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Potassium 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:

Calcium (Ca) 4 atoms
Chlorine (Cl) 4 atoms
Copper (Cu) 24 atoms
Sodium (Na) 4 atoms

Potassium Binding Sites:

The binding sites of Potassium 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 Potassium atom.
In total 4 binding sites of Potassium where determined in the Recombinant Pseudomonas Stutzeri Nitrous Oxide Reductase, Form I, PDB code: 6rl0:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 6rl0

Go back to Potassium Binding Sites List in 6rl0
Potassium 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 Potassium with other atoms in the K 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:K707

b:34.8
occ:0.67
 OE2 A:GLU469 2.2 23.5 0.5
O A:HOH1055 2.4 35.6 1.0
O D:HOH948 2.4 33.4 1.0
O A:LYS454 2.5 22.9 1.0
O D:HOH851 2.6 30.7 1.0
O A:HOH985 2.6 32.5 1.0
OE1 A:GLU469 2.8 26.1 0.5
CD A:GLU469 2.8 25.7 0.5
C A:LYS454 3.7 25.1 1.0
OD1 D:ASP580 4.1 40.0 1.0
NE1 D:TRP620 4.1 43.2 1.0
CD1 D:TRP620 4.2 40.8 1.0
CG A:GLU469 4.3 26.1 0.5
CA A:LYS454 4.3 21.1 1.0
O A:HIS467 4.4 24.7 1.0
O A:PRO468 4.5 26.1 1.0
O D:HOH955 4.6 28.5 1.0
N A:PHE455 4.7 22.7 1.0
CB A:LYS454 4.7 24.9 1.0
CD1 A:PHE455 4.7 28.2 1.0
CA A:PHE455 4.8 26.1 1.0
O A:HOH1022 4.8 37.3 1.0
CA A:GLU469 4.8 22.7 0.5
CA A:GLU469 4.8 24.1 0.5
N A:GLU469 4.8 24.5 1.0
C A:PRO468 4.8 25.3 1.0
O D:PHE621 4.9 32.6 1.0
OE1 A:GLU492 5.0 29.3 1.0

Potassium binding site 2 out of 4 in 6rl0

Go back to Potassium Binding Sites List in 6rl0
Potassium 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 Potassium with other atoms in the K 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:K707

b:35.5
occ:0.67
 OE1 B:GLU469 2.2 26.7 0.5
O B:LYS454 2.4 26.0 1.0
O B:HOH983 2.5 33.0 1.0
O C:HOH850 2.6 36.2 1.0
O B:HOH843 2.6 31.3 1.0
O C:HOH859 2.7 31.3 1.0
CD B:GLU469 2.9 26.6 0.5
OE2 B:GLU469 3.0 25.4 0.5
C B:LYS454 3.6 24.8 1.0
OD2 C:ASP580 4.1 40.6 1.0
CD1 C:TRP620 4.1 42.3 1.0
NE1 C:TRP620 4.2 42.5 1.0
CA B:LYS454 4.3 24.8 1.0
CG B:GLU469 4.3 27.0 0.5
O B:HIS467 4.5 26.4 1.0
O B:PRO468 4.6 25.5 1.0
O C:HOH855 4.6 26.5 1.0
N B:PHE455 4.6 25.6 1.0
O C:HOH879 4.7 37.0 1.0
CB B:LYS454 4.7 24.6 1.0
CA B:GLU469 4.8 23.1 0.5
CA B:GLU469 4.8 24.4 0.5
CA B:PHE455 4.8 25.8 1.0
CD1 B:PHE455 4.8 30.1 1.0
N B:GLU469 4.8 23.3 1.0
C B:PRO468 4.8 26.1 1.0
O C:PHE621 4.9 28.3 1.0
CB B:GLU469 5.0 25.0 0.5

Potassium binding site 3 out of 4 in 6rl0

Go back to Potassium Binding Sites List in 6rl0
Potassium 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 Potassium with other atoms in the K 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:K708

b:30.4
occ:0.83
 OE2 C:GLU469 2.3 22.8 0.5
O C:LYS454 2.4 25.5 1.0
O C:HOH898 2.5 30.1 1.0
O B:HOH818 2.5 26.2 1.0
O B:HOH980 2.5 28.4 1.0
O C:HOH973 2.5 31.4 1.0
OE1 C:GLU469 2.6 24.9 0.5
CD C:GLU469 2.9 23.6 0.5
C C:LYS454 3.6 24.0 1.0
OD1 B:ASP580 4.1 30.1 1.0
CD1 B:TRP620 4.1 32.7 1.0
NE1 B:TRP620 4.2 36.1 1.0
CA C:LYS454 4.3 23.1 1.0
CG C:GLU469 4.4 22.6 0.5
O B:HOH982 4.5 21.9 1.0
O C:HIS467 4.5 22.6 1.0
O C:PRO468 4.6 22.6 1.0
N C:PHE455 4.6 19.9 1.0
CD1 C:PHE455 4.6 27.5 1.0
CB C:LYS454 4.7 23.6 1.0
CA C:PHE455 4.7 24.0 1.0
OE1 C:GLU492 4.7 21.6 1.0
O B:HOH941 4.8 33.0 1.0
CA C:GLU469 4.8 21.7 0.5
CA C:GLU469 4.9 20.9 0.5
O B:PHE621 4.9 27.1 1.0
N C:GLU469 4.9 21.2 1.0
C C:PRO468 4.9 21.7 1.0
CE1 C:PHE455 5.0 27.8 1.0

Potassium binding site 4 out of 4 in 6rl0

Go back to Potassium Binding Sites List in 6rl0
Potassium 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 Potassium with other atoms in the K 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:K707

b:30.2
occ:0.84
 OE2 D:GLU469 2.3 23.5 0.5
O D:HOH898 2.4 24.6 1.0
O D:LYS454 2.4 26.5 1.0
O A:HOH958 2.4 32.8 1.0
O D:HOH951 2.5 31.0 1.0
O A:HOH832 2.5 24.2 1.0
OE1 D:GLU469 2.8 26.6 0.5
CD D:GLU469 2.9 24.5 0.5
C D:LYS454 3.6 24.9 1.0
CD1 A:TRP620 4.1 31.6 1.0
NE1 A:TRP620 4.2 32.5 1.0
OD1 A:ASP580 4.2 30.8 1.0
CA D:LYS454 4.3 22.4 1.0
CG D:GLU469 4.4 25.6 0.5
O A:HOH986 4.6 26.7 1.0
O D:HIS467 4.6 21.4 1.0
O A:HOH973 4.6 32.8 1.0
N D:PHE455 4.6 20.2 1.0
CB D:LYS454 4.6 23.9 1.0
O D:PRO468 4.6 24.1 1.0
CD1 D:PHE455 4.7 26.9 1.0
CA D:PHE455 4.8 23.0 1.0
OE1 D:GLU492 4.8 28.4 1.0
O A:PHE621 4.8 24.1 1.0
CA D:GLU469 4.9 22.3 0.5
CA D:GLU469 4.9 20.6 0.5
N D:GLU469 4.9 21.7 1.0
C D:PRO468 5.0 21.8 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: Mon Aug 12 17:28:47 2024

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