Calcium in PDB 6tnj: Crystal Structure of the Vwf Domain of the Type V Pili Tip Protein MFA5 From Porphyromonas Gingivalis

The structure of Crystal Structure of the Vwf Domain of the Type V Pili Tip Protein MFA5 From Porphyromonas Gingivalis, PDB code: 6tnj was solved by T.V.Heidler, R.Claesson, K.Persson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.80 / 1.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	35.198, 110.080, 38.178, 90.00, 98.11, 90.00
R / Rfree (%)	13.3 / 17.9

The binding sites of Calcium atom in the Crystal Structure of the Vwf Domain of the Type V Pili Tip Protein MFA5 From Porphyromonas Gingivalis (pdb code 6tnj). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of the Vwf Domain of the Type V Pili Tip Protein MFA5 From Porphyromonas Gingivalis, PDB code: 6tnj:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of the Vwf Domain of the Type V Pili Tip Protein MFA5 From Porphyromonas 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 the Vwf Domain of the Type V Pili Tip Protein MFA5 From Porphyromonas Gingivalis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:32.3 occ:1.00 O A:HOH637 1.9 12.7 1.0 OG A:SER154 2.1 10.1 1.0 OG A:SER152 2.2 7.1 0.5 O A:HOH907 2.3 15.9 1.0 OD1 A:ASP252 2.4 6.7 1.0 HB2 A:SER152 2.6 9.2 0.5 O A:HOH823 2.9 22.9 1.0 CB A:SER154 3.1 6.8 1.0 HB3 A:SER154 3.1 8.2 1.0 CG A:ASP252 3.2 7.8 1.0 HA3 A:GLY253 3.2 13.5 1.0 CB A:SER152 3.4 7.7 0.5 CB A:SER152 3.4 7.7 0.5 HB2 A:SER152 3.5 9.2 0.5 HB2 A:SER154 3.5 8.2 1.0 HB3 A:SER152 3.5 9.2 0.5 OD2 A:ASP252 3.5 8.4 1.0 HB3 A:SER152 3.7 9.2 0.5 HG1 A:THR224 3.7 9.5 1.0 O A:HOH885 3.8 12.4 1.0 H A:SER154 3.8 9.2 1.0 OD2 A:ASP150 3.8 2.4 0.2 C A:ASP252 3.9 7.1 1.0 O A:ASP252 3.9 5.2 1.0 OD2 A:ASP150 3.9 2.9 0.8 N A:GLY253 4.0 6.1 1.0 OG A:SER152 4.0 7.8 0.5 CA A:GLY253 4.0 11.2 1.0 OG1 A:THR224 4.0 7.9 1.0 H A:ASP252 4.2 4.6 1.0 CA A:SER154 4.3 8.0 1.0 H A:GLY253 4.3 7.3 1.0 O A:HOH716 4.3 12.4 1.0 N A:SER154 4.4 7.7 1.0 HG2 A:MET155 4.4 11.1 1.0 CB A:ASP252 4.4 6.8 1.0 CG A:ASP150 4.5 7.7 0.2 OD1 A:ASP150 4.5 12.2 0.2 CA A:ASP252 4.6 8.7 1.0 HG21 A:THR224 4.6 4.3 1.0 H A:SER152 4.6 6.2 0.5 H A:SER152 4.6 6.2 0.5 CA A:SER152 4.6 4.8 0.5 HA2 A:GLY253 4.6 13.5 1.0 CA A:SER152 4.6 4.8 0.5 CG A:ASP150 4.6 5.4 0.8 OD1 A:ASP150 4.6 11.8 0.8 N A:ASP252 4.7 3.9 1.0 HG A:SER152 4.7 9.4 0.5 