Calcium in PDB 6za2: Crystal Structure of Dimeric Latent Poru From Poprhyromonas Gingivalis

The structure of Crystal Structure of Dimeric Latent Poru From Poprhyromonas Gingivalis, PDB code: 6za2 was solved by F.X.Gomis-Ruth, T.Goulas, T.Guevara, A.Rodriguez-Banqueri, J.Potempa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	88.48 / 3.35
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	171.7, 171.7, 440.4, 90, 90, 120
R / Rfree (%)	20.2 / 24.3

The binding sites of Calcium atom in the Crystal Structure of Dimeric Latent Poru From Poprhyromonas Gingivalis (pdb code 6za2). 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 Dimeric Latent Poru From Poprhyromonas Gingivalis, PDB code: 6za2:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Dimeric Latent Poru From Poprhyromonas Gingivalis


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 Dimeric Latent Poru From Poprhyromonas Gingivalis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2001 b:106.9 occ:1.00 O A:LEU185 2.4 104.5 1.0 OD1 A:ASP293 2.4 102.1 1.0 OE1 A:GLU174 2.4 102.2 1.0 O A:HOH2102 2.4 89.8 1.0 OE1 A:GLU172 2.4 124.2 1.0 O A:HOH2101 2.4 108.9 1.0 H A:LEU185 3.1 95.9 0.0 CD A:GLU174 3.3 103.2 1.0 CD A:GLU172 3.4 122.8 1.0 OE2 A:GLU174 3.4 86.4 1.0 C A:LEU185 3.5 106.0 1.0 HG3 A:GLU172 3.5 97.7 0.0 CG A:ASP293 3.5 105.5 1.0 HB3 A:ASP184 3.7 102.8 0.0 HD2 A:PHE294 3.8 100.7 0.0 N A:LEU185 3.8 98.7 1.0 CG A:GLU172 3.9 98.5 1.0 HB2 A:LEU185 4.0 93.8 0.0 HA A:TYR186 4.0 105.9 0.0 OD2 A:ASP293 4.0 114.5 1.0 HG2 A:GLU172 4.1 97.4 0.0 CA A:LEU185 4.2 98.2 1.0 O A:ASP293 4.3 106.4 1.0 OE2 A:GLU172 4.3 110.5 1.0 HA A:ASP293 4.5 99.4 0.0 HA A:GLU174 4.5 90.3 0.0 HA A:ASP184 4.5 99.8 0.0 N A:TYR186 4.5 106.8 1.0 CB A:LEU185 4.6 96.1 1.0 HB3 A:PHE294 4.6 99.2 0.0 CB A:ASP184 4.6 105.2 1.0 CG A:GLU174 4.7 87.4 1.0 CA A:TYR186 4.7 108.2 1.0 HG21 A:VAL127 4.7 101.5 0.0 CB A:ASP293 4.8 101.3 1.0 C A:ASP293 4.8 105.8 1.0 C A:ASP184 4.8 105.7 1.0 CD2 A:PHE294 4.8 101.6 1.0 HG22 A:VAL127 4.8 101.8 0.0 HG2 A:GLU174 4.9 85.3 0.0 CA A:ASP293 4.9 100.4 1.0 HB3 A:LEU185 4.9 94.8 0.0 CA A:ASP184 4.9 102.8 1.0 OD2 A:ASP184 5.0 126.0 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Dimeric Latent Poru From Poprhyromonas Gingivalis


