Calcium in PDB 6rkz: Recombinant Pseudomonas Stutzeri Nitrous Oxide Reductase, Form II

Enzymatic activity of Recombinant Pseudomonas Stutzeri Nitrous Oxide Reductase, Form II

All present enzymatic activity of Recombinant Pseudomonas Stutzeri Nitrous Oxide Reductase, Form II:
1.7.2.4;

Protein crystallography data

The structure of Recombinant Pseudomonas Stutzeri Nitrous Oxide Reductase, Form II, PDB code: 6rkz 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) 59.70 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 68.887, 76.789, 108.823, 90.00, 93.33, 90.00
R / Rfree (%) 15.2 / 19.1

Other elements in 6rkz:

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

Potassium (K) 2 atoms
Chlorine (Cl) 3 atoms
Copper (Cu) 12 atoms
Sodium (Na) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Recombinant Pseudomonas Stutzeri Nitrous Oxide Reductase, Form II (pdb code 6rkz). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Recombinant Pseudomonas Stutzeri Nitrous Oxide Reductase, Form II, PDB code: 6rkz:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 6rkz

Go back to Calcium Binding Sites List in 6rkz
Calcium binding site 1 out of 2 in the Recombinant Pseudomonas Stutzeri Nitrous Oxide Reductase, Form II


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 II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca703

b:20.5
occ:0.61
OE2 A:GLU259 2.3 40.0 1.0
O A:TYR256 2.3 31.2 1.0
OD1 A:ASN324 2.4 30.7 1.0
O A:MET267 2.5 42.2 1.0
OD2 A:ASP273 2.5 34.4 1.0
OD1 A:ASP273 2.5 34.8 1.0
O A:HOH867 2.5 32.5 1.0
OE1 A:GLU259 2.8 41.1 1.0
CG A:ASP273 2.8 36.1 1.0
CD A:GLU259 2.9 43.1 1.0
CG A:ASN324 3.4 30.6 1.0
C A:TYR256 3.4 33.3 1.0
C A:MET267 3.6 44.3 1.0
ND2 A:ASN324 3.9 27.6 1.0
N A:ASN257 4.2 30.8 1.0
CA A:ASN257 4.2 36.7 1.0
CA A:MET268 4.3 43.7 1.0
CA A:TYR256 4.3 33.2 1.0
N A:SER258 4.3 34.0 1.0
N A:MET268 4.3 34.4 1.0
CB A:ASP273 4.4 29.6 1.0
CG A:GLU259 4.4 37.3 1.0
OG A:SER258 4.5 40.8 1.0
N A:ASN324 4.5 22.5 1.0
CA A:ASN324 4.5 25.3 1.0
CA A:MET267 4.5 42.8 1.0
CB A:ASN324 4.6 25.8 1.0
C A:MET268 4.7 44.0 1.0
C A:ASN257 4.7 39.8 1.0
O A:ASN270 4.8 36.8 1.0
N A:ARG269 4.8 48.0 1.0
N A:ASN270 4.9 43.3 1.0
CB A:ASN270 4.9 36.6 1.0
CB A:TYR256 5.0 33.0 1.0

Calcium binding site 2 out of 2 in 6rkz

Go back to Calcium Binding Sites List in 6rkz
Calcium binding site 2 out of 2 in the Recombinant Pseudomonas Stutzeri Nitrous Oxide Reductase, Form II


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 II within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca703

b:26.1
occ:0.78
O B:HOH821 2.3 37.5 1.0
O B:MET267 2.3 35.8 1.0
O B:TYR256 2.4 31.8 1.0
OE2 B:GLU259 2.5 34.6 1.0
OD1 B:ASN324 2.5 31.1 1.0
OD2 B:ASP273 2.5 32.5 1.0
OE1 B:GLU259 2.7 30.1 1.0
OD1 B:ASP273 2.7 28.6 1.0
CD B:GLU259 2.9 31.8 1.0
CG B:ASP273 3.0 34.6 1.0
CG B:ASN324 3.4 29.8 1.0
C B:TYR256 3.5 27.8 1.0
C B:MET267 3.5 34.7 1.0
ND2 B:ASN324 3.9 26.5 1.0
N B:MET268 4.3 30.2 1.0
N B:ASN257 4.3 35.7 1.0
CA B:TYR256 4.3 27.7 1.0
CA B:MET268 4.3 36.2 1.0
N B:SER258 4.4 32.2 1.0
OG B:SER258 4.4 36.9 1.0
CA B:ASN257 4.4 34.6 1.0
CA B:MET267 4.4 36.9 1.0
CG B:GLU259 4.4 30.3 1.0
CB B:ASP273 4.5 30.9 1.0
C B:MET268 4.6 35.8 1.0
N B:ASN324 4.7 28.1 1.0
CB B:ASN324 4.7 29.0 1.0
CA B:ASN324 4.7 24.1 1.0
N B:ARG269 4.8 38.0 1.0
O B:ASN270 4.8 35.4 1.0
N B:ASN270 4.8 32.4 1.0
C B:ASN257 4.9 34.5 1.0
CB B:TYR256 4.9 27.9 1.0
CB B:ASN270 5.0 32.0 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: Sat Dec 12 07:30:55 2020

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