Atomistry » Sodium » PDB 6rca-6rmx » 6rl0
Atomistry »
  Sodium »
    PDB 6rca-6rmx »
      6rl0 »

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

Last articles

Tb in 6TVY
Si in 6Y7O
Rh in 6WRM
Rh in 6WRL
Ni in 6Y8Z
Ni in 6Y8Y
Na in 6ZXZ
Na in 7ACG
Na in 6YLS
Na in 6Y8Z
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy