Calcium in PDB 3cvg: Crystal Structure of A Periplasmic Putative Metal Binding Protein

The structure of Crystal Structure of A Periplasmic Putative Metal Binding Protein, PDB code: 3cvg was solved by R.Agarwal, S.K.Burley, S.Swaminathan, New York Sgx Research Center Forstructural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.14 / 1.97
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	150.782, 150.782, 116.687, 90.00, 90.00, 90.00
R / Rfree (%)	25.9 / 28.9

The binding sites of Calcium atom in the Crystal Structure of A Periplasmic Putative Metal Binding Protein (pdb code 3cvg). 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 Periplasmic Putative Metal Binding Protein, PDB code: 3cvg:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of A Periplasmic Putative Metal Binding Protein


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 Periplasmic Putative Metal Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:32.7 occ:1.00 OG1 A:THR174 3.0 24.7 1.0 NH1 A:ARG168 3.2 25.5 1.0 N A:THR174 3.3 18.9 1.0 O A:HOH524 3.5 40.7 1.0 O A:HOH534 3.7 39.3 1.0 CB A:THR174 3.7 21.7 1.0 N A:ALA173 3.7 18.3 1.0 CB A:SER172 3.7 21.0 1.0 O A:HOH458 3.8 34.2 1.0 OG A:SER172 3.8 22.4 1.0 CB A:ALA173 3.9 18.5 1.0 CA A:THR174 4.1 18.6 1.0 CA A:ALA173 4.1 18.5 1.0 CZ A:ARG168 4.1 25.2 1.0 C A:ALA173 4.2 17.2 1.0 NH2 A:ARG168 4.2 26.7 1.0 C A:SER172 4.4 18.0 1.0 CA A:SER172 4.7 19.0 1.0 O A:HOH504 4.7 42.8 1.0 O A:HOH506 4.8 36.0 1.0 O A:HOH513 5.0 46.1 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of A Periplasmic Putative Metal Binding Protein


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 Periplasmic Putative Metal Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:49.8 occ:1.00 O B:HOH409 2.6 29.9 1.0 O B:HOH403 2.9 17.5 1.0 OG1 B:THR174 3.0 24.9 1.0 NH1 B:ARG168 3.1 21.3 1.0 O B:HOH402 3.4 17.0 1.0 N B:THR174 3.5 21.8 1.0 N B:ALA173 3.9 23.7 1.0 CB B:THR174 3.9 23.1 1.0 CB B:SER172 3.9 22.2 1.0 OG B:SER172 4.0 23.8 1.0 CB B:ALA173 4.1 26.1 1.0 CZ B:ARG168 4.2 21.4 1.0 CA B:THR174 4.3 22.2 1.0 NH2 B:ARG168 4.3 20.7 1.0 CA B:ALA173 4.3 24.0 1.0 C B:ALA173 4.4 21.2 1.0 C B:SER172 4.6 23.8 1.0 CG B:PRO205 4.7 25.9 1.0 CD2 B:TYR99 4.8 34.7 1.0 CA B:SER172 4.8 23.0 1.0 O B:HOH436 4.9 23.1 1.0 CE2 B:TYR99 4.9 34.6 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of A Periplasmic Putative Metal Binding Protein


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 Periplasmic Putative Metal Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca401 b:35.8 occ:1.00 OG1 C:THR174 3.0 23.4 1.0 NH1 C:ARG168 3.3 20.9 1.0 N C:THR174 3.4 22.3 1.0 O C:HOH443 3.5 36.2 1.0 CB C:THR174 3.8 20.6 1.0 N C:ALA173 3.8 21.6 1.0 CB C:ALA173 3.9 23.4 1.0 CB C:SER172 3.9 19.5 1.0 O C:HOH472 3.9 26.2 1.0 OG C:SER172 4.1 20.6 1.0 CA C:ALA173 4.2 23.1 1.0 CA C:THR174 4.2 21.1 1.0 C C:ALA173 4.2 23.2 1.0 CZ C:ARG168 4.3 20.6 1.0 NH2 C:ARG168 4.3 22.0 1.0 C C:SER172 4.6 20.6 1.0 O C:HOH489 4.6 51.6 1.0 CG C:PRO205 4.7 25.9 1.0 CA C:SER172 4.8 19.9 1.0 O C:HOH478 4.9 24.2 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of A Periplasmic Putative Metal Binding Protein


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 Periplasmic Putative Metal Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca401 b:39.8 occ:1.00 OG1 D:THR174 3.0 29.1 1.0 O D:HOH479 3.2 36.3 1.0 NH1 D:ARG168 3.2 24.0 1.0 N D:THR174 3.5 24.8 1.0 CB D:SER172 3.7 25.3 1.0 N D:ALA173 3.8 26.5 1.0 CB D:THR174 3.8 25.3 1.0 O D:HOH457 3.8 38.3 1.0 OG D:SER172 3.9 23.3 1.0 O D:HOH471 4.0 52.6 1.0 CB D:ALA173 4.1 25.6 1.0 CZ D:ARG168 4.2 23.4 1.0 NH2 D:ARG168 4.2 23.9 1.0 CA D:THR174 4.2 24.9 1.0 CA D:ALA173 4.3 25.5 1.0 C D:ALA173 4.3 24.8 1.0 C D:SER172 4.5 26.0 1.0 O D:HOH432 4.5 34.6 1.0 CA D:SER172 4.7 25.6 1.0 CG D:PRO205 5.0 27.1 1.0

R.Agarwal, S.K.Burley, S.Swaminathan. Crystal Structure of A Periplasmic Putative Metal Binding Protein. To Be Published.