Calcium in PDB 5i5m: Shewanella Denitrificans Nitrous Oxide Reductase, CA2+-Reconstituted Form

All present enzymatic activity of Shewanella Denitrificans Nitrous Oxide Reductase, CA2+-Reconstituted Form:
1.7.2.4;

The structure of Shewanella Denitrificans Nitrous Oxide Reductase, CA2+-Reconstituted Form, PDB code: 5i5m was solved by L.K.Schneider, O.Einsle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	157.52 / 1.37
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	124.756, 56.978, 163.524, 90.00, 105.58, 90.00
R / Rfree (%)	16.3 / 18.1

The binding sites of Calcium atom in the Shewanella Denitrificans Nitrous Oxide Reductase, CA2+-Reconstituted Form (pdb code 5i5m). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Shewanella Denitrificans Nitrous Oxide Reductase, CA2+-Reconstituted Form, PDB code: 5i5m:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Shewanella Denitrificans Nitrous Oxide Reductase, CA2+-Reconstituted Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Shewanella Denitrificans Nitrous Oxide Reductase, CA2+-Reconstituted Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:5.4 occ:1.00 O A:TYR252 2.3 5.9 1.0 O A:HOH1209 2.3 6.9 1.0 O A:MET263 2.3 6.8 1.0 OE2 A:GLU255 2.4 6.4 1.0 OD2 A:ASP269 2.5 5.6 1.0 OD1 A:ASP269 2.5 5.5 1.0 OE1 A:GLU255 2.6 6.8 1.0 CD A:GLU255 2.9 6.9 1.0 CG A:ASP269 2.9 5.6 1.0 OG A:SER316 2.9 5.5 1.0 C A:MET263 3.5 7.6 1.0 C A:TYR252 3.5 5.8 1.0 O B:HOH1135 4.0 8.0 1.0 CB A:SER316 4.1 5.3 1.0 CA A:ILE264 4.2 8.9 1.0 N A:ILE264 4.2 8.2 1.0 N A:ASN253 4.3 6.1 1.0 CA A:SER316 4.3 5.3 1.0 CA A:ASN253 4.3 6.4 1.0 CB A:ASP269 4.4 5.6 1.0 CG A:GLU255 4.4 7.0 1.0 CA A:TYR252 4.4 5.6 1.0 N A:SER316 4.4 5.3 1.0 CA A:MET263 4.5 7.5 1.0 N A:SER254 4.5 6.5 1.0 CB A:ALA266 4.6 8.5 1.0 O A:ALA266 4.6 8.6 1.0 N A:ALA266 4.7 9.0 1.0 C A:ILE264 4.7 9.4 1.0 OG A:SER254 4.8 6.5 1.0 N A:THR265 4.9 9.6 1.0 C A:ASN253 4.9 6.6 1.0

Calcium binding site 2 out of 2 in the Shewanella Denitrificans Nitrous Oxide Reductase, CA2+-Reconstituted Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Shewanella Denitrificans Nitrous Oxide Reductase, CA2+-Reconstituted Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1001 b:7.5 occ:1.00 O B:TYR252 2.3 7.4 1.0 O B:MET263 2.3 8.9 1.0 OE2 B:GLU255 2.5 8.3 1.0 O B:HOH1145 2.5 7.9 1.0 OD1 B:ASP269 2.5 7.5 1.0 OE1 B:GLU255 2.6 8.2 1.0 OD2 B:ASP269 2.6 8.1 1.0 OG B:SER316 2.9 7.3 1.0 CD B:GLU255 2.9 8.3 1.0 CG B:ASP269 2.9 7.9 1.0 C B:TYR252 3.4 7.2 1.0 C B:MET263 3.5 9.5 1.0 O A:HOH1129 4.0 10.2 1.0 CB B:SER316 4.1 7.2 1.0 N B:ASN253 4.2 7.5 1.0 CA B:ILE264 4.2 10.8 1.0 CA B:ASN253 4.3 7.8 1.0 N B:ILE264 4.3 10.2 1.0 CA B:SER316 4.3 7.2 1.0 CG B:GLU255 4.4 8.7 1.0 N B:SER254 4.4 8.7 1.0 CB B:ASP269 4.4 7.9 1.0 CA B:TYR252 4.4 6.9 1.0 N B:SER316 4.4 7.3 1.0 CA B:MET263 4.5 9.4 1.0 CB B:ALA266 4.6 12.2 1.0 O B:ALA266 4.6 11.6 1.0 N B:ALA266 4.7 12.8 1.0 OG B:SER254 4.7 8.9 1.0 C B:ILE264 4.8 11.6 1.0 C B:ASN253 4.9 8.2 1.0 N B:THR265 4.9 12.3 1.0

L.K.Schneider, O.Einsle. Role of Calcium in Secondary Structure Stabilization During Maturation of Nitrous Oxide Reductase. Biochemistry V. 55 1433 2016.
ISSN: ISSN 0006-2960
PubMed: 26885878
DOI: 10.1021/ACS.BIOCHEM.5B01278