Calcium in PDB 7thw: Crystal Structure of the Soluble Domain of the Putative Ompa -Family Membrane Protein YPO0514 From Yersinia Pestis

The structure of Crystal Structure of the Soluble Domain of the Putative Ompa -Family Membrane Protein YPO0514 From Yersinia Pestis, PDB code: 7thw was solved by Y.Kim, C.Tesar, G.Chhor, S.Clancy, G.Babnigg, O.Schneewind, A.Joachimiak, 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)	49.59 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.861, 123.099, 54.183, 90, 89.97, 90
R / Rfree (%)	22.6 / 26.9

The binding sites of Calcium atom in the Crystal Structure of the Soluble Domain of the Putative Ompa -Family Membrane Protein YPO0514 From Yersinia Pestis (pdb code 7thw). 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 the Soluble Domain of the Putative Ompa -Family Membrane Protein YPO0514 From Yersinia Pestis, PDB code: 7thw:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of the Soluble Domain of the Putative Ompa -Family Membrane Protein YPO0514 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 the Soluble Domain of the Putative Ompa -Family Membrane Protein YPO0514 From Yersinia Pestis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:91.0 occ:1.00 O A:GLY138 2.4 68.2 1.0 O A:HOH502 2.5 73.8 1.0 OD1 A:ASP141 2.9 74.9 1.0 O A:HOH510 3.1 70.8 1.0 OE2 D:GLU168 3.1 111.0 1.0 C A:GLY138 3.4 73.8 1.0 OE2 A:GLU255 3.4 75.9 1.0 OD2 A:ASP141 3.5 94.0 1.0 CG A:ASP141 3.6 87.0 1.0 OE1 A:GLU255 3.6 68.1 1.0 CA A:GLY138 3.7 81.4 1.0 CD A:GLU255 3.9 76.2 1.0 CD D:GLU168 4.0 109.4 1.0 CG D:GLU168 4.2 105.0 1.0 NE A:ARG251 4.5 83.5 1.0 N A:ALA139 4.6 76.2 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of the Soluble Domain of the Putative Ompa -Family Membrane Protein YPO0514 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 the Soluble Domain of the Putative Ompa -Family Membrane Protein YPO0514 From Yersinia Pestis within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:112.1 occ:1.00 O B:GLY138 2.4 94.4 1.0 OD1 B:ASP141 2.6 84.8 1.0 OD2 B:ASP141 2.9 98.0 1.0 CG B:ASP141 3.1 94.4 1.0 C B:GLY138 3.3 86.2 1.0 CA B:GLY138 3.5 95.5 1.0 OE2 B:GLU252 3.7 89.9 1.0 OE2 B:GLU255 4.0 85.8 1.0 OE1 B:GLU255 4.4 82.8 1.0 N B:ALA139 4.5 87.4 1.0 CB B:ASP141 4.6 90.3 1.0 CD B:GLU255 4.6 84.0 1.0 N B:GLY138 4.8 87.0 1.0 CD B:GLU252 4.9 88.8 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of the Soluble Domain of the Putative Ompa -Family Membrane Protein YPO0514 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 the Soluble Domain of the Putative Ompa -Family Membrane Protein YPO0514 From Yersinia Pestis within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca401 b:91.9 occ:1.00 O C:GLY138 2.4 74.2 1.0 OD1 C:ASP141 2.6 72.7 1.0 OD2 C:ASP141 3.0 89.1 1.0 CG C:ASP141 3.2 83.3 1.0 C C:GLY138 3.3 76.3 1.0 CA C:GLY138 3.5 79.2 1.0 OE2 C:GLU255 3.8 73.8 1.0 OE1 C:GLU255 4.0 66.4 1.0 CD C:GLU255 4.3 69.6 1.0 N C:ALA139 4.5 79.2 1.0 OE2 B:GLU168 4.6 113.2 1.0 CB C:ASP141 4.7 80.4 1.0 O C:LEU137 4.8 77.0 1.0 CG B:GLU168 4.8 96.8 1.0 N C:GLY138 4.9 78.0 1.0 NE C:ARG251 4.9 81.4 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of the Soluble Domain of the Putative Ompa -Family Membrane Protein YPO0514 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 the Soluble Domain of the Putative Ompa -Family Membrane Protein YPO0514 From Yersinia Pestis within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca401 b:99.5 occ:1.00 O D:GLY138 2.5 83.8 1.0 OD1 D:ASP141 2.8 102.7 1.0 OD2 D:ASP141 3.1 102.7 1.0 C D:GLY138 3.3 91.0 1.0 CG D:ASP141 3.3 101.1 1.0 CA D:GLY138 3.5 98.1 1.0 OE2 D:GLU255 3.8 89.3 1.0 OE1 D:GLU255 4.0 69.1 1.0 OE2 D:GLU252 4.1 95.2 1.0 CD D:GLU255 4.3 80.1 1.0 N D:ALA139 4.5 91.5 1.0 CB D:ASP141 4.8 95.7 1.0 N D:GLY138 4.9 96.7 1.0

Y.Kim, C.Tesar, G.Chhor, S.Clancy, G.Babnigg, O.Schneewind, A.Joachimiak, Center For Structural Genomics Of Infectious Diseases(Csgid). Crystal Structure of the Soluble Domain of the Putative Ompa -Family Membrane Protein YPO0514 From Yersinia Pestis To Be Published.