Calcium in PDB 4q0t: Free Form of Tvnir, Low Dose Data Set

The structure of Free Form of Tvnir, Low Dose Data Set, PDB code: 4q0t 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)	59.01 / 1.70
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	195.480, 195.480, 195.480, 90.00, 90.00, 90.00
R / Rfree (%)	15.8 / 17

The structure of Free Form of Tvnir, Low Dose Data Set also contains other interesting chemical elements:

Iron

(Fe)

16 atoms

The binding sites of Calcium atom in the Free Form of Tvnir, Low Dose Data Set (pdb code 4q0t). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Free Form of Tvnir, Low Dose Data Set, PDB code: 4q0t:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Free Form of Tvnir, Low 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 Free Form of Tvnir, Low Dose Data Set within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca609 b:18.3 occ:1.00 OE1 A:GLN360 2.3 22.3 1.0 O A:LYS358 2.3 16.7 1.0 OE2 A:GLU302 2.3 16.6 1.0 O A:TYR303 2.3 15.8 1.0 O A:HOH895 2.4 16.5 1.0 OE1 A:GLU302 2.4 15.9 1.0 O A:HOH894 2.6 17.6 1.0 CD A:GLU302 2.7 16.7 1.0 CD A:GLN360 3.5 21.9 1.0 C A:TYR303 3.5 15.7 1.0 C A:LYS358 3.5 15.5 1.0 N A:TYR303 3.9 14.5 1.0 NE2 A:GLN360 4.0 21.9 1.0 CA A:LEU359 4.2 14.5 1.0 OH A:TYR335 4.2 15.4 1.0 CG A:GLU302 4.3 16.1 1.0 OD1 A:ASN304 4.3 16.6 0.7 N A:GLN360 4.3 14.6 1.0 N A:LEU359 4.3 14.6 1.0 CA A:TYR303 4.4 15.6 1.0 OD1 A:ASP346 4.4 16.5 1.0 N A:ASN304 4.5 15.2 1.0 CE1 A:PHE328 4.5 17.4 1.0 OD2 A:ASP346 4.5 17.9 1.0 C A:LEU359 4.5 14.1 1.0 CA A:LYS358 4.6 14.9 1.0 CB A:LYS358 4.7 14.7 1.0 CA A:ASN304 4.7 16.1 1.0 CG A:GLN360 4.7 19.3 1.0 CG A:ASP346 4.8 16.0 1.0 N A:LYS358 4.8 15.5 1.0 CB A:GLN360 4.9 17.0 1.0 OD1 A:ASN304 4.9 16.3 0.3 C A:GLU302 4.9 14.9 1.0 CG A:LYS358 5.0 14.5 1.0

Calcium binding site 2 out of 2 in the Free Form of Tvnir, Low 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 Free Form of Tvnir, Low Dose Data Set within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca609 b:16.9 occ:1.00 OE1 B:GLN360 2.3 21.2 1.0 OE2 B:GLU302 2.3 14.0 1.0 O B:LYS358 2.3 13.6 1.0 O B:TYR303 2.4 14.1 1.0 O B:HOH921 2.4 15.9 1.0 OE1 B:GLU302 2.5 13.4 1.0 O B:HOH920 2.6 15.0 1.0 CD B:GLU302 2.8 12.9 1.0 CD B:GLN360 3.5 21.1 1.0 C B:TYR303 3.5 13.7 1.0 C B:LYS358 3.5 13.3 1.0 N B:TYR303 4.0 12.5 1.0 NE2 B:GLN360 4.1 20.6 1.0 CA B:LEU359 4.2 12.1 1.0 OH B:TYR335 4.3 13.9 1.0 CG B:GLU302 4.3 12.0 1.0 OD1 B:ASN304 4.3 14.4 0.5 N B:LEU359 4.3 12.3 1.0 OD1 B:ASP346 4.4 13.8 1.0 N B:GLN360 4.4 12.7 1.0 CA B:TYR303 4.4 13.6 1.0 OD2 B:ASP346 4.5 14.3 1.0 N B:ASN304 4.5 14.0 1.0 CE2 B:PHE328 4.5 13.6 1.0 C B:LEU359 4.5 12.2 1.0 CA B:LYS358 4.6 13.5 1.0 CB B:LYS358 4.7 13.2 1.0 CA B:ASN304 4.7 14.7 1.0 CG B:GLN360 4.7 18.3 1.0 CG B:ASP346 4.8 13.7 1.0 OD1 B:ASN304 4.8 18.9 0.5 CB B:GLN360 4.8 15.5 1.0 N B:LYS358 4.8 13.3 1.0 CG B:LYS358 4.9 12.2 1.0 C B:GLU302 5.0 12.6 1.0 CD1 B:TYR303 5.0 14.3 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.