Calcium in PDB 4nhf: Crystal Structure of the Soluble Domain of Trwg Type IV Secretion Machinery From Bartonella Grahamii

The structure of Crystal Structure of the Soluble Domain of Trwg Type IV Secretion Machinery From Bartonella Grahamii, PDB code: 4nhf was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	62.950, 87.650, 191.830, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 24

The binding sites of Calcium atom in the Crystal Structure of the Soluble Domain of Trwg Type IV Secretion Machinery From Bartonella Grahamii (pdb code 4nhf). 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 Trwg Type IV Secretion Machinery From Bartonella Grahamii, PDB code: 4nhf:
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 Trwg Type IV Secretion Machinery From Bartonella Grahamii


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 Trwg Type IV Secretion Machinery From Bartonella Grahamii within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:31.9 occ:1.00 OD2 B:ASP115 2.3 27.6 1.0 O B:HOH481 2.4 28.1 1.0 O A:HOH406 2.4 18.8 1.0 OD2 A:ASP115 2.4 26.7 1.0 O B:HOH428 2.6 22.0 1.0 OD1 B:ASP113 2.6 23.5 1.0 CG B:ASP113 3.4 23.0 1.0 CG B:ASP115 3.4 26.6 1.0 OD2 B:ASP113 3.4 25.4 1.0 CG A:ASP115 3.4 25.0 1.0 CB B:ASP115 3.8 24.6 1.0 CB A:ASP115 3.9 22.6 1.0 O A:HOH353 4.2 43.0 1.0 CD B:ARG155 4.4 28.5 1.0 OD1 A:ASP113 4.5 22.6 1.0 OD1 B:ASP115 4.5 27.6 1.0 OD1 A:ASP115 4.5 25.7 1.0 N B:ASP115 4.5 23.0 1.0 OD2 A:ASP113 4.6 24.0 1.0 OD1 B:ASN152 4.7 26.1 1.0 CA B:ASP115 4.8 23.5 1.0 CB B:ASP113 4.8 20.4 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of the Soluble Domain of Trwg Type IV Secretion Machinery From Bartonella Grahamii


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 Trwg Type IV Secretion Machinery From Bartonella Grahamii within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca301 b:46.3 occ:1.00 O D:HOH382 2.3 12.6 1.0 OD2 C:ASP115 2.5 42.7 1.0 OD1 C:ASP113 2.6 34.2 1.0 OD2 D:ASP115 2.6 31.7 1.0 O C:HOH446 2.7 18.2 1.0 O D:HOH395 2.9 54.7 1.0 CG C:ASP113 3.3 33.2 1.0 OD2 C:ASP113 3.3 32.2 1.0 CG C:ASP115 3.5 41.0 1.0 CG D:ASP115 3.5 28.4 1.0 CB C:ASP115 3.9 37.5 1.0 CB D:ASP115 3.9 26.0 1.0 O D:HOH394 4.0 40.2 1.0 OD1 D:ASP115 4.4 29.0 1.0 OD2 D:ASP113 4.4 31.8 1.0 OD1 C:ASP115 4.5 44.8 1.0 OD1 D:ASP113 4.5 28.3 1.0 N C:ASP115 4.5 35.8 1.0 CD C:ARG155 4.6 45.5 1.0 CB C:ASP113 4.8 31.0 1.0 CA C:ASP115 4.9 35.9 1.0 O C:HOH423 4.9 30.9 1.0 NE C:ARG155 4.9 46.0 1.0 CG D:ASP113 4.9 28.1 1.0 CG C:ARG155 5.0 43.7 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of the Soluble Domain of Trwg Type IV Secretion Machinery From Bartonella Grahamii


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 Trwg Type IV Secretion Machinery From Bartonella Grahamii within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca301 b:45.4 occ:1.00 O E:HOH409 2.3 39.8 1.0 O F:HOH471 2.4 40.3 1.0 O E:SER182 2.6 52.2 1.0 O F:HOH472 2.7 43.2 1.0 C E:SER182 3.7 53.0 1.0 OD1 F:ASP115 4.3 31.2 1.0 CA E:SER182 4.4 51.9 1.0 CB E:SER182 4.5 55.4 1.0 O E:HOH464 4.7 40.6 1.0 OD2 F:ASP115 4.7 31.5 1.0 N E:SER183 4.8 53.0 1.0 O F:HOH470 5.0 46.2 1.0 CG F:ASP115 5.0 30.4 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of the Soluble Domain of Trwg Type IV Secretion Machinery From Bartonella Grahamii


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 Trwg Type IV Secretion Machinery From Bartonella Grahamii within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca301 b:42.7 occ:1.00 O F:HOH469 2.2 16.6 1.0 OD2 F:ASP115 2.5 31.5 1.0 O E:HOH447 2.5 23.6 1.0 OD2 E:ASP115 2.6 48.1 1.0 OD1 F:ASP113 2.6 31.4 1.0 O F:HOH417 2.6 40.5 1.0 OD2 F:ASP113 2.7 31.3 1.0 CG F:ASP113 3.0 29.9 1.0 CG F:ASP115 3.3 30.4 1.0 CG E:ASP115 3.6 44.1 1.0 CB F:ASP115 3.6 27.6 1.0 CB E:ASP115 4.0 39.8 1.0 O F:HOH472 4.0 43.2 1.0 OD1 E:ASP113 4.3 38.7 1.0 OD1 F:ASP115 4.4 31.2 1.0 N F:ASP115 4.5 26.7 1.0 CB F:ASP113 4.5 27.4 1.0 OD2 E:ASP113 4.5 36.8 1.0 O F:HOH470 4.6 46.2 1.0 NE F:ARG155 4.6 40.6 1.0 CA F:ASP115 4.7 27.1 1.0 CD F:ARG155 4.7 39.4 1.0 OD1 E:ASP115 4.7 46.1 1.0 CG E:ASP113 4.9 36.2 1.0

T.E.Edwards, M.C.Clifton, I.Phan, A.Pulliainen, Seattle Structural Genomics Center For Infectious Disease(Ssgcid). Crystal Structure of the Soluble Domain of Trwg Type IV Secretion Machinery From Bartonella Grahamii To Be Published.