Calcium in PDB 9fzc: Structure of Ompa-Short in Complex with Nanobody NB01

The structure of Structure of Ompa-Short in Complex with Nanobody NB01, PDB code: 9fzc was solved by F.Ackle, M.Sorgenfrei, M.A.Seeger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	107.79 / 2.27
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.048, 55.296, 107.805, 90, 91.09, 90
R / Rfree (%)	20.8 / 23.4

The binding sites of Calcium atom in the Structure of Ompa-Short in Complex with Nanobody NB01 (pdb code 9fzc). 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 Ompa-Short in Complex with Nanobody NB01, PDB code: 9fzc:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of Ompa-Short in Complex with Nanobody NB01


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Ompa-Short in Complex with Nanobody NB01 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca207 b:34.1 occ:1.00 OD1 A:ASN146 2.3 20.2 1.0 O A:HOH350 2.4 25.9 1.0 OD1 A:ASP158 2.5 25.3 1.0 OD2 A:ASP158 2.5 20.9 1.0 O A:HOH308 2.5 24.1 1.0 O A:HOH314 2.7 23.6 1.0 CG A:ASP158 2.8 23.5 1.0 CG A:ASN146 3.5 22.1 1.0 H A:ASN146 3.8 25.7 1.0 OD1 A:ASN145 4.0 26.9 1.0 HD21 A:ASN146 4.0 30.9 1.0 HD21 A:ASN145 4.0 37.0 1.0 HA A:ASN146 4.2 29.2 1.0 ND2 A:ASN146 4.2 25.1 1.0 O A:HOH306 4.3 24.5 1.0 CB A:ASP158 4.4 20.4 1.0 N A:ASN146 4.4 20.7 1.0 ND2 A:ASN145 4.4 30.1 1.0 CG A:ASN145 4.4 27.4 1.0 HB3 A:ASP20 4.5 28.9 1.0 OD2 A:ASP20 4.5 24.1 1.0 CA A:ASN146 4.6 23.6 1.0 HZ2 A:TRP143 4.7 22.8 1.0 CB A:ASN146 4.7 22.4 1.0 HB2 A:ASP158 4.7 25.3 1.0 O A:ARG156 4.8 22.3 1.0 HD3 A:ARG156 4.8 37.0 1.0 HB3 A:ASP158 4.8 25.3 1.0 H A:ASP158 4.8 27.6 1.0 HB2 A:ASP20 4.8 28.9 1.0 HA A:ASN145 4.9 26.3 1.0 N A:ASP158 4.9 22.3 1.0

Calcium binding site 2 out of 2 in the Structure of Ompa-Short in Complex with Nanobody NB01


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Ompa-Short in Complex with Nanobody NB01 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca212 b:26.0 occ:1.00 OD1 B:ASN146 2.4 18.7 1.0 O B:HOH318 2.4 25.3 1.0 OD2 B:ASP158 2.5 25.9 1.0 OD1 B:ASP158 2.5 21.9 1.0 O B:HOH306 2.5 25.1 1.0 O B:HOH362 2.6 30.3 1.0 CG B:ASP158 2.8 21.6 1.0 CG B:ASN146 3.6 22.3 1.0 H B:ASN146 3.9 24.0 1.0 HD21 B:ASN146 4.1 32.1 1.0 HD22 B:ASN145 4.1 30.8 1.0 OD1 B:ASN145 4.1 27.7 1.0 O B:HOH301 4.1 29.8 1.0 O B:HOH319 4.1 26.1 1.0 HB3 B:ASP20 4.2 32.5 1.0 OD2 B:ASP20 4.2 29.9 1.0 HA B:ASN146 4.2 26.8 1.0 ND2 B:ASN146 4.3 26.1 1.0 CB B:ASP158 4.3 20.3 1.0 O B:HOH352 4.4 27.5 1.0 N B:ASN146 4.5 19.3 1.0 ND2 B:ASN145 4.5 24.9 1.0 CG B:ASN145 4.5 24.4 1.0 HB2 B:ASP20 4.6 32.5 1.0 O B:ARG156 4.6 22.7 1.0 H B:ASP158 4.6 27.8 1.0 HZ2 B:TRP143 4.7 25.0 1.0 HB2 B:ASP158 4.7 25.2 1.0 CA B:ASN146 4.7 21.6 1.0 CB B:ASP20 4.8 26.3 1.0 HB3 B:ASP158 4.8 25.2 1.0 CB B:ASN146 4.8 21.8 1.0 N B:ASP158 4.8 22.5 1.0 CG B:ASP20 4.9 30.1 1.0 HA B:ASN145 5.0 27.8 1.0

M.Sorgenfrei, L.M.Hurlimann, A.Printz, F.Wegner, D.Morger, F.Ackle, M.M.Remy, G.Montowski, H.Keserue, A.Cuenod, F.Imkamp, A.Egli, P.M.Keller, M.A.Seeger. Rapid Detection and Capture of Clinical Escherichia Coli Strains Mediated By Ompa-Targeting Nanobodies To Be Published.