Calcium in PDB 8pxc: Structure of FAP1, A Domain of the Accessory Sec-Dependent Serine-Rich Glycoprotein Adhesin From Streptococcus Oralis, Solved at Wavelength 3.06 A

The structure of Structure of FAP1, A Domain of the Accessory Sec-Dependent Serine-Rich Glycoprotein Adhesin From Streptococcus Oralis, Solved at Wavelength 3.06 A, PDB code: 8pxc was solved by K.El Omari, R.Duman, V.Mykhaylyk, C.Orr, C.D.Owen, M.A.Walsh, A.Wagner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	65.53 / 1.97
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	132.81, 30.4, 90.6, 90, 127.04, 90
R / Rfree (%)	18.1 / 22

The binding sites of Calcium atom in the Structure of FAP1, A Domain of the Accessory Sec-Dependent Serine-Rich Glycoprotein Adhesin From Streptococcus Oralis, Solved at Wavelength 3.06 A (pdb code 8pxc). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of FAP1, A Domain of the Accessory Sec-Dependent Serine-Rich Glycoprotein Adhesin From Streptococcus Oralis, Solved at Wavelength 3.06 A, PDB code: 8pxc:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of FAP1, A Domain of the Accessory Sec-Dependent Serine-Rich Glycoprotein Adhesin From Streptococcus Oralis, Solved at Wavelength 3.06 A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of FAP1, A Domain of the Accessory Sec-Dependent Serine-Rich Glycoprotein Adhesin From Streptococcus Oralis, Solved at Wavelength 3.06 A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:14.6 occ:1.00 O A:SER280 2.4 12.7 1.0 OD1 A:ASP364 2.4 12.4 1.0 O A:TYR283 2.4 11.5 1.0 OD2 A:ASP364 2.4 11.5 1.0 O A:HOH809 2.6 14.1 1.0 CG A:ASP364 2.7 11.4 1.0 C A:SER280 3.5 11.3 1.0 C A:TYR283 3.6 12.1 1.0 CA A:SER280 4.2 10.7 1.0 CB A:ASP364 4.2 11.1 1.0 N A:TYR283 4.5 11.4 1.0 CB A:SER280 4.5 10.8 1.0 N A:GLU284 4.5 11.6 1.0 CA A:GLU284 4.6 12.0 1.0 N A:GLU281 4.6 11.8 1.0 CD A:PRO285 4.6 11.0 1.0 CA A:TYR283 4.6 12.0 1.0 CA A:GLU281 4.7 12.3 1.0 C A:GLU281 4.8 12.5 1.0 OH A:TYR358 4.8 10.7 1.0 O A:GLU281 4.9 13.7 1.0

Calcium binding site 2 out of 2 in the Structure of FAP1, A Domain of the Accessory Sec-Dependent Serine-Rich Glycoprotein Adhesin From Streptococcus Oralis, Solved at Wavelength 3.06 A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of FAP1, A Domain of the Accessory Sec-Dependent Serine-Rich Glycoprotein Adhesin From Streptococcus Oralis, Solved at Wavelength 3.06 A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:19.4 occ:1.00 OD2 A:ASP247 2.3 17.9 1.0 OD1 A:ASN165 2.4 18.3 1.0 OD1 A:ASP164 2.4 16.8 1.0 OD2 A:ASP126 2.4 20.2 1.0 OD2 A:ASP164 2.4 17.4 1.0 O A:GLU128 2.4 18.4 1.0 OD1 A:ASP126 2.5 21.1 1.0 CG A:ASP164 2.7 16.8 1.0 CG A:ASP126 2.7 21.5 1.0 CG A:ASP247 3.4 17.5 1.0 CG A:ASN165 3.5 18.0 1.0 C A:GLU128 3.6 18.3 1.0 CB A:ASP247 3.8 16.8 1.0 ND2 A:ASN165 4.0 18.3 1.0 CB A:ASP164 4.2 16.2 1.0 ND2 A:ASN251 4.2 18.4 1.0 CB A:ASP126 4.2 22.6 1.0 N A:GLU128 4.3 20.8 1.0 CB A:GLU128 4.3 21.5 1.0 CA A:GLU128 4.3 19.8 1.0 N A:ASN165 4.3 16.9 1.0 N A:SER166 4.4 17.0 1.0 O A:HOH678 4.5 20.4 1.0 OD1 A:ASP247 4.5 17.6 1.0 C A:LYS129 4.6 15.2 1.0 OG A:SER166 4.6 16.1 1.0 O A:HOH713 4.6 11.4 1.0 N A:LYS129 4.7 16.8 1.0 N A:PRO130 4.7 15.2 1.0 CB A:ASN165 4.7 18.1 1.0 CB A:SER166 4.7 16.8 1.0 CD A:PRO130 4.7 15.0 1.0 CA A:ASN165 4.9 17.6 1.0 CA A:LYS129 4.9 15.7 1.0 CB A:ASN251 4.9 16.8 1.0 CA A:ASP164 4.9 16.5 1.0 O A:LYS129 4.9 14.5 1.0 CG A:GLU128 5.0 22.0 1.0 C A:ASP164 5.0 16.9 1.0

K.El Omari, R.Duman, V.Mykhaylyk, C.M.Orr, M.Latimer-Smith, G.Winter, V.Grama, F.Qu, K.Bountra, H.S.Kwong, M.Romano, R.I.Reis, L.Vogeley, L.Vecchia, C.D.Owen, S.Wittmann, M.Renner, M.Senda, N.Matsugaki, Y.Kawano, T.A.Bowden, I.Moraes, J.M.Grimes, E.J.Mancini, M.A.Walsh, C.R.Guzzo, R.J.Owens, E.Y.Jones, D.G.Brown, D.I.Stuart, K.Beis, A.Wagner. Experimental Phasing Opportunities For Macromolecular Crystallography at Very Long Wavelengths. Commun Chem V. 6 219 2023.
ISSN: ESSN 2399-3669
PubMed: 37828292
DOI: 10.1038/S42004-023-01014-0