Calcium in PDB 3ge4: Crystal Structure of Ferritin:Dna-Binding Protein Dps From Brucella Melitensis

The structure of Crystal Structure of Ferritin:Dna-Binding Protein Dps From Brucella Melitensis, PDB code: 3ge4 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)	19.86 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	95.240, 98.330, 105.450, 90.00, 89.98, 90.00
R / Rfree (%)	14.3 / 17.9

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Ferritin:Dna-Binding Protein Dps From Brucella Melitensis (pdb code 3ge4). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the Crystal Structure of Ferritin:Dna-Binding Protein Dps From Brucella Melitensis, PDB code: 3ge4:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 12 in the Crystal Structure of Ferritin:Dna-Binding Protein Dps From Brucella Melitensis


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 Ferritin:Dna-Binding Protein Dps From Brucella Melitensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca167 b:25.7 occ:1.00 OE2 A:GLU75 2.1 24.5 1.0 OD2 A:ASP71 2.3 15.3 0.5 O B:HOH1925 2.3 27.3 1.0 NE2 B:HIS44 2.4 20.8 1.0 OD1 A:ASP71 2.4 19.4 0.5 CG A:ASP71 2.6 15.2 0.5 CD A:GLU75 3.0 22.8 1.0 O B:HOH1742 3.2 31.9 1.0 CE1 B:HIS44 3.3 18.4 1.0 CD2 B:HIS44 3.4 20.3 1.0 OE1 A:GLU75 3.6 23.6 1.0 CG A:ASP71 3.7 15.6 0.5 NZ B:LYS41 3.8 16.1 1.0 OD1 A:ASP71 3.8 17.8 0.5 OD2 B:ASP60 4.0 22.6 1.0 OD2 A:ASP71 4.0 19.7 0.5 CB A:ASP71 4.1 14.3 0.5 CG A:GLU75 4.1 17.3 1.0 CB A:ASP71 4.1 14.0 0.5 NE2 B:HIS56 4.2 17.5 1.0 CE1 B:HIS56 4.2 17.1 1.0 NE1 B:TRP45 4.3 15.1 1.0 OD1 B:ASP60 4.4 18.1 1.0 CD1 B:TRP45 4.4 16.6 1.0 ND1 B:HIS44 4.5 18.8 1.0 CG B:HIS44 4.5 17.7 1.0 CG B:ASP60 4.6 19.1 1.0 O A:HOH2013 4.8 39.8 1.0 CA A:ASP71 5.0 14.2 0.5 CA A:ASP71 5.0 14.1 0.5

Calcium binding site 2 out of 12 in the Crystal Structure of Ferritin:Dna-Binding Protein Dps From Brucella Melitensis


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 Ferritin:Dna-Binding Protein Dps From Brucella Melitensis within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca167 b:24.9 occ:1.00 OE2 B:GLU75 2.2 21.6 1.0 O A:HOH2031 2.2 26.1 1.0 NE2 A:HIS44 2.3 14.0 1.0 OD2 B:ASP71 2.3 26.4 1.0 OD1 B:ASP71 2.5 27.1 1.0 CG B:ASP71 2.7 22.7 1.0 O A:HOH576 2.8 24.0 1.0 CD B:GLU75 3.0 20.7 1.0 CE1 A:HIS44 3.2 15.6 1.0 CD2 A:HIS44 3.4 16.7 1.0 OE1 B:GLU75 3.5 20.3 1.0 NZ A:LYS41 3.9 17.6 1.0 OD2 A:ASP60 4.0 18.6 1.0 NE2 A:HIS56 4.1 16.7 1.0 CG B:GLU75 4.2 15.9 1.0 CE1 A:HIS56 4.2 14.8 1.0 CB B:ASP71 4.2 15.7 1.0 NE1 A:TRP45 4.3 14.2 1.0 OD1 A:ASP60 4.4 19.0 1.0 ND1 A:HIS44 4.4 14.4 1.0 O D:HOH1814 4.5 38.4 1.0 CG A:HIS44 4.5 14.7 1.0 CD1 A:TRP45 4.5 15.0 1.0 CG A:ASP60 4.6 15.3 1.0 O B:HOH1233 5.0 38.4 1.0

