Calcium in PDB 6bgc: The Crystal Structure of the W145A Variant of Tpmglb-2 (TP0684) with Bound Glucose

The structure of The Crystal Structure of the W145A Variant of Tpmglb-2 (TP0684) with Bound Glucose, PDB code: 6bgc was solved by C.A.Brautigam, M.V.Norgard, R.K.Deka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.73 / 2.08
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	42.257, 61.592, 70.350, 80.22, 77.58, 72.72
R / Rfree (%)	18 / 22

The binding sites of Calcium atom in the The Crystal Structure of the W145A Variant of Tpmglb-2 (TP0684) with Bound Glucose (pdb code 6bgc). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the The Crystal Structure of the W145A Variant of Tpmglb-2 (TP0684) with Bound Glucose, PDB code: 6bgc:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the The Crystal Structure of the W145A Variant of Tpmglb-2 (TP0684) with Bound Glucose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Crystal Structure of the W145A Variant of Tpmglb-2 (TP0684) with Bound Glucose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:35.1 occ:1.00 OD1 A:ASP71 2.3 39.0 1.0 O A:ILE77 2.3 34.7 1.0 O A:HOH503 2.5 23.4 1.0 OD1 A:ASN73 2.5 42.2 1.0 O A:HOH568 2.5 25.1 1.0 OD1 A:ASP75 2.5 46.1 1.0 OD2 A:ASP166 2.6 35.0 1.0 CG A:ASP75 3.4 46.1 1.0 CG A:ASN73 3.4 43.8 1.0 HD21 A:ASN73 3.4 53.3 1.0 CG A:ASP71 3.4 40.1 1.0 CG A:ASP166 3.5 34.4 1.0 C A:ILE77 3.5 35.4 1.0 H A:ILE77 3.6 46.5 1.0 H A:ASN73 3.6 53.9 1.0 H A:ASP75 3.6 52.8 1.0 OD1 A:ASP166 3.6 36.6 1.0 HA A:ASP71 3.7 44.6 1.0 OD2 A:ASP75 3.7 46.4 1.0 ND2 A:ASN73 3.8 44.4 1.0 H A:GLY79 3.8 33.6 1.0 HB A:ILE77 3.9 46.3 1.0 HA A:ILE78 4.0 37.1 1.0 H A:ARG72 4.0 44.9 1.0 HA A:LYS164 4.1 50.6 1.0 O A:LYS164 4.2 41.4 1.0 OD2 A:ASP71 4.2 42.8 1.0 H A:GLY74 4.2 50.2 1.0 N A:ILE77 4.2 38.8 1.0 CA A:ASP71 4.3 37.2 1.0 N A:ASN73 4.3 44.9 1.0 CA A:ILE77 4.3 37.8 1.0 N A:ARG72 4.4 37.5 1.0 N A:ASP75 4.4 44.0 1.0 CB A:ASP71 4.4 38.6 1.0 C A:ASP71 4.5 38.6 1.0 N A:GLY79 4.6 28.0 1.0 N A:ILE78 4.6 31.4 1.0 HD22 A:ASN73 4.6 53.3 1.0 CB A:ILE77 4.6 38.6 1.0 CB A:ASP75 4.6 45.9 1.0 HD13 A:ILE78 4.6 40.2 1.0 N A:GLY74 4.7 41.9 1.0 CB A:ASN73 4.7 45.3 1.0 H A:GLY76 4.7 41.6 1.0 HB2 A:ASP71 4.7 46.3 1.0 O A:ASP163 4.7 45.3 1.0 CA A:ILE78 4.7 30.9 1.0 HB3 A:ASP75 4.8 55.1 1.0 CB A:ASP166 4.9 31.5 1.0 CA A:ASN73 4.9 46.5 1.0 C A:LYS164 4.9 41.2 1.0 CA A:LYS164 4.9 42.1 1.0 HG22 A:ILE77 4.9 46.0 1.0 HB2 A:ARG72 4.9 46.0 1.0 HB3 A:ASN73 5.0 54.3 1.0 CA A:ASP75 5.0 45.1 1.0