C A:SER152 4.8 3.9 1.0 HG A:SER251 4.8 9.8 1.0 HB2 A:ASP252 4.9 8.2 1.0 H A:MET155 4.9 4.9 1.0 C A:SER154 4.9 11.0 1.0 HH11 A:ARG162 4.9 7.6 1.0 C A:GLY253 5.0 10.8 1.0 HG23 A:THR224 5.0 4.3 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of the Vwf Domain of the Type V Pili Tip Protein MFA5 From Porphyromonas 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 the Vwf Domain of the Type V Pili Tip Protein MFA5 From Porphyromonas Gingivalis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:24.2 occ:1.00 O A:ASN298 2.2 7.4 1.0 O A:LEU303 2.3 10.2 0.4 OG1 A:THR301 2.3 12.9 1.0 O A:LEU303 2.4 9.4 0.6 OD2 A:ASP336 2.4 9.7 1.0 O A:THR301 2.5 8.1 1.0 O A:HOH774 2.6 16.5 1.0 H A:THR301 3.1 10.5 1.0 O A:HOH651 3.1 9.8 1.0 C A:THR301 3.2 10.7 1.0 HB3 A:ASN298 3.2 8.1 1.0 H A:LEU303 3.3 15.7 0.4 C A:LEU303 3.3 14.2 0.4 C A:ASN298 3.4 14.3 1.0 C A:LEU303 3.4 14.2 0.6 HB2 A:LEU303 3.4 10.3 0.6 N A:LEU303 3.5 13.1 0.4 CG A:ASP336 3.5 13.2 1.0 H A:LEU303 3.5 15.7 0.6 H A:ASN298 3.5 6.5 1.0 HB3 A:LEU303 3.5 10.3 0.4 CB A:THR301 3.5 11.6 1.0 N A:LEU303 3.5 13.1 0.6 CA A:THR301 3.7 6.6 1.0 N A:THR301 3.7 8.7 1.0 CA A:LEU303 3.8 11.9 0.4 O A:HOH608 3.9 31.2 1.0 CA A:LEU303 3.9 11.9 0.6 OD1 A:ASP336 3.9 12.8 1.0 HA A:PRO299 4.0 15.7 1.0 C A:PRO302 4.0 13.8 1.0 CB A:ASN298 4.0 6.7 1.0 CA A:ASN298 4.1 7.4 1.0 N A:PRO302 4.1 11.2 1.0 N A:ASN298 4.1 5.4 1.0 CB A:LEU303 4.1 8.6 0.6 CB A:LEU303 4.2 8.6 0.4 HB A:THR301 4.2 13.9 1.0 HG23 A:THR301 4.2 24.1 1.0 HA A:THR304 4.3 15.1 0.6 N A:PRO299 4.4 10.3 1.0 HA A:THR304 4.4 14.9 0.4 CA A:PRO302 4.4 12.9 1.0 CG2 A:THR301 4.5 20.1 1.0 CA A:PRO299 4.5 13.1 1.0 N A:THR304 4.5 11.7 0.6 N A:THR304 4.5 11.7 0.4 HA A:PRO302 4.5 15.5 1.0 C A:PRO299 4.6 17.3 1.0 HA A:THR301 4.6 8.0 1.0 HB3 A:LEU303 4.6 10.3 0.6 O A:PRO302 4.7 16.6 1.0 HB2 A:LEU303 4.7 10.3 0.4 CB A:ASP336 4.7 3.1 1.0 CG A:ASN298 4.7 11.1 1.0 HA A:LEU303 4.7 14.3 0.4 HB2 A:ASN298 4.8 8.1 1.0 HB3 A:ASP336 4.8 3.7 1.0 HG21 A:THR301 4.8 24.1 1.0 HA A:LEU303 4.8 14.2 0.6 H A:SER300 4.8 13.6 1.0 N A:SER300 4.8 11.3 1.0 CA A:THR304 4.9 12.6 0.6 HB2 A:ASP336 4.9 3.7 1.0 CA A:THR304 5.0 12.5 0.4 HA A:ASN298 5.0 8.9 1.0 C A:SER300 5.0 21.6 1.0

T.V.Heidler, R.Claesson, K.Persson. Structure of Porphyromonas Gingivalis MFA5 Reveals Unexpected Divergence For A Gram-Negative Fimbrial Tip Protein To Be Published.