Calcium binding site 3 out of 12 in the Crystal Structure of Ferritin:Dna-Binding Protein Dps From Brucella Melitensis


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 Ferritin:Dna-Binding Protein Dps From Brucella Melitensis within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca167 b:23.4 occ:1.00 OE2 C:GLU75 2.1 20.6 1.0 O I:HOH2051 2.1 21.6 1.0 OD2 C:ASP71 2.2 9.9 0.5 NE2 I:HIS44 2.4 10.9 1.0 OD1 C:ASP71 2.5 14.2 0.5 CG C:ASP71 2.7 11.9 0.5 O I:HOH1235 2.8 28.9 1.0 CD C:GLU75 3.1 17.0 1.0 CE1 I:HIS44 3.4 11.0 1.0 CD2 I:HIS44 3.4 10.9 1.0 OE1 C:GLU75 3.5 20.4 1.0 CG C:ASP71 3.8 12.9 0.5 OD2 C:ASP71 3.8 16.8 0.5 NZ I:LYS41 3.9 15.4 1.0 OD2 I:ASP60 3.9 19.4 1.0 OD1 C:ASP71 4.1 17.2 0.5 NE2 I:HIS56 4.2 10.7 1.0 CB C:ASP71 4.2 11.1 0.5 CB C:ASP71 4.2 11.6 0.5 CG C:GLU75 4.2 13.4 1.0 NE1 I:TRP45 4.3 11.9 1.0 CE1 I:HIS56 4.3 11.1 1.0 O E:HOH1825 4.4 43.2 1.0 OD1 I:ASP60 4.4 18.6 1.0 CD1 I:TRP45 4.4 11.9 1.0 ND1 I:HIS44 4.5 11.6 1.0 CG I:HIS44 4.5 9.4 1.0 CG I:ASP60 4.6 14.3 1.0

Calcium binding site 4 out of 12 in the Crystal Structure of Ferritin:Dna-Binding Protein Dps From Brucella Melitensis


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 Ferritin:Dna-Binding Protein Dps From Brucella Melitensis within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca167 b:25.2 occ:1.00 OE2 D:GLU75 2.1 23.3 1.0 O J:HOH2073 2.2 22.4 1.0 OD2 D:ASP71 2.4 18.2 0.5 OD1 D:ASP71 2.4 13.8 0.5 NE2 J:HIS44 2.4 12.3 1.0 CG D:ASP71 2.7 14.4 0.5 O D:HOH1096 3.0 29.4 1.0 CD D:GLU75 3.0 18.4 1.0 CE1 J:HIS44 3.4 12.7 1.0 CD2 J:HIS44 3.4 12.2 1.0 OE1 D:GLU75 3.4 18.6 1.0 NZ J:LYS41 3.9 14.4 1.0 CG D:ASP71 4.0 14.6 0.5 OD2 J:ASP60 4.0 18.1 1.0 OD1 D:ASP71 4.0 18.0 0.5 CG D:GLU75 4.1 14.6 1.0 NE2 J:HIS56 4.1 12.2 1.0 CB D:ASP71 4.2 11.8 0.5 CB D:ASP71 4.2 12.1 0.5 CE1 J:HIS56 4.3 11.3 1.0 NE1 J:TRP45 4.3 10.9 1.0 OD2 D:ASP71 4.3 19.2 0.5 O L:HOH1859 4.4 36.7 1.0 O D:HOH1346 4.4 44.0 1.0 OD1 J:ASP60 4.4 18.2 1.0 CD1 J:TRP45 4.5 9.5 1.0 ND1 J:HIS44 4.5 10.6 1.0 CG J:HIS44 4.5 11.5 1.0 CG J:ASP60 4.7 14.2 1.0