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 Dimeric Latent Poru From Poprhyromonas Gingivalis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2002 b:169.8 occ:1.00 OD2 A:ASP936 2.4 195.3 1.0 O A:THR938 2.4 167.7 1.0 OD1 A:ASP936 2.4 194.1 1.0 OD1 A:ASP1035 2.4 159.8 1.0 OD1 A:ASP970 2.4 147.7 1.0 OD1 A:ASN1039 2.4 194.6 1.0 CG A:ASP936 2.6 194.4 1.0 CG A:ASP970 3.1 144.5 1.0 OD2 A:ASP970 3.1 148.8 1.0 CG A:ASP1035 3.3 155.4 1.0 HA A:PRO939 3.5 160.4 0.0 C A:THR938 3.6 170.9 1.0 CG A:ASN1039 3.6 192.2 1.0 HB2 A:ASN1039 3.8 150.2 0.0 CB A:ASP936 4.0 196.2 1.0 HB3 A:ASP1035 4.0 142.0 0.0 OD2 A:ASP1035 4.0 155.4 1.0 HB2 A:ASP1035 4.1 143.5 0.0 CB A:ASP1035 4.1 144.0 1.0 HD22 A:ASN972 4.1 147.5 0.0 CA A:PRO939 4.2 161.1 1.0 HB3 A:ASP936 4.2 188.1 0.0 H A:THR938 4.2 175.8 0.0 O A:ASP936 4.3 197.3 1.0 HD3 A:PRO940 4.3 156.6 0.0 CB A:ASN1039 4.4 153.2 1.0 N A:PRO939 4.4 165.2 1.0 C A:PRO939 4.4 162.0 1.0 N A:THR938 4.4 178.0 1.0 C A:ASP936 4.4 198.5 1.0 HB A:THR938 4.5 182.5 0.0 HB2 A:ASN972 4.5 140.4 0.0 CA A:THR938 4.5 174.6 1.0 H A:ASN972 4.6 135.2 0.0 CB A:ASP970 4.6 127.6 1.0 ND2 A:ASN1039 4.6 185.8 1.0 CA A:ASP936 4.7 202.6 1.0 HB2 A:ASP936 4.7 187.9 0.0 HD21 A:ASN1039 4.7 186.9 0.0 N A:PRO940 4.7 154.6 1.0 HA A:ASP936 4.7 189.6 0.0 O A:PRO939 4.7 163.0 1.0 HB2 A:ASP970 4.8 126.6 0.0 HG3 A:PRO940 4.8 156.1 0.0 H A:ASN1039 4.9 147.8 0.0 CB A:THR938 5.0 185.0 1.0 CD A:PRO940 5.0 155.0 1.0 HB3 A:ASN1039 5.0 155.6 0.0

Calcium binding site 3 out of 4 in the Crystal Structure of Dimeric Latent Poru From Poprhyromonas Gingivalis


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 Dimeric Latent Poru From Poprhyromonas Gingivalis within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2001 b:103.1 occ:1.00 O B:LEU185 2.4 99.7 1.0 OD1 B:ASP293 2.4 97.2 1.0 O B:HOH2101 2.4 73.2 1.0 O B:HOH2102 2.4 105.7 1.0 OE1 B:GLU174 2.4 120.0 1.0 OE1 B:GLU172 2.4 94.5 1.0 H B:LEU185 3.1 101.0 0.0 CD B:GLU174 3.3 109.9 1.0 CD B:GLU172 3.4 121.4 1.0 OE2 B:GLU174 3.4 89.4 1.0 C B:LEU185 3.5 102.8 1.0 CG B:ASP293 3.5 101.1 1.0 HG3 B:GLU172 3.5 100.5 0.0 HB3 B:ASP184 3.7 109.3 0.0 N B:LEU185 3.8 101.8 1.0 HD2 B:PHE294 3.8 98.1 0.0 CG B:GLU172 3.9 100.5 1.0 HA B:TYR186 4.0 102.9 0.0 HB2 B:LEU185 4.0 97.5 0.0 OD2 B:ASP293 4.0 113.8 1.0 HG2 B:GLU172 4.1 101.0 0.0 CA B:LEU185 4.2 99.7 1.0 O B:ASP293 4.3 98.1 1.0 OE2 B:GLU172 4.3 115.4 1.0 HA B:ASP293 4.5 95.7 0.0 HA B:GLU174 4.5 94.2 0.0 N B:TYR186 4.5 102.9 1.0 HB3 B:PHE294 4.5 93.0 0.0 HA B:ASP184 4.5 107.3 0.0 CB B:LEU185 4.6 98.4 1.0 CB B:ASP184 4.7 109.8 1.0 CG B:GLU174 4.7 100.2 1.0 CA B:TYR186 4.7 104.1 1.0 HG21 B:VAL127 4.7 92.3 0.0 CB B:ASP293 4.8 95.4 1.0 C B:ASP293 4.8 97.6 1.0 C B:ASP184 4.8 108.5 1.0 HG22 B:VAL127 4.8 92.6 0.0 CD2 B:PHE294 4.9 98.1 1.0 HG2 B:GLU174 4.9 99.7 0.0 HB3 B:LEU185 4.9 98.4 0.0 CA B:ASP293 4.9 95.0 1.0 CA B:ASP184 4.9 108.2 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Dimeric Latent Poru From Poprhyromonas Gingivalis


