Calcium in PDB 6bgd: 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: 6bgd 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)	37.90 / 1.47
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	75.834, 110.199, 89.304, 90.00, 90.00, 90.00
R / Rfree (%)	11.4 / 14.4

The binding sites of Calcium atom in the The Crystal Structure of the W145A Variant of Tpmglb-2 (TP0684) with Bound Glucose (pdb code 6bgd). 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 Crystal Structure of the W145A Variant of Tpmglb-2 (TP0684) with Bound Glucose, PDB code: 6bgd:

Calcium binding site 1 out of 1 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:Ca411 b:13.1 occ:1.00 O A:ILE77 2.3 13.2 1.0 OD1 A:ASP71 2.3 14.3 1.0 O A:HOH558 2.4 12.8 1.0 O A:HOH513 2.4 12.8 1.0 OD1 A:ASP75 2.5 16.6 1.0 OD1 A:ASN73 2.6 15.0 1.0 OD2 A:ASP166 2.6 11.3 1.0 CG A:ASP75 3.4 17.7 1.0 CG A:ASP71 3.5 14.0 1.0 H A:ASP75 3.5 20.3 1.0 CG A:ASN73 3.5 15.7 1.0 C A:ILE77 3.5 13.4 1.0 H A:ILE77 3.5 17.3 1.0 H A:ASN73 3.5 18.2 1.0 CG A:ASP166 3.6 11.4 1.0 HD21 A:ASN73 3.7 21.1 1.0 HB A:ILE77 3.7 19.1 1.0 HA A:ASP71 3.7 16.0 1.0 OD2 A:ASP75 3.7 18.3 1.0 H A:GLY79 3.8 13.6 1.0 OD1 A:ASP166 3.8 12.2 1.0 HA A:ILE78 3.9 13.5 1.0 ND2 A:ASN73 4.0 17.6 1.0 HA A:LYS164 4.1 14.2 1.0 H A:ARG72 4.2 15.9 1.0 N A:ILE77 4.2 14.4 1.0 OD2 A:ASP71 4.2 14.6 1.0 CA A:ILE77 4.3 14.3 1.0 N A:ASP75 4.3 16.9 1.0 H A:GLY74 4.3 19.7 1.0 CA A:ASP71 4.3 13.3 1.0 N A:ASN73 4.3 15.2 1.0 O A:LYS164 4.4 11.7 1.0 CB A:ASP71 4.4 13.2 1.0 CB A:ILE77 4.4 15.9 1.0 N A:ARG72 4.4 13.3 1.0 C A:ASP71 4.5 13.6 1.0 N A:GLY79 4.5 11.3 1.0 O A:HOH590 4.5 20.1 1.0 N A:ILE78 4.5 12.2 1.0 HD13 A:ILE78 4.6 17.7 1.0 H A:GLY76 4.6 19.4 1.0 CB A:ASP75 4.6 17.5 1.0 CA A:ILE78 4.6 11.2 1.0 HG22 A:ILE77 4.7 18.3 1.0 N A:GLY74 4.7 16.4 1.0 CB A:ASN73 4.7 15.9 1.0 HB2 A:ASP71 4.7 15.8 1.0 HD22 A:ASN73 4.8 21.1 1.0 CA A:ASP75 4.8 17.5 1.0 HB3 A:ASP75 4.9 21.0 1.0 O A:ASP163 4.9 13.8 1.0 CA A:ASN73 4.9 15.4 1.0 N A:GLY76 4.9 16.2 1.0 HB3 A:ASN73 4.9 19.1 1.0 CA A:LYS164 5.0 11.8 1.0 CB A:ASP166 5.0 10.6 1.0 C A:ASN73 5.0 16.9 1.0 C A:LYS164 5.0 11.3 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