Calcium binding site 5 out of 12 in the Crystal Structure of Ferritin:Dna-Binding Protein Dps From Brucella Melitensis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Ferritin:Dna-Binding Protein Dps From Brucella Melitensis within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca167 b:23.1 occ:1.00 OE2 E:GLU75 2.2 20.6 1.0 OD2 E:ASP71 2.3 14.8 0.5 O F:HOH2089 2.3 26.7 1.0 NE2 F:HIS44 2.4 12.2 1.0 OD1 E:ASP71 2.4 11.3 0.5 CG E:ASP71 2.6 12.5 0.5 O E:HOH1017 2.9 27.2 1.0 CD E:GLU75 3.0 16.4 1.0 O E:HOH1869 3.0 35.2 1.0 CE1 F:HIS44 3.3 12.3 1.0 CD2 F:HIS44 3.3 11.9 1.0 OE1 E:GLU75 3.4 17.7 1.0 CG E:ASP71 3.9 12.6 0.5 NZ F:LYS41 3.9 14.6 1.0 OD2 E:ASP71 4.0 17.9 0.5 OD2 F:ASP60 4.0 15.2 1.0 OD1 E:ASP71 4.0 14.3 0.5 NE2 F:HIS56 4.1 13.0 1.0 CB E:ASP71 4.2 10.4 0.5 CG E:GLU75 4.2 12.1 1.0 CE1 F:HIS56 4.2 10.4 1.0 NE1 F:TRP45 4.2 12.9 1.0 CB E:ASP71 4.2 11.2 0.5 OD1 F:ASP60 4.4 15.7 1.0 CD1 F:TRP45 4.4 12.4 1.0 ND1 F:HIS44 4.5 12.0 1.0 CG F:HIS44 4.5 11.5 1.0 CG F:ASP60 4.6 14.6 1.0 O F:HOH1413 4.9 39.2 1.0 O E:HOH2090 4.9 41.2 1.0

Calcium binding site 6 out of 12 in the Crystal Structure of Ferritin:Dna-Binding Protein Dps From Brucella Melitensis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Ferritin:Dna-Binding Protein Dps From Brucella Melitensis within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca167 b:20.9 occ:1.00 O E:HOH2082 2.1 22.6 1.0 OE2 F:GLU75 2.1 17.9 1.0 OD1 F:ASP71 2.2 3.1 0.3 OD2 F:ASP71 2.3 2.5 0.3 NE2 E:HIS44 2.3 10.4 1.0 CG F:ASP71 2.6 5.3 0.3 O E:HOH1747 2.9 28.5 1.0 CD F:GLU75 3.0 14.6 1.0 O F:HOH1448 3.1 35.4 1.0 OD1 F:ASP71 3.2 22.7 0.7 CD2 E:HIS44 3.3 10.3 1.0 CE1 E:HIS44 3.3 12.8 1.0 OE1 F:GLU75 3.4 15.3 1.0 CG F:ASP71 3.7 17.0 0.7 NZ E:LYS41 3.9 16.1 1.0 OD2 E:ASP60 4.0 14.0 1.0 NE2 E:HIS56 4.1 11.1 1.0 CG F:GLU75 4.1 11.8 1.0 CB F:ASP71 4.2 7.6 0.3 OD2 F:ASP71 4.2 25.7 0.7 CB F:ASP71 4.2 10.9 0.7 CE1 E:HIS56 4.2 10.2 1.0 NE1 E:TRP45 4.3 9.7 1.0 ND1 E:HIS44 4.4 9.9 1.0 CG E:HIS44 4.5 8.2 1.0 OD1 E:ASP60 4.5 15.1 1.0 CD1 E:TRP45 4.5 10.2 1.0 O F:HOH825 4.6 29.0 1.0 CG E:ASP60 4.6 13.3 1.0 O E:HOH1260 4.8 36.0 1.0

