Calcium in PDB 3b3d: B.Subtilis Ytbe

The structure of B.Subtilis Ytbe, PDB code: 3b3d was solved by Y.F.Zhou, L.F.Li, Y.H.Liang, X.-D.Su, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	83.106, 89.170, 115.687, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 26

The binding sites of Calcium atom in the B.Subtilis Ytbe (pdb code 3b3d). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the B.Subtilis Ytbe, PDB code: 3b3d:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the B.Subtilis Ytbe


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of B.Subtilis Ytbe within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca281 b:23.6 occ:1.00 O A:HOH361 2.9 22.0 1.0 N A:LYS236 3.2 20.0 1.0 N A:LEU196 3.5 27.0 1.0 CD A:PRO195 3.7 24.9 1.0 CA A:PRO235 3.7 22.9 1.0 CA A:SER194 3.7 26.8 1.0 N A:PRO195 3.7 25.6 1.0 C A:SER194 3.7 26.1 1.0 CB A:LEU196 3.8 27.2 1.0 CD A:LYS236 3.8 20.0 1.0 C A:PRO235 3.9 24.1 1.0 CB A:LYS236 4.1 20.0 1.0 CA A:LEU196 4.1 28.2 1.0 CA A:LYS236 4.1 20.0 1.0 CG A:PRO195 4.1 25.4 1.0 CG A:LEU196 4.2 26.1 1.0 CB A:PRO235 4.2 22.2 1.0 N A:MET197 4.3 31.1 1.0 O A:LYS236 4.4 25.9 1.0 CG A:LYS236 4.4 20.0 1.0 O A:SER194 4.4 25.3 1.0 CB A:SER194 4.5 26.9 1.0 C A:PRO195 4.5 26.1 1.0 C A:LEU196 4.6 28.9 1.0 CA A:PRO195 4.6 25.4 1.0 N A:SER194 4.6 26.6 1.0 OG A:SER194 4.7 30.0 1.0 CD1 A:LEU196 4.7 25.5 1.0 C A:LYS236 4.8 20.0 1.0 O A:ILE234 4.8 23.7 1.0 N A:PRO235 4.9 23.4 1.0 O A:HOH329 4.9 19.8 1.0 CB A:PRO195 5.0 24.5 1.0

Calcium binding site 2 out of 4 in the B.Subtilis Ytbe


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of B.Subtilis Ytbe within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca282 b:51.1 occ:1.00 OD2 A:ASP88 4.4 27.2 1.0 OD1 A:ASP88 4.8 20.7 1.0

Calcium binding site 3 out of 4 in the B.Subtilis Ytbe


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of B.Subtilis Ytbe within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca281 b:32.0 occ:1.00 O B:HOH314 2.4 16.1 1.0 N B:LYS236 3.4 29.1 0.5 N B:LYS236 3.4 29.1 0.5 N B:LEU196 3.5 29.1 1.0 CD B:LYS236 3.6 39.5 0.5 CD B:PRO195 3.6 25.5 1.0 N B:PRO195 3.7 26.9 1.0 CA B:PRO235 3.8 27.0 1.0 CG B:PRO195 3.8 27.2 1.0 CB B:LEU196 3.8 29.6 1.0 C B:SER194 3.9 26.7 1.0 CA B:SER194 3.9 27.6 1.0 CG B:LYS236 4.0 35.5 0.5 CG B:LEU196 4.0 30.1 1.0 C B:PRO235 4.1 27.8 1.0 CB B:LYS236 4.1 31.6 0.5 CD B:LYS236 4.2 39.5 0.5 CA B:LEU196 4.2 29.8 1.0 CD1 B:LEU196 4.3 26.9 1.0 CA B:LYS236 4.3 31.0 0.5 CB B:LYS236 4.3 31.6 0.5 CE B:LYS236 4.3 34.8 0.5 CB B:PRO235 4.3 26.8 1.0 CA B:LYS236 4.3 31.0 0.5 CG B:LYS236 4.3 35.5 0.5 O B:LYS236 4.4 32.9 0.5 C B:PRO195 4.5 28.2 1.0 O B:LYS236 4.5 32.9 0.5 CA B:PRO195 4.5 27.4 1.0 O B:SER194 4.6 26.1 1.0 CB B:PRO195 4.8 28.1 1.0 C B:LYS236 4.8 31.3 0.5 N B:SER194 4.8 28.1 1.0 C B:LEU196 4.8 30.4 1.0 C B:LYS236 4.8 31.3 0.5 CB B:SER194 4.9 28.6 1.0 N B:PRO235 4.9 26.2 1.0 OG B:SER194 5.0 31.1 1.0 O B:ILE234 5.0 25.1 1.0

Calcium binding site 4 out of 4 in the B.Subtilis Ytbe


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of B.Subtilis Ytbe within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca281 b:25.2 occ:1.00 O C:HOH399 2.9 30.7 1.0 N C:LYS236 3.1 23.1 0.5 N C:LYS236 3.1 22.9 0.5 N C:LEU196 3.4 28.6 1.0 CD C:PRO195 3.5 25.6 1.0 CA C:SER194 3.6 28.0 1.0 N C:PRO195 3.6 26.7 1.0 C C:SER194 3.7 26.8 1.0 CA C:PRO235 3.7 22.7 1.0 CG C:PRO195 3.7 26.7 1.0 CB C:LEU196 3.7 29.8 1.0 CB C:LYS236 3.8 24.2 0.5 C C:PRO235 3.9 22.8 1.0 CB C:LYS236 4.0 23.9 0.5 CA C:LYS236 4.0 23.6 0.5 CA C:LEU196 4.1 29.9 1.0 CA C:LYS236 4.1 23.2 0.5 CG C:LEU196 4.2 28.0 1.0 NZ C:LYS236 4.2 27.4 0.5 CG C:LYS236 4.3 24.1 0.5 CD C:LYS236 4.4 24.5 0.5 CB C:PRO235 4.4 21.5 1.0 C C:PRO195 4.4 27.2 1.0 O C:SER194 4.4 26.3 1.0 N C:MET197 4.4 33.8 0.5 O C:LYS236 4.5 23.8 0.5 CG C:LYS236 4.5 25.2 0.5 CA C:PRO195 4.5 27.0 1.0 CB C:SER194 4.5 27.8 1.0 N C:SER194 4.5 28.8 1.0 N C:MET197 4.5 33.8 0.5 C C:LEU196 4.6 31.4 1.0 O C:LYS236 4.6 22.9 0.5 O C:HOH365 4.6 22.0 1.0 CD1 C:LEU196 4.6 24.2 1.0 O C:ILE234 4.7 24.6 1.0 CB C:PRO195 4.7 27.7 1.0 C C:LYS236 4.8 23.6 0.5 CD C:LYS236 4.8 23.2 0.5 C C:LYS236 4.8 23.1 0.5 N C:PRO235 4.9 22.4 1.0 CE C:LYS236 4.9 26.3 0.5

J.Lei, Y.F.Zhou, L.F.Li, X.-D.Su. Structural and Biochemical Analyses of Yvgn and Ytbe From Bacillus Subtilis Protein Sci. V. 18 1792 2009.
ISSN: ISSN 0961-8368
PubMed: 19585557
DOI: 10.1002/PRO.178