Calcium in PDB 8bgw: Cryoem Structure of Quinol-Dependent Nitric Oxide Reductase (Qnor) From Alcaligenes Xylosoxidans at 2.2 A Resolution

All present enzymatic activity of Cryoem Structure of Quinol-Dependent Nitric Oxide Reductase (Qnor) From Alcaligenes Xylosoxidans at 2.2 A Resolution:
1.7.2.5;

The structure of Cryoem Structure of Quinol-Dependent Nitric Oxide Reductase (Qnor) From Alcaligenes Xylosoxidans at 2.2 A Resolution also contains other interesting chemical elements:

Iron

(Fe)

6 atoms

The binding sites of Calcium atom in the Cryoem Structure of Quinol-Dependent Nitric Oxide Reductase (Qnor) From Alcaligenes Xylosoxidans at 2.2 A Resolution (pdb code 8bgw). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Cryoem Structure of Quinol-Dependent Nitric Oxide Reductase (Qnor) From Alcaligenes Xylosoxidans at 2.2 A Resolution, PDB code: 8bgw:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Cryoem Structure of Quinol-Dependent Nitric Oxide Reductase (Qnor) From Alcaligenes Xylosoxidans at 2.2 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cryoem Structure of Quinol-Dependent Nitric Oxide Reductase (Qnor) From Alcaligenes Xylosoxidans at 2.2 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca804 b:32.7 occ:1.00 OE2 A:GLU407 2.1 36.8 1.0 O1D A:HEM801 2.2 38.4 1.0 OE1 A:GLU407 2.2 33.3 1.0 O A:HOH963 2.3 28.3 1.0 O2A A:HEM802 2.3 39.4 1.0 O A:GLY76 2.3 30.8 1.0 OH A:TYR78 2.5 45.1 1.0 CD A:GLU407 2.5 33.0 1.0 C A:GLY76 3.3 25.1 1.0 CZ A:TYR78 3.3 41.4 1.0 CGD A:HEM801 3.3 40.2 1.0 CGA A:HEM802 3.3 38.3 1.0 O1A A:HEM802 3.5 37.2 1.0 N A:GLY76 3.6 27.7 1.0 CA A:GLY76 3.7 23.5 1.0 O2D A:HEM801 3.7 45.9 1.0 NH2 A:ARG328 3.7 28.4 1.0 O A:HOH903 3.9 37.3 1.0 CE2 A:TYR78 4.0 37.9 1.0 CG A:GLU407 4.0 38.6 1.0 CE1 A:TYR78 4.0 44.3 1.0 OH A:TYR408 4.0 43.0 1.0 O A:HOH967 4.1 36.3 1.0 NH1 A:ARG328 4.4 26.7 1.0 N A:ALA77 4.5 31.0 1.0 CZ A:ARG328 4.5 27.2 1.0 CBD A:HEM801 4.6 36.9 1.0 CE2 A:TYR408 4.6 34.9 1.0 CBA A:HEM802 4.6 38.6 1.0 CZ A:TYR408 4.7 35.4 1.0 CB A:GLU407 4.8 37.2 1.0 C A:HIS75 4.8 31.2 1.0 CAA A:HEM802 4.8 42.0 1.0 CAD A:HEM801 4.8 33.9 1.0 CG2 A:THR626 4.9 40.1 1.0 CA A:ALA77 4.9 29.3 1.0

Calcium binding site 2 out of 2 in the Cryoem Structure of Quinol-Dependent Nitric Oxide Reductase (Qnor) From Alcaligenes Xylosoxidans at 2.2 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cryoem Structure of Quinol-Dependent Nitric Oxide Reductase (Qnor) From Alcaligenes Xylosoxidans at 2.2 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca805 b:32.6 occ:1.00 OE2 B:GLU407 2.1 36.7 1.0 O1D B:HEM802 2.2 38.3 1.0 OE1 B:GLU407 2.2 33.1 1.0 O B:HOH958 2.3 28.1 1.0 O2A B:HEM803 2.3 39.3 1.0 O B:GLY76 2.3 30.9 1.0 OH B:TYR78 2.5 45.0 1.0 CD B:GLU407 2.5 33.0 1.0 C B:GLY76 3.3 25.1 1.0 CZ B:TYR78 3.3 41.5 1.0 CGD B:HEM802 3.3 40.3 1.0 CGA B:HEM803 3.3 38.4 1.0 O1A B:HEM803 3.5 37.0 1.0 N B:GLY76 3.6 27.8 1.0 CA B:GLY76 3.7 23.5 1.0 O2D B:HEM802 3.7 45.7 1.0 NH2 B:ARG328 3.7 28.5 1.0 O B:HOH902 3.9 37.6 1.0 CE2 B:TYR78 4.0 37.8 1.0 CG B:GLU407 4.0 38.8 1.0 CE1 B:TYR78 4.0 44.3 1.0 OH B:TYR408 4.0 43.0 1.0 O B:HOH951 4.1 36.0 1.0 NH1 B:ARG328 4.4 26.7 1.0 N B:ALA77 4.5 31.0 1.0 CZ B:ARG328 4.5 27.2 1.0 CBD B:HEM802 4.6 36.8 1.0 CE2 B:TYR408 4.6 34.9 1.0 CBA B:HEM803 4.6 38.6 1.0 CZ B:TYR408 4.7 35.4 1.0 CB B:GLU407 4.8 37.4 1.0 C B:HIS75 4.8 31.3 1.0 CAA B:HEM803 4.8 41.9 1.0 CAD B:HEM802 4.8 33.9 1.0 CG2 B:THR626 4.9 40.4 1.0 CA B:ALA77 4.9 29.4 1.0

A.J.Flynn, S.V.Antonyuk, R.R.Eady, S.P.Muench, S.S.Hasnain. A 2.2 Angstrom Cryoem Structure of A Quinol-Dependent No Reductase Shows Close Similarity to Respiratory Oxidases. Nat Commun V. 14 3416 2023.
ISSN: ESSN 2041-1723
PubMed: 37296134
DOI: 10.1038/S41467-023-39140-X