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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:

Potassium (K) 4 atoms
Calcium (Ca) 4 atoms
Chlorine (Cl) 4 atoms
Copper (Cu) 24 atoms

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


Mono view


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


Mono view


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


Mono view


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


Mono view


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

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