Calcium binding site 2 out of 2 in the The Crystal Structure of the W145A Variant of Tpmglb-2 (TP0684) with Bound Glucose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Crystal Structure of the W145A Variant of Tpmglb-2 (TP0684) with Bound Glucose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:19.6 occ:1.00 O B:ILE77 2.3 20.3 1.0 OD1 B:ASP71 2.4 22.0 1.0 O B:HOH520 2.4 14.9 1.0 OD1 B:ASN73 2.5 26.1 1.0 O B:HOH509 2.5 14.3 1.0 OD1 B:ASP75 2.5 28.0 1.0 OD2 B:ASP166 2.6 23.3 1.0 CG B:ASP75 3.3 28.1 1.0 CG B:ASN73 3.4 26.5 1.0 H B:ASP75 3.5 32.9 1.0 C B:ILE77 3.5 20.9 1.0 CG B:ASP166 3.5 21.8 1.0 CG B:ASP71 3.5 22.8 1.0 H B:ILE77 3.6 28.9 1.0 H B:ASN73 3.6 30.1 1.0 HD21 B:ASN73 3.6 32.6 1.0 OD2 B:ASP75 3.6 27.6 1.0 OD1 B:ASP166 3.7 21.9 1.0 H B:GLY79 3.8 27.2 1.0 HA B:ASP71 3.8 25.1 1.0 HB B:ILE77 3.8 28.4 1.0 ND2 B:ASN73 3.9 27.1 1.0 HA B:ILE78 4.1 25.2 1.0 H B:GLY74 4.1 31.2 1.0 HA B:LYS164 4.1 26.5 1.0 N B:ILE77 4.2 24.1 1.0 O B:LYS164 4.2 20.3 1.0 OD2 B:ASP71 4.3 24.2 1.0 CA B:ILE77 4.3 22.6 1.0 H B:ARG72 4.3 29.4 1.0 O B:HOH510 4.3 17.5 1.0 N B:ASP75 4.3 27.4 1.0 N B:ASN73 4.4 25.1 1.0 CA B:ASP71 4.4 20.9 1.0 CB B:ILE77 4.5 23.6 1.0 CB B:ASP71 4.5 22.0 1.0 N B:GLY79 4.5 22.6 1.0 N B:ARG72 4.5 24.5 1.0 N B:ILE78 4.5 20.9 1.0 C B:ASP71 4.5 21.4 1.0 N B:GLY74 4.6 26.0 1.0 CB B:ASN73 4.6 26.2 1.0 HD13 B:ILE78 4.6 24.7 1.0 HG22 B:ILE77 4.6 28.2 1.0 CB B:ASP75 4.6 28.6 1.0 HD22 B:ASN73 4.7 32.6 1.0 CA B:ILE78 4.7 21.0 1.0 HB3 B:ASN73 4.7 31.5 1.0 HB2 B:ASP71 4.8 26.4 1.0 O B:ASP163 4.8 23.4 1.0 CA B:ASN73 4.9 26.1 1.0 H B:GLY76 4.9 28.9 1.0 C B:LYS164 4.9 20.8 1.0 HB3 B:ASP75 4.9 34.3 1.0 CA B:ASP75 4.9 28.2 1.0 CB B:ASP166 4.9 19.7 1.0 CA B:LYS164 5.0 22.1 1.0

C.A.Brautigam, R.K.Deka, W.Z.Liu, M.V.Norgard. Crystal Structures of Mglb-2 (TP0684), A Topologically Variant D-Glucose-Binding Protein From Treponema Pallidum, Reveal A Ligand-Induced Conformational Change. Protein Sci. V. 27 880 2018.
ISSN: ESSN 1469-896X
PubMed: 29318719
DOI: 10.1002/PRO.3373