Calcium in PDB 5zl1: Hexameric Structure of Copper-Containing Nitrite Reductase of An Anammox Organism Ksu-1

The structure of Hexameric Structure of Copper-Containing Nitrite Reductase of An Anammox Organism Ksu-1, PDB code: 5zl1 was solved by D.Hira, M.Matsumura, R.Kitamura, T.Fujii, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 3.20
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	270.217, 270.217, 128.909, 90.00, 90.00, 120.00
R / Rfree (%)	24 / 25.4

The structure of Hexameric Structure of Copper-Containing Nitrite Reductase of An Anammox Organism Ksu-1 also contains other interesting chemical elements:

Copper

(Cu)

9 atoms

The binding sites of Calcium atom in the Hexameric Structure of Copper-Containing Nitrite Reductase of An Anammox Organism Ksu-1 (pdb code 5zl1). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Hexameric Structure of Copper-Containing Nitrite Reductase of An Anammox Organism Ksu-1, PDB code: 5zl1:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Hexameric Structure of Copper-Containing Nitrite Reductase of An Anammox Organism Ksu-1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Hexameric Structure of Copper-Containing Nitrite Reductase of An Anammox Organism Ksu-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:42.4 occ:1.00 O A:PRO272 2.3 44.7 1.0 O A:ALA292 2.3 36.9 1.0 O A:ALA143 2.3 38.9 1.0 C A:PRO272 3.3 45.1 1.0 C A:ALA292 3.5 34.5 1.0 C A:ALA143 3.6 37.1 1.0 CA A:GLY273 3.9 47.7 1.0 N A:ALA292 4.0 33.6 1.0 N A:GLY273 4.0 46.1 1.0 CA A:PRO272 4.2 44.5 1.0 CA A:ALA292 4.2 34.1 1.0 CA A:ALA143 4.4 36.9 1.0 N A:ALA143 4.5 36.9 1.0 N A:ALA293 4.5 34.3 1.0 N A:TYR144 4.5 36.7 1.0 CB A:PRO272 4.5 44.6 1.0 CB A:ALA143 4.6 36.9 1.0 CA A:TYR144 4.6 36.3 1.0 CB A:ALA292 4.7 34.1 1.0 CA A:ALA293 4.7 34.0 1.0

Calcium binding site 2 out of 4 in the Hexameric Structure of Copper-Containing Nitrite Reductase of An Anammox Organism Ksu-1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Hexameric Structure of Copper-Containing Nitrite Reductase of An Anammox Organism Ksu-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca404 b:49.2 occ:1.00 O B:ALA292 2.3 44.0 1.0 O B:ALA143 2.3 46.4 1.0 O B:PRO272 2.3 50.9 1.0 OE2 C:GLU283 2.4 49.2 1.0 O C:HOH504 2.4 36.2 1.0 C B:PRO272 3.4 50.6 1.0 CD C:GLU283 3.4 48.4 1.0 C B:ALA292 3.5 41.7 1.0 C B:ALA143 3.6 45.4 1.0 OE1 C:GLU282 3.8 51.0 1.0 N B:ALA292 3.9 41.5 1.0 CG C:GLU283 4.0 48.0 1.0 CA B:GLY273 4.0 53.0 1.0 N B:GLY273 4.1 51.7 1.0 CA B:ALA292 4.2 41.9 1.0 CA B:PRO272 4.3 49.8 1.0 OE1 C:GLU283 4.4 48.6 1.0 CA B:ALA143 4.5 45.5 1.0 N B:TYR144 4.5 45.2 1.0 N B:ALA293 4.5 40.9 1.0 N B:ALA143 4.5 45.6 1.0 CA B:TYR144 4.5 45.1 1.0 CB B:PRO272 4.5 49.8 1.0 CB B:ALA143 4.6 45.6 1.0 CB B:ALA292 4.6 42.1 1.0 CA B:ALA293 4.8 40.2 1.0 CB C:GLU283 4.8 47.6 1.0 N C:GLU283 4.9 47.5 1.0 O C:ASN281 4.9 48.2 1.0 C B:SER291 5.0 41.2 1.0 CD C:GLU282 5.0 50.4 1.0