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 Dimeric Latent Poru From Poprhyromonas Gingivalis within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2002 b:213.2 occ:1.00 OD2 B:ASP936 2.4 250.9 1.0 OD1 B:ASP1035 2.4 242.0 1.0 OD1 B:ASP936 2.4 251.2 1.0 O B:THR938 2.4 238.8 1.0 OD1 B:ASP970 2.4 211.2 1.0 OD1 B:ASN1039 2.4 259.3 1.0 CG B:ASP936 2.6 250.5 1.0 CG B:ASP1035 3.1 242.2 1.0 CG B:ASP970 3.2 209.4 1.0 OD2 B:ASP970 3.3 214.7 1.0 HA B:PRO939 3.5 237.1 0.0 C B:THR938 3.6 241.3 1.0 CG B:ASN1039 3.6 262.3 1.0 OD2 B:ASP1035 3.7 249.2 1.0 HB2 B:ASN1039 3.9 247.0 0.0 CB B:ASP936 4.0 247.1 1.0 HB2 B:ASP1035 4.0 234.1 0.0 CB B:ASP1035 4.1 233.1 1.0 HB3 B:ASP1035 4.2 231.7 0.0 HD22 B:ASN972 4.2 217.4 0.0 CA B:PRO939 4.2 236.7 1.0 H B:THR938 4.2 244.0 0.0 HB3 B:ASP936 4.3 245.9 0.0 O B:ASP936 4.3 253.7 1.0 HD3 B:PRO940 4.3 234.4 0.0 C B:PRO939 4.4 233.2 1.0 N B:PRO939 4.4 238.9 1.0 CB B:ASN1039 4.4 250.1 1.0 N B:THR938 4.4 245.3 1.0 C B:ASP936 4.5 254.2 1.0 HB B:THR938 4.5 237.1 0.0 HB2 B:ASN972 4.5 213.0 0.0 CA B:THR938 4.6 242.8 1.0 CB B:ASP970 4.6 193.8 1.0 H B:ASN972 4.6 193.0 0.0 ND2 B:ASN1039 4.6 261.6 1.0 HD21 B:ASN1039 4.6 262.1 0.0 HB2 B:ASP970 4.7 194.2 0.0 CA B:ASP936 4.7 250.0 1.0 N B:PRO940 4.7 226.9 1.0 HB2 B:ASP936 4.7 243.8 0.0 HA B:ASP936 4.7 250.0 0.0 O B:PRO939 4.7 232.5 1.0 HG3 B:PRO940 4.8 228.3 0.0 H B:ASN1039 4.9 248.6 0.0 CB B:THR938 5.0 240.0 1.0

D.Mizgalska, T.Goulas, A.Rodriguez-Banqueri, F.Veillard, M.Madej, E.Malecka, K.Szczesniak, M.Ksiazek, M.Wiedzolek, T.Guevara, U.Eckhard, M.Sola, J.Potempa, F.X.Gomis-Ruth. Intermolecular Latency Regulates the Essential C-Terminal Signal Peptidase and Sortase of the P. Gingivalis Type-IX Secretion System To Be Published.