Calcium in PDB 3ojc: Crystal Structure of A Putative Asp/Glu Racemase From Yersinia Pestis

The structure of Crystal Structure of A Putative Asp/Glu Racemase From Yersinia Pestis, PDB code: 3ojc was solved by S.M.Anderson, Z.Wawrzak, M.Kudritska, K.Kwon, W.F.Anderson, A.Savchenko, Center For Structural Genomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.77 / 1.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	66.520, 95.410, 142.620, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 20.2

The binding sites of Calcium atom in the Crystal Structure of A Putative Asp/Glu Racemase From Yersinia Pestis (pdb code 3ojc). 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 A Putative Asp/Glu Racemase From Yersinia Pestis, PDB code: 3ojc:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of A Putative Asp/Glu Racemase From Yersinia Pestis


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 A Putative Asp/Glu Racemase From Yersinia Pestis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca232 b:27.5 occ:1.00 O A:HOH291 2.8 38.2 1.0 OG1 A:THR129 3.0 24.9 1.0 N A:THR126 3.1 16.5 1.0 C A:GLY197 3.4 15.3 1.0 CB A:THR129 3.4 23.4 1.0 O A:GLY197 3.5 16.8 1.0 CA A:GLY125 3.5 12.0 1.0 CB A:CYS198 3.6 17.7 1.0 OG1 A:THR126 3.7 23.4 1.0 N A:CYS198 3.8 15.6 1.0 SG A:CYS198 3.8 19.6 1.0 CG2 A:THR129 3.8 31.4 1.0 C A:GLY125 3.8 13.8 1.0 CA A:GLY197 3.9 14.0 1.0 CG2 A:THR126 3.9 26.9 1.0 CB A:THR126 4.2 23.8 1.0 ND2 A:ASN85 4.2 48.6 1.0 CA A:THR126 4.2 20.8 1.0 CA A:CYS198 4.2 13.3 1.0 O A:HOH619 4.6 37.0 1.0 O A:THR126 4.8 20.1 1.0 N A:GLY197 4.9 12.7 1.0 CG A:ASN85 4.9 47.6 1.0 CA A:THR129 4.9 21.7 1.0 N A:GLY125 4.9 13.3 1.0 O A:LEU124 5.0 17.0 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of A Putative Asp/Glu Racemase From Yersinia Pestis


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 A Putative Asp/Glu Racemase From Yersinia Pestis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca233 b:35.5 occ:1.00 O A:HOH387 2.8 49.0 1.0 O A:HOH299 3.2 28.9 1.0 N A:VAL214 3.3 13.5 1.0 CA A:PRO213 3.5 17.2 1.0 CG2 A:VAL214 3.9 26.3 1.0 C A:PRO213 4.0 16.4 1.0 CB A:ALA207 4.0 22.3 1.0 CB A:PRO213 4.1 16.4 1.0 O A:VAL214 4.2 14.1 1.0 O A:HOH292 4.3 36.6 1.0 CA A:VAL214 4.4 13.2 1.0 CB A:VAL214 4.7 16.2 1.0 O A:VAL212 4.7 15.7 1.0 N A:PRO213 4.7 16.8 1.0 C A:VAL214 4.8 10.8 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of A Putative Asp/Glu Racemase From Yersinia Pestis


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 A Putative Asp/Glu Racemase From Yersinia Pestis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca234 b:27.0 occ:1.00 O A:HOH646 2.3 32.2 1.0 O A:GLY144 2.3 20.1 1.0 O A:HOH620 2.4 18.4 1.0 O A:HOH479 2.4 23.3 1.0 OD1 A:ASP119 2.5 21.7 1.0 OD2 A:ASP119 2.5 24.0 1.0 O A:HOH253 2.7 28.8 1.0 CG A:ASP119 2.8 21.1 1.0 C A:GLY144 3.5 20.0 1.0 O A:HOH702 3.6 21.1 1.0 O A:HOH535 3.9 54.2 1.0 CA A:GLY144 4.2 20.6 1.0 CB A:ASP119 4.3 18.7 1.0 O A:HOH302 4.4 27.3 1.0 N A:ILE145 4.5 16.4 1.0 O A:ASP119 4.6 22.4 1.0 CA A:ILE145 4.7 18.9 1.0 O A:HOH583 4.7 34.6 1.0 O A:HOH274 4.8 28.5 1.0 O A:HOH580 4.8 45.9 1.0 O A:HOH529 4.9 43.8 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of A Putative Asp/Glu Racemase From Yersinia Pestis


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 A Putative Asp/Glu Racemase From Yersinia Pestis within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca232 b:22.8 occ:1.00 OG1 B:THR129 3.0 18.2 1.0 O B:HOH306 3.1 19.0 1.0 N B:THR126 3.2 13.3 1.0 CB B:THR129 3.5 13.9 1.0 CA B:GLY125 3.6 12.7 1.0 C B:GLY197 3.6 13.4 1.0 O B:GLY197 3.7 16.1 1.0 CG2 B:THR129 3.8 14.8 1.0 OG1 B:THR126 3.8 18.0 1.0 CG2 B:THR126 3.8 14.9 1.0 CA B:GLY197 3.9 12.6 1.0 C B:GLY125 3.9 13.1 1.0 CB B:CYS198 3.9 22.9 1.0 SG B:CYS198 4.0 20.9 1.0 CB B:ASN85 4.0 13.7 1.0 N B:CYS198 4.0 10.3 1.0 OG1 B:THR86 4.1 10.1 0.5 CB B:THR126 4.2 11.2 1.0 CA B:THR126 4.3 12.9 1.0 ND2 B:ASN85 4.3 18.3 1.0 CG B:ASN85 4.4 20.7 1.0 CA B:CYS198 4.5 15.2 1.0 N B:THR86 4.8 17.4 1.0 CA B:THR129 4.9 13.1 1.0 N B:GLY125 5.0 11.9 1.0 N B:GLY197 5.0 11.2 1.0 O B:THR126 5.0 14.2 1.0

S.M.Anderson, Z.Wawrzak, M.Kudritska, K.Kwon, W.F.Anderson, A.Savchenko, Center For Structural Genomics Of Infectiousdiseases (Csgid). Crystal Structure of A Putative Asp/Glu Racemase From Yersinia Pestis To Be Published.