Calcium in PDB 4q5b: Tvnir in Complex with Sulfite, High Dose Data Set

The structure of Tvnir in Complex with Sulfite, High Dose Data Set, PDB code: 4q5b was solved by V.A.Lazarenko, K.M.Polyakov, A.A.Trofimov, A.N.Popov, T.V.Tikhonova, A.V.Tikhonov, V.O.Popov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.36 / 1.80
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	195.270, 195.270, 195.270, 90.00, 90.00, 90.00
R / Rfree (%)	15.2 / 16.5

The structure of Tvnir in Complex with Sulfite, High Dose Data Set also contains other interesting chemical elements:

Iron

(Fe)

16 atoms

The binding sites of Calcium atom in the Tvnir in Complex with Sulfite, High Dose Data Set (pdb code 4q5b). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Tvnir in Complex with Sulfite, High Dose Data Set, PDB code: 4q5b:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Tvnir in Complex with Sulfite, High Dose Data Set


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tvnir in Complex with Sulfite, High Dose Data Set within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca610 b:21.0 occ:1.00 OE1 A:GLN360 2.4 22.6 1.0 O A:LYS358 2.4 20.7 1.0 O A:TYR303 2.4 19.5 1.0 O A:HOH800 2.4 22.4 1.0 O A:HOH748 2.4 24.8 1.0 OE2 A:GLU302 2.4 22.8 1.0 OE1 A:GLU302 2.5 22.2 1.0 CD A:GLU302 2.8 21.7 1.0 CD A:GLN360 3.5 23.4 1.0 C A:TYR303 3.6 20.8 1.0 C A:LYS358 3.6 20.7 1.0 NE2 A:GLN360 4.0 26.9 1.0 N A:TYR303 4.0 18.5 1.0 CA A:LEU359 4.2 19.4 1.0 N A:LEU359 4.3 18.6 1.0 CG A:GLU302 4.4 20.6 1.0 OH A:TYR335 4.4 23.4 1.0 N A:GLN360 4.4 18.8 1.0 OD1 A:ASN304 4.4 34.5 1.0 CA A:TYR303 4.4 19.8 1.0 N A:ASN304 4.5 21.4 1.0 OD2 A:ASP346 4.5 28.2 1.0 OD1 A:ASP346 4.5 26.3 1.0 C A:LEU359 4.6 20.1 1.0 CA A:LYS358 4.6 20.6 1.0 CE1 A:PHE328 4.7 22.9 1.0 CA A:ASN304 4.7 22.3 1.0 CB A:LYS358 4.7 22.9 1.0 CG A:GLN360 4.7 21.2 1.0 CG A:ASP346 4.8 25.7 1.0 N A:LYS358 4.9 21.4 1.0 CB A:GLN360 4.9 20.2 1.0 C A:GLU302 5.0 18.9 1.0

Calcium binding site 2 out of 2 in the Tvnir in Complex with Sulfite, High Dose Data Set


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tvnir in Complex with Sulfite, High Dose Data Set within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca610 b:18.8 occ:1.00 O B:LYS358 2.3 18.5 1.0 OE1 B:GLN360 2.3 21.1 1.0 O B:TYR303 2.4 18.1 1.0 OE2 B:GLU302 2.4 19.2 1.0 O B:HOH824 2.4 19.2 1.0 OE1 B:GLU302 2.5 19.8 1.0 O B:HOH772 2.5 23.4 1.0 CD B:GLU302 2.8 18.9 1.0 CD B:GLN360 3.5 22.4 1.0 C B:LYS358 3.5 19.2 1.0 C B:TYR303 3.6 17.9 1.0 NE2 B:GLN360 4.0 26.5 1.0 N B:TYR303 4.0 17.5 1.0 CA B:LEU359 4.2 18.9 1.0 N B:LEU359 4.3 18.1 1.0 CG B:GLU302 4.4 18.7 1.0 N B:GLN360 4.4 17.6 1.0 OH B:TYR335 4.4 21.2 1.0 OD1 B:ASN304 4.4 37.1 1.0 CA B:TYR303 4.4 17.9 1.0 OD1 B:ASP346 4.5 24.2 1.0 N B:ASN304 4.5 18.9 1.0 OD2 B:ASP346 4.5 26.7 1.0 C B:LEU359 4.5 18.7 1.0 CA B:LYS358 4.5 18.9 1.0 CB B:LYS358 4.7 19.9 1.0 CA B:ASN304 4.7 21.4 1.0 CE2 B:PHE328 4.7 19.2 1.0 CG B:GLN360 4.7 21.1 1.0 N B:LYS358 4.8 19.4 1.0 CG B:ASP346 4.8 24.0 1.0 CB B:GLN360 4.9 19.5 1.0 C B:GLU302 5.0 18.4 1.0

V.A.Lazarenko, K.M.Polyakov, A.A.Trofimov, A.N.Popov, T.V.Tikhonova, A.V.Tikhonov, V.O.Popov. X-Ray-Induced Changes in the Active Site Structure of Octaheme Cytochrome C Nitrite Reductase and Its Substrate Complexes To Be Published.