Calcium in PDB 6qq5: Cryo-Em Structure of Dimeric Quinol Dependent Nitric Oxide Reductase (Qnor) From Alcaligenes Xylosoxidans

All present enzymatic activity of Cryo-Em Structure of Dimeric Quinol Dependent Nitric Oxide Reductase (Qnor) From Alcaligenes Xylosoxidans:
1.7.2.5;

The structure of Cryo-Em Structure of Dimeric Quinol Dependent Nitric Oxide Reductase (Qnor) From Alcaligenes Xylosoxidans also contains other interesting chemical elements:

Iron

(Fe)

6 atoms

The binding sites of Calcium atom in the Cryo-Em Structure of Dimeric Quinol Dependent Nitric Oxide Reductase (Qnor) From Alcaligenes Xylosoxidans (pdb code 6qq5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Cryo-Em Structure of Dimeric Quinol Dependent Nitric Oxide Reductase (Qnor) From Alcaligenes Xylosoxidans, PDB code: 6qq5:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Cryo-Em Structure of Dimeric Quinol Dependent Nitric Oxide Reductase (Qnor) From Alcaligenes Xylosoxidans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cryo-Em Structure of Dimeric Quinol Dependent Nitric Oxide Reductase (Qnor) From Alcaligenes Xylosoxidans within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca804 b:32.6 occ:1.00 O1D A:HEM801 2.3 40.1 1.0 O A:GLY76 2.4 25.9 1.0 OE2 A:GLU407 2.5 32.6 1.0 O2A A:HEM802 2.6 40.1 1.0 OH A:TYR78 2.6 23.9 1.0 O2D A:HEM801 2.7 40.1 1.0 CGD A:HEM801 2.8 40.1 1.0 OE1 A:GLU407 2.9 32.6 1.0 CD A:GLU407 3.0 32.6 1.0 CZ A:TYR78 3.3 23.9 1.0 CGA A:HEM802 3.5 40.1 1.0 C A:GLY76 3.5 25.9 1.0 O1A A:HEM802 3.8 40.1 1.0 NH2 A:ARG328 3.8 26.9 1.0 CE2 A:TYR78 3.9 23.9 1.0 CE1 A:TYR78 4.0 23.9 1.0 N A:GLY76 4.1 25.9 1.0 CA A:GLY76 4.2 25.9 1.0 CBD A:HEM801 4.3 40.1 1.0 CG A:GLU407 4.5 32.6 1.0 N A:ALA77 4.6 25.1 1.0 CE2 A:TYR408 4.7 40.1 1.0 CZ A:ARG328 4.8 26.9 1.0 CAD A:HEM801 4.8 40.1 1.0 OH A:TYR408 4.8 40.1 1.0 NH1 A:ARG328 4.8 26.9 1.0 CBA A:HEM802 4.9 40.1 1.0 CA A:ALA77 4.9 25.1 1.0

Calcium binding site 2 out of 2 in the Cryo-Em Structure of Dimeric Quinol Dependent Nitric Oxide Reductase (Qnor) From Alcaligenes Xylosoxidans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cryo-Em Structure of Dimeric Quinol Dependent Nitric Oxide Reductase (Qnor) From Alcaligenes Xylosoxidans within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca804 b:34.9 occ:1.00 O1D B:HEM801 2.3 40.1 1.0 O B:GLY76 2.4 25.9 1.0 OE2 B:GLU407 2.5 33.0 1.0 O2A B:HEM802 2.6 40.1 1.0 OH B:TYR78 2.6 24.8 1.0 O2D B:HEM801 2.7 40.1 1.0 CGD B:HEM801 2.8 40.1 1.0 OE1 B:GLU407 2.9 33.0 1.0 CD B:GLU407 3.0 33.0 1.0 CZ B:TYR78 3.3 24.8 1.0 CGA B:HEM802 3.5 40.1 1.0 C B:GLY76 3.5 25.9 1.0 O1A B:HEM802 3.7 40.1 1.0 NH2 B:ARG328 3.9 27.3 1.0 CE2 B:TYR78 4.0 24.8 1.0 CE1 B:TYR78 4.0 24.8 1.0 N B:GLY76 4.1 25.9 1.0 CA B:GLY76 4.2 25.9 1.0 CBD B:HEM801 4.3 40.1 1.0 CG B:GLU407 4.5 33.0 1.0 N B:ALA77 4.6 25.7 1.0 CE2 B:TYR408 4.7 40.1 1.0 CAD B:HEM801 4.8 40.1 1.0 NH1 B:ARG328 4.8 27.3 1.0 CZ B:ARG328 4.8 27.3 1.0 CBA B:HEM802 4.9 40.1 1.0 OH B:TYR408 4.9 40.1 1.0 CA B:ALA77 4.9 25.7 1.0

C.C.Gopalasingam, R.M.Johnson, G.N.Chiduza, T.Tosha, M.Yamamoto, Y.Shiro, S.V.Antonyuk, S.P.Muench, S.S.Hasnain. Dimeric Structures of Quinol-Dependent Nitric Oxide Reductases (Qnors) Revealed By Cryo-Electron Microscopy. Sci Adv V. 5 X1803 2019.
ISSN: ESSN 2375-2548
PubMed: 31489376
DOI: 10.1126/SCIADV.AAX1803