Calcium in PDB 5nf3: The Fimbrial Shaft Protein MFA1 From Porphyromonas Gingivalis-C- Terminal Deletion

The structure of The Fimbrial Shaft Protein MFA1 From Porphyromonas Gingivalis-C- Terminal Deletion, PDB code: 5nf3 was solved by M.Hall, Y.Hasegawa, K.Persson, F.Yoshimura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.65 / 1.97
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	66.262, 66.262, 286.607, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 22

The binding sites of Calcium atom in the The Fimbrial Shaft Protein MFA1 From Porphyromonas Gingivalis-C- Terminal Deletion (pdb code 5nf3). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the The Fimbrial Shaft Protein MFA1 From Porphyromonas Gingivalis-C- Terminal Deletion, PDB code: 5nf3:

Calcium binding site 1 out of 1 in the The Fimbrial Shaft Protein MFA1 From Porphyromonas Gingivalis-C- Terminal Deletion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Fimbrial Shaft Protein MFA1 From Porphyromonas Gingivalis-C- Terminal Deletion within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:23.7 occ:1.00 O A:GLU514 2.3 20.7 1.0 O A:ASP509 2.3 26.5 1.0 OD1 A:ASN512 2.4 21.9 1.0 OD1 A:ASP509 2.5 25.8 1.0 O A:ASN512 2.5 22.9 1.0 OD1 A:ASP507 2.5 21.9 1.0 OD2 A:ASP507 2.6 24.6 1.0 CG A:ASP507 2.9 23.0 1.0 C A:ASP509 3.3 23.7 1.0 CG A:ASP509 3.4 21.6 1.0 C A:ASN512 3.4 28.7 1.0 H A:ASN512 3.4 28.3 1.0 C A:GLU514 3.4 21.9 1.0 CG A:ASN512 3.5 24.2 1.0 H A:ASP509 3.5 37.0 1.0 H A:GLU514 3.8 27.9 1.0 N A:GLU514 3.8 23.3 1.0 HB2 A:ASN515 3.9 20.0 1.0 HA A:PRO510 3.9 30.9 1.0 CA A:ASP509 4.0 23.4 1.0 HB2 A:GLU514 4.0 34.4 1.0 N A:ASN512 4.1 23.6 1.0 C A:PRO513 4.1 24.5 1.0 CA A:ASN512 4.1 28.1 1.0 CA A:GLU514 4.1 26.6 1.0 CB A:ASP509 4.1 23.8 1.0 N A:ASP509 4.1 30.9 1.0 HD21 A:ASN512 4.2 30.1 1.0 N A:PRO510 4.2 21.1 1.0 OD2 A:ASP509 4.2 26.9 1.0 ND2 A:ASN512 4.3 25.1 1.0 HA A:ASN515 4.3 25.3 1.0 HB2 A:ASP509 4.3 28.6 1.0 N A:PRO513 4.3 24.2 1.0 CB A:ASN512 4.4 25.9 1.0 CB A:ASP507 4.4 21.9 1.0 CA A:PRO510 4.4 25.7 1.0 N A:ASN515 4.5 20.1 1.0 HA A:PRO513 4.5 29.8 1.0 CA A:PRO513 4.5 24.8 1.0 CB A:GLU514 4.6 28.6 1.0 O A:PRO513 4.6 25.2 1.0 CB A:ASN515 4.7 16.7 1.0 CA A:ASN515 4.7 21.1 1.0 HB3 A:ASP507 4.7 26.3 1.0 C A:PRO510 4.7 33.4 1.0 O A:HOH853 4.8 20.7 1.0 HB2 A:ASP507 4.8 26.3 1.0 HB2 A:ASN512 4.8 31.1 1.0 HD2 A:PRO508 4.9 50.6 1.0 HA A:ASP509 4.9 28.1 1.0 H A:SER511 5.0 44.6 1.0 HB3 A:GLU514 5.0 34.4 1.0

M.Hall, Y.Hasegawa, F.Yoshimura, K.Persson. Structural and Functional Characterization of Shaft, Anchor, and Tip Proteins of the MFA1 Fimbria From the Periodontal Pathogen Porphyromonas Gingivalis. Sci Rep V. 8 1793 2018.
ISSN: ESSN 2045-2322
PubMed: 29379120
DOI: 10.1038/S41598-018-20067-Z