Calcium binding site 3 out of 4 in the Hexameric Structure of Copper-Containing Nitrite Reductase of An Anammox Organism Ksu-1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Hexameric Structure of Copper-Containing Nitrite Reductase of An Anammox Organism Ksu-1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca403 b:56.7 occ:1.00 O C:PRO272 2.3 56.7 1.0 O C:ALA143 2.3 54.3 1.0 OE2 D:GLU283 2.3 56.7 1.0 O C:ALA292 2.3 49.6 1.0 CD D:GLU283 3.3 55.8 1.0 C C:PRO272 3.5 56.1 1.0 C C:ALA292 3.5 46.4 1.0 C C:ALA143 3.6 53.9 1.0 OE1 D:GLU282 3.8 63.7 1.0 N C:ALA292 3.8 44.5 1.0 CG D:GLU283 3.9 55.7 1.0 CA C:ALA292 4.1 45.8 1.0 CA C:PRO272 4.3 55.0 1.0 OE1 D:GLU283 4.3 55.1 1.0 N C:GLY273 4.4 57.2 1.0 N C:TYR144 4.4 53.7 1.0 CA C:GLY273 4.4 58.1 1.0 CA C:TYR144 4.5 53.2 1.0 CA C:ALA143 4.5 54.0 1.0 N C:ALA293 4.5 46.0 1.0 CB C:PRO272 4.6 54.7 1.0 N C:ALA143 4.6 54.7 1.0 CB C:ALA292 4.6 46.0 1.0 CB C:ALA143 4.6 54.2 1.0 CB D:GLU283 4.7 55.5 1.0 N D:GLU283 4.8 55.7 1.0 CA C:ALA293 4.8 45.5 1.0 C C:SER291 4.9 43.4 1.0 O D:ASN281 4.9 57.3 1.0 CD D:GLU282 5.0 62.0 1.0 CD2 C:TYR144 5.0 51.1 1.0

Calcium binding site 4 out of 4 in the Hexameric Structure of Copper-Containing Nitrite Reductase of An Anammox Organism Ksu-1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Hexameric Structure of Copper-Containing Nitrite Reductase of An Anammox Organism Ksu-1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca403 b:53.1 occ:1.00 O D:PRO272 2.3 54.0 1.0 OE2 B:GLU283 2.3 50.4 1.0 O D:ALA143 2.3 53.2 1.0 O D:ALA292 2.3 50.5 1.0 C D:PRO272 3.3 53.8 1.0 CD B:GLU283 3.3 49.6 1.0 C D:ALA292 3.4 48.3 1.0 C D:ALA143 3.5 52.8 1.0 N D:ALA292 3.7 47.6 1.0 OE1 B:GLU282 3.8 51.2 1.0 CG B:GLU283 3.9 49.2 1.0 N D:GLY273 3.9 54.6 1.0 CA D:ALA292 4.1 47.8 1.0 OE1 B:GLU283 4.3 50.1 1.0 CA D:TYR144 4.4 52.3 1.0 CA D:PRO272 4.4 53.3 1.0 N D:TYR144 4.4 52.3 1.0 CB D:ALA292 4.5 47.7 1.0 CA D:ALA143 4.5 53.0 1.0 N D:ALA293 4.5 48.0 1.0 CB D:PRO272 4.7 53.1 1.0 N D:ALA143 4.7 53.0 1.0 CB B:GLU283 4.7 48.5 1.0 CB D:ALA143 4.7 53.2 1.0 C D:SER291 4.8 47.3 1.0 N B:GLU283 4.8 48.2 1.0 CA D:ALA293 4.9 48.2 1.0 CD2 D:TYR144 4.9 51.7 1.0 CB D:SER291 4.9 46.7 1.0 CA D:SER291 4.9 46.9 1.0 O B:ASN281 5.0 50.5 1.0

D.Hira, M.Matsumura, R.Kitamura, T.Fujii. Hexameric Structure of Copper-Containing Nitrite Reductase of An Anammox Organism Ksu-1 To Be Published.