Calcium binding site 7 out of 12 in the Crystal Structure of Ferritin:Dna-Binding Protein Dps From Brucella Melitensis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Ferritin:Dna-Binding Protein Dps From Brucella Melitensis within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca167 b:22.9 occ:1.00 O H:HOH1976 2.2 20.2 1.0 OE2 G:GLU75 2.3 19.6 1.0 OD1 G:ASP71 2.3 12.8 0.5 OD2 G:ASP71 2.3 11.1 0.5 NE2 H:HIS44 2.4 12.5 1.0 CG G:ASP71 2.7 11.6 0.5 O H:HOH219 2.9 26.7 1.0 CD G:GLU75 3.1 19.4 1.0 CE1 H:HIS44 3.3 11.4 1.0 CD2 H:HIS44 3.4 9.9 1.0 OE1 G:GLU75 3.5 20.4 1.0 NZ H:LYS41 3.8 15.2 1.0 CG G:ASP71 3.9 11.6 0.5 OD2 H:ASP60 3.9 15.3 1.0 OD1 G:ASP71 3.9 15.2 0.5 CB G:ASP71 4.2 9.7 0.5 CG G:GLU75 4.2 14.7 1.0 CB G:ASP71 4.2 9.6 0.5 NE2 H:HIS56 4.2 11.7 1.0 OD2 G:ASP71 4.2 15.6 0.5 CE1 H:HIS56 4.3 12.5 1.0 NE1 H:TRP45 4.3 9.4 1.0 OD1 H:ASP60 4.4 14.1 1.0 ND1 H:HIS44 4.4 9.3 1.0 CD1 H:TRP45 4.4 10.9 1.0 CG H:HIS44 4.5 8.7 1.0 CG H:ASP60 4.5 14.2 1.0 O H:HOH1756 4.7 34.3 1.0 O G:HOH1308 5.0 39.6 1.0

Calcium binding site 8 out of 12 in the Crystal Structure of Ferritin:Dna-Binding Protein Dps From Brucella Melitensis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Ferritin:Dna-Binding Protein Dps From Brucella Melitensis within 5.0Å range: probe atom residue distance (Å) B Occ H:Ca167 b:18.2 occ:1.00 OE2 H:GLU75 2.1 15.1 1.0 O G:HOH2134 2.2 25.4 1.0 OD2 H:ASP71 2.2 12.8 0.5 OD1 H:ASP71 2.4 11.4 0.5 NE2 G:HIS44 2.4 12.1 1.0 CG H:ASP71 2.6 10.3 0.5 O G:HOH178 2.7 23.9 1.0 CD H:GLU75 3.0 15.2 1.0 O H:HOH2135 3.2 40.6 1.0 CD2 G:HIS44 3.3 11.9 1.0 OE1 H:GLU75 3.4 15.6 1.0 CE1 G:HIS44 3.4 11.5 1.0 NZ G:LYS41 3.9 14.1 1.0 CG H:ASP71 3.9 10.7 0.5 OD1 H:ASP71 4.0 12.6 0.5 OD2 G:ASP60 4.0 14.4 1.0 CB H:ASP71 4.1 9.2 0.5 OD2 H:ASP71 4.1 15.5 0.5 CB H:ASP71 4.2 9.5 0.5 CG H:GLU75 4.2 11.9 1.0 NE2 G:HIS56 4.2 8.4 1.0 NE1 G:TRP45 4.3 8.5 1.0 CE1 G:HIS56 4.3 10.5 1.0 CD1 G:TRP45 4.4 8.8 1.0 OD1 G:ASP60 4.4 15.9 1.0 CG G:HIS44 4.5 9.4 1.0 ND1 G:HIS44 4.5 8.6 1.0 CG G:ASP60 4.6 12.6 1.0 O H:HOH1095 4.7 29.9 1.0

