOH1029
|
2.5
|
28.3
|
1.0
|
O
|
C:HOH1016
|
2.5
|
24.1
|
1.0
|
C
|
C:MET168
|
3.6
|
22.5
|
1.0
|
O
|
C:HOH1160
|
3.8
|
37.1
|
1.0
|
O
|
C:HOH1090
|
4.0
|
33.6
|
1.0
|
O
|
C:ILE116
|
4.0
|
20.7
|
1.0
|
O
|
C:HOH1026
|
4.1
|
34.8
|
1.0
|
N
|
C:MET168
|
4.1
|
20.6
|
1.0
|
O
|
C:HOH1077
|
4.2
|
46.4
|
1.0
|
O
|
C:HOH1149
|
4.2
|
29.4
|
1.0
|
O
|
C:HOH1023
|
4.4
|
38.8
|
1.0
|
O
|
C:HOH1024
|
4.4
|
23.1
|
1.0
|
N
|
C:ILE169
|
4.4
|
19.9
|
1.0
|
CA
|
C:ILE169
|
4.5
|
20.2
|
1.0
|
CA
|
C:MET168
|
4.5
|
20.1
|
1.0
|
O
|
C:HOH1107
|
4.8
|
31.1
|
1.0
|
CB
|
C:ILE169
|
4.9
|
20.4
|
1.0
|
O
|
C:MET227
|
5.0
|
24.0
|
1.0
|
|
Sodium binding site 4 out
of 4 in 6rl0
Go back to
Sodium Binding Sites List in 6rl0
Sodium binding site 4 out
of 4 in the Recombinant Pseudomonas Stutzeri Nitrous Oxide Reductase, Form I
![](/pictures/NA/pdb/rl/6rl0-NA-sphere_04.jpg) Mono view
![](/pictures/NA/pdb/rl/6rl0-NA-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Recombinant Pseudomonas Stutzeri Nitrous Oxide Reductase, Form I within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na708
b:34.2
occ:0.85
|
O
|
D:MET168
|
2.3
|
21.4
|
1.0
|
O
|
D:HOH1050
|
2.4
|
36.8
|
1.0
|
O
|
D:HOH987
|
2.4
|
37.7
|
1.0
|
O
|
D:HOH956
|
2.4
|
39.0
|
1.0
|
O
|
D:HOH1019
|
2.5
|
26.7
|
1.0
|
C
|
D:MET168
|
3.5
|
23.6
|
1.0
|
O
|
D:ILE116
|
4.0
|
22.2
|
1.0
|
N
|
D:MET168
|
4.1
|
22.4
|
1.0
|
N
|
D:ILE169
|
4.4
|
22.1
|
1.0
|
O
|
D:HOH1080
|
4.4
|
36.2
|
1.0
|
CA
|
D:MET168
|
4.4
|
22.5
|
1.0
|
CA
|
D:ILE169
|
4.4
|
22.7
|
1.0
|
O
|
D:HOH983
|
4.6
|
27.4
|
1.0
|
O
|
D:HOH1054
|
4.7
|
30.6
|
1.0
|
CB
|
D:ILE169
|
4.8
|
24.7
|
1.0
|
O
|
D:MET227
|
4.9
|
28.6
|
1.0
|
|
Reference:
L.Zhang,
A.Wust,
B.Prasser,
C.Muller,
O.Einsle.
Functional Assembly of Nitrous Oxide Reductase Provides Insights Into Copper Site Maturation. Proc.Natl.Acad.Sci.Usa V. 116 12822 2019.
ISSN: ESSN 1091-6490
PubMed: 31189605
DOI: 10.1073/PNAS.1903819116
Page generated: Tue Dec 15 12:55:01 2020
|