Calcium in PDB 6rl0: 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;

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

The structure of Recombinant Pseudomonas Stutzeri Nitrous Oxide Reductase, Form I also contains other interesting chemical elements:

Potassium	(K)	4 atoms
Chlorine	(Cl)	4 atoms
Copper	(Cu)	24 atoms
Sodium	(Na)	4 atoms

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

Calcium 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 Calcium with other atoms in the Ca 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:Ca703 b:27.3 occ:0.68 O A:MET267 2.3 47.0 1.0 OD1 A:ASN324 2.3 32.5 1.0 O A:TYR256 2.4 31.0 1.0 O A:HOH825 2.4 38.3 1.0 OE2 A:GLU259 2.5 37.5 1.0 OE1 A:GLU259 2.6 39.4 1.0 OD1 A:ASP273 2.7 31.2 1.0 OD2 A:ASP273 2.7 32.2 1.0 CD A:GLU259 2.9 45.9 1.0 CG A:ASP273 3.0 33.5 1.0 CG A:ASN324 3.2 30.4 1.0 C A:MET267 3.4 45.3 1.0 C A:TYR256 3.5 33.7 1.0 ND2 A:ASN324 3.7 32.6 1.0 N A:MET268 4.2 42.5 1.0 CA A:MET268 4.2 45.6 1.0 CA A:ASN257 4.3 42.5 1.0 N A:ASN257 4.3 40.4 1.0 CA A:MET267 4.4 42.4 1.0 CA A:TYR256 4.4 32.5 1.0 CB A:ASN324 4.4 25.8 1.0 CG A:GLU259 4.5 49.8 1.0 N A:SER258 4.5 40.8 1.0 CA A:ASN324 4.5 27.4 1.0 N A:ASN324 4.5 27.1 1.0 CB A:ASP273 4.6 29.4 1.0 OG A:SER258 4.6 43.8 1.0 O A:ASN270 4.7 42.0 1.0 C A:MET268 4.8 44.2 1.0 CB A:TYR256 4.9 32.1 1.0 C A:ASN257 4.9 42.2 1.0 CB A:MET267 4.9 44.1 1.0 N A:ARG269 5.0 44.4 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca703 b:27.3 occ:0.65 OD1 B:ASN324 2.3 32.1 1.0 O B:HOH821 2.4 32.0 1.0 O B:TYR256 2.4 38.3 1.0 O B:MET267 2.4 44.6 1.0 OD1 B:ASP273 2.5 29.3 1.0 OE2 B:GLU259 2.5 37.8 1.0 OD2 B:ASP273 2.6 31.1 1.0 OE1 B:GLU259 2.6 42.3 1.0 CG B:ASP273 2.8 32.0 1.0 CD B:GLU259 2.9 45.7 1.0 CG B:ASN324 3.3 31.4 1.0 C B:TYR256 3.5 36.6 1.0 C B:MET267 3.5 43.5 1.0 ND2 B:ASN324 3.8 29.4 1.0 CA B:MET268 4.3 48.6 1.0 N B:MET268 4.3 44.6 1.0 CA B:TYR256 4.3 34.7 1.0 N B:ASN257 4.3 39.3 1.0 CA B:ASN257 4.3 35.4 1.0 N B:ASN324 4.4 29.3 1.0 CB B:ASP273 4.4 30.4 1.0 CA B:ASN324 4.4 28.1 1.0 N B:SER258 4.4 40.6 1.0 CB B:ASN324 4.4 27.8 1.0 CG B:GLU259 4.5 47.7 1.0 CA B:MET267 4.5 44.5 1.0 OG B:SER258 4.6 49.4 1.0 O B:ASN270 4.7 48.0 1.0 CB B:TYR256 4.8 35.3 1.0 C B:ASN257 4.9 41.6 1.0 C B:MET268 4.9 49.9 1.0 N B:ASN270 5.0 48.0 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca703 b:23.0 occ:1.00 O C:MET267 2.4 23.9 1.0 OD1 C:ASN324 2.4 21.9 1.0 O C:HOH823 2.5 21.9 1.0 O C:TYR256 2.5 24.0 1.0 OD2 C:ASP273 2.5 22.7 1.0 OE2 C:GLU259 2.6 25.3 1.0 OD1 C:ASP273 2.6 19.1 1.0 OE1 C:GLU259 2.6 23.9 1.0 CG C:ASP273 2.9 21.8 1.0 CD C:GLU259 2.9 26.1 1.0 CG C:ASN324 3.4 20.9 1.0 C C:MET267 3.5 24.5 1.0 C C:TYR256 3.5 21.2 1.0 ND2 C:ASN324 3.9 20.7 1.0 CA C:MET268 4.2 26.1 1.0 N C:MET268 4.2 27.3 1.0 N C:ASN257 4.3 21.5 1.0 CA C:TYR256 4.4 21.0 1.0 CA C:ASN257 4.4 22.8 1.0 CB C:ASP273 4.4 20.2 1.0 N C:SER258 4.4 22.8 1.0 CA C:MET267 4.5 25.7 1.0 CG C:GLU259 4.5 29.0 1.0 OG C:SER258 4.5 26.1 1.0 N C:ASN324 4.5 21.2 1.0 CA C:ASN324 4.6 20.9 1.0 CB C:ASN324 4.6 20.9 1.0 O C:ASN270 4.6 26.6 1.0 C C:MET268 4.8 28.6 1.0 C C:ASN257 4.9 23.3 1.0 N C:ARG269 4.9 29.3 1.0 CB C:TYR256 5.0 22.9 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca703 b:26.0 occ:1.00 O D:MET267 2.3 26.2 1.0 O D:TYR256 2.4 28.8 1.0 OD1 D:ASN324 2.4 27.6 1.0 OE1 D:GLU259 2.5 26.9 1.0 O D:HOH843 2.5 28.6 1.0 OD2 D:ASP273 2.5 25.1 1.0 OE2 D:GLU259 2.6 30.2 1.0 OD1 D:ASP273 2.6 27.4 1.0 CG D:ASP273 2.9 27.0 1.0 CD D:GLU259 2.9 32.9 1.0 CG D:ASN324 3.4 27.6 1.0 C D:MET267 3.4 30.0 1.0 C D:TYR256 3.5 25.9 1.0 ND2 D:ASN324 3.9 26.3 1.0 CA D:MET268 4.2 31.6 1.0 N D:MET268 4.2 29.4 1.0 N D:ASN257 4.3 24.0 1.0 CA D:ASN257 4.3 26.5 1.0 N D:SER258 4.4 30.3 1.0 CA D:TYR256 4.4 25.0 1.0 CG D:GLU259 4.4 38.2 1.0 CB D:ASP273 4.4 28.1 1.0 CA D:MET267 4.4 31.5 1.0 OG D:SER258 4.5 28.0 1.0 N D:ASN324 4.5 22.1 1.0 CA D:ASN324 4.5 23.5 1.0 CB D:ASN324 4.6 22.9 1.0 O D:ASN270 4.8 26.9 1.0 C D:ASN257 4.9 28.1 1.0 C D:MET268 4.9 29.2 1.0 CB D:TYR256 5.0 26.3 1.0 CB D:MET267 5.0 30.2 1.0

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