Calcium binding site 9 out of 12 in the Crystal Structure of Ferritin:Dna-Binding Protein Dps From Brucella Melitensis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Ferritin:Dna-Binding Protein Dps From Brucella Melitensis within 5.0Å range: probe atom residue distance (Å) B Occ I:Ca167 b:26.6 occ:1.00 OE2 I:GLU75 2.2 23.2 1.0 O C:HOH2047 2.2 26.4 1.0 OD1 I:ASP71 2.3 13.7 0.5 OD2 I:ASP71 2.4 14.7 0.5 NE2 C:HIS44 2.4 13.0 1.0 CG I:ASP71 2.7 14.3 0.5 O C:HOH1137 3.0 24.2 1.0 CD I:GLU75 3.1 18.8 1.0 CD2 C:HIS44 3.3 12.2 1.0 CE1 C:HIS44 3.4 15.2 1.0 OE1 I:GLU75 3.6 20.7 1.0 NZ C:LYS41 3.8 13.1 1.0 OD1 I:ASP71 3.9 18.3 0.5 CG I:ASP71 3.9 13.6 0.5 OD2 C:ASP60 4.0 15.7 1.0 CG I:GLU75 4.2 14.4 1.0 CB I:ASP71 4.2 11.2 0.5 CB I:ASP71 4.2 11.4 0.5 NE2 C:HIS56 4.2 13.2 1.0 OD2 I:ASP71 4.2 18.5 0.5 NE1 C:TRP45 4.3 13.7 1.0 CE1 C:HIS56 4.4 14.7 1.0 CD1 C:TRP45 4.4 13.7 1.0 OD1 C:ASP60 4.5 14.2 1.0 ND1 C:HIS44 4.5 11.5 1.0 CG C:HIS44 4.5 13.2 1.0 O I:HOH1249 4.6 41.7 1.0 O K:HOH2046 4.6 38.3 1.0 CG C:ASP60 4.6 16.0 1.0 O C:HOH959 5.0 35.7 1.0

Calcium binding site 10 out of 12 in the Crystal Structure of Ferritin:Dna-Binding Protein Dps From Brucella Melitensis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of Ferritin:Dna-Binding Protein Dps From Brucella Melitensis within 5.0Å range: probe atom residue distance (Å) B Occ J:Ca167 b:22.7 occ:1.00 O D:HOH2071 2.1 25.2 1.0 OE2 J:GLU75 2.2 19.6 1.0 OD1 J:ASP71 2.3 13.6 0.5 OD2 J:ASP71 2.3 13.6 0.5 NE2 D:HIS44 2.3 11.9 1.0 CG J:ASP71 2.6 13.4 0.5 O D:HOH924 3.1 31.0 1.0 CD J:GLU75 3.1 17.0 1.0 CD2 D:HIS44 3.3 10.6 1.0 CE1 D:HIS44 3.3 13.8 1.0 OE1 J:GLU75 3.5 17.2 1.0 CG J:ASP71 3.9 14.6 0.5 OD2 D:ASP60 3.9 16.7 1.0 NZ D:LYS41 3.9 15.3 1.0 OD1 J:ASP71 4.0 18.1 0.5 OD2 J:ASP71 4.1 18.8 0.5 NE2 D:HIS56 4.1 12.4 1.0 CB J:ASP71 4.2 10.9 0.5 CG J:GLU75 4.2 13.1 1.0 CB J:ASP71 4.3 11.7 0.5 CE1 D:HIS56 4.3 13.0 1.0 NE1 D:TRP45 4.3 11.8 1.0 OD1 D:ASP60 4.4 16.4 1.0 ND1 D:HIS44 4.4 13.2 1.0 CD1 D:TRP45 4.5 11.5 1.0 CG D:HIS44 4.5 12.0 1.0 CG D:ASP60 4.6 14.7 1.0 O J:HOH1357 4.8 30.2 1.0

Seattle Structural Genomics Center For Infectiousdisease (Ssgcid), Seattle Structural Genomics Center For Infectious Disease(Ssgcid). N/A N/A.