Calcium in PDB 7vmk: Crystal Structure of Tubulin with 3

The structure of Crystal Structure of Tubulin with 3, PDB code: 7vmk was solved by Z.Jifa, T.Lun, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.73 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.831, 157.513, 182.187, 90, 90, 90
R / Rfree (%)	19.4 / 23.2

The structure of Crystal Structure of Tubulin with 3 also contains other interesting chemical elements:

Magnesium	(Mg)	4 atoms
Fluorine	(F)	3 atoms

The binding sites of Calcium atom in the Crystal Structure of Tubulin with 3 (pdb code 7vmk). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Tubulin with 3, PDB code: 7vmk:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Tubulin with 3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Tubulin with 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:54.6 occ:1.00 OD2 A:ASP39 2.3 58.6 1.0 OE2 A:GLU55 2.3 59.7 1.0 OG1 A:THR41 2.3 69.5 1.0 OD1 A:ASP39 2.4 49.6 1.0 O A:GLY44 2.5 58.2 1.0 CG A:ASP39 2.6 57.2 1.0 O A:THR41 2.7 57.5 1.0 CD A:GLU55 3.1 56.9 1.0 OE1 A:GLU55 3.2 58.9 1.0 CB A:THR41 3.5 56.1 1.0 C A:GLY44 3.6 53.2 1.0 C A:THR41 3.6 62.0 1.0 CA A:THR41 3.9 56.1 1.0 CA A:GLY45 4.1 60.9 1.0 OD2 A:ASP47 4.1 58.7 1.0 CB A:ASP39 4.1 51.7 1.0 N A:THR41 4.2 52.2 1.0 CZ A:PHE49 4.2 52.7 1.0 N A:GLY45 4.3 54.6 1.0 CG A:GLU55 4.5 50.4 1.0 N A:GLY44 4.5 57.9 1.0 CA A:GLY44 4.6 49.7 1.0 CG2 A:THR41 4.7 60.4 1.0 OD1 A:ASN50 4.7 50.7 1.0 ND2 A:ASN50 4.8 47.5 1.0 NE2 A:HIS61 4.8 54.4 1.0 N A:ILE42 4.8 56.0 1.0 CA A:ASP39 5.0 54.0 1.0 C A:ASP39 5.0 58.2 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Tubulin with 3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Tubulin with 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:110.2 occ:1.00 OD2 E:ASP44 3.6 74.8 1.0 OG A:SER158 4.0 45.9 1.0 NZ A:LYS166 4.1 35.1 1.0 O A:GLU196 4.2 48.4 1.0 OD1 A:ASP199 4.6 41.8 1.0 CA A:HIS197 4.7 38.8 1.0 CG E:ASP44 4.7 75.3 1.0 O A:HIS197 4.8 33.7 1.0 CB A:SER158 4.8 35.7 1.0 O A:GLY162 4.8 50.9 1.0 C A:HIS197 4.9 34.2 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Tubulin with 3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Tubulin with 3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:91.1 occ:1.00 OE1 B:GLU111 2.5 68.2 1.0 CD B:GLU111 3.6 70.7 1.0 OE2 B:GLU111 3.9 77.8 1.0 OE1 B:GLU108 4.1 49.7 1.0 OE2 B:GLU108 4.8 49.2 1.0 CG B:GLU111 4.8 46.8 1.0 CD B:GLU108 4.8 46.8 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Tubulin with 3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Tubulin with 3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:43.3 occ:1.00 OE2 C:GLU55 1.9 50.3 1.0 OD2 C:ASP39 2.1 43.4 1.0 OG1 C:THR41 2.1 53.6 1.0 O C:GLY44 2.6 48.4 1.0 OD1 C:ASP39 2.7 49.7 1.0 CG C:ASP39 2.7 45.9 1.0 CD C:GLU55 2.9 43.4 1.0 O C:THR41 3.1 53.7 1.0 OE1 C:GLU55 3.1 44.2 1.0 C C:GLY44 3.4 45.4 1.0 OD2 C:ASP47 3.5 53.2 1.0 CB C:THR41 3.6 43.0 1.0 CA C:GLY45 3.7 35.6 1.0 OD1 C:ASN50 3.8 33.4 1.0 N C:GLY45 3.9 36.2 1.0 C C:THR41 4.0 43.5 1.0 CZ C:PHE49 4.2 36.2 1.0 CB C:ASP39 4.2 35.3 1.0 CA C:THR41 4.3 37.6 1.0 CG C:GLU55 4.3 33.9 1.0 CE1 C:PHE49 4.4 35.6 1.0 CG2 C:THR41 4.5 43.0 1.0 N C:THR41 4.5 42.0 1.0 ND2 C:ASN50 4.6 28.3 1.0 CG C:ASN50 4.6 27.8 1.0 CA C:GLY44 4.6 42.7 1.0 CG C:ASP47 4.6 40.2 1.0 C C:GLY45 4.7 42.6 1.0 N C:GLY44 4.8 40.4 1.0 NE2 C:HIS61 5.0 40.1 1.0

Z.Jifa, T.Lun. Crystal Structure of Tubulin with 3 To Be Published.