Calcium in PDB 6kgd: Crystal Structure of CADOC0917(R49D)-CACOHA2 Complex at pH 8.0

The structure of Crystal Structure of CADOC0917(R49D)-CACOHA2 Complex at pH 8.0, PDB code: 6kgd was solved by Y.Feng, X.Yao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.12 / 1.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	31.110, 62.500, 100.320, 90.00, 90.00, 90.00
R / Rfree (%)	15.2 / 18.8

The binding sites of Calcium atom in the Crystal Structure of CADOC0917(R49D)-CACOHA2 Complex at pH 8.0 (pdb code 6kgd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of CADOC0917(R49D)-CACOHA2 Complex at pH 8.0, PDB code: 6kgd:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of CADOC0917(R49D)-CACOHA2 Complex at pH 8.0


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of CADOC0917(R49D)-CACOHA2 Complex at pH 8.0 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca101 b:17.3 occ:1.00 O B:VAL12 2.3 21.9 1.0 OD1 B:ASP6 2.4 23.1 1.0 O B:HOH215 2.4 14.4 1.0 OD1 B:ASN8 2.4 19.9 1.0 OD1 B:ASP10 2.4 21.7 1.0 OD2 B:ASP17 2.5 13.4 1.0 OD1 B:ASP17 2.5 16.0 1.0 CG B:ASP17 2.8 12.5 1.0 CG B:ASP10 3.3 29.3 1.0 HA B:ASP6 3.3 26.2 1.0 CG B:ASN8 3.4 18.5 1.0 HD21 B:ASN8 3.4 38.0 1.0 H B:ASP10 3.4 31.9 1.0 CG B:ASP6 3.5 30.4 1.0 C B:VAL12 3.5 18.9 1.0 H B:ASN8 3.6 25.7 1.0 H B:VAL12 3.6 34.1 1.0 HA B:VAL13 3.6 30.9 1.0 OD2 B:ASP10 3.6 20.7 1.0 HG23 B:VAL12 3.7 35.9 1.0 ND2 B:ASN8 3.7 31.7 1.0 CA B:ASP6 4.0 21.8 1.0 H B:ASN14 4.1 18.2 1.0 H B:LEU7 4.1 26.2 1.0 HG22 B:VAL12 4.1 35.9 1.0 CB B:ASP6 4.2 24.1 1.0 N B:VAL12 4.2 28.5 1.0 H B:ASP9 4.3 31.6 1.0 N B:ASP10 4.3 26.6 1.0 CB B:ASP17 4.3 10.4 1.0 HB2 B:ASP6 4.3 28.9 1.0 C B:ASP6 4.4 27.0 1.0 N B:VAL13 4.4 24.5 1.0 OD2 B:ASP6 4.4 28.8 1.0 N B:ASN8 4.4 21.4 1.0 CG2 B:VAL12 4.4 29.9 1.0 CA B:VAL13 4.4 25.8 1.0 N B:LEU7 4.4 21.9 1.0 CA B:VAL12 4.5 23.6 1.0 H B:GLY11 4.5 33.9 1.0 CB B:ASP10 4.5 30.4 1.0 OD1 B:ASN14 4.5 13.4 1.0 H B:ASP17 4.5 15.3 1.0 HB2 B:ARG16 4.6 16.3 1.0 HD22 B:ASN8 4.6 38.0 1.0 N B:ASP9 4.6 26.3 1.0 CB B:ASN8 4.7 23.5 1.0 HB3 B:ASP10 4.7 36.5 1.0 HB2 B:ASP17 4.7 12.4 1.0 N B:ASN14 4.7 15.2 1.0 HB3 B:ASP17 4.8 12.4 1.0 CA B:ASP10 4.8 24.1 1.0 N B:GLY11 4.8 28.3 1.0 HG22 B:VAL13 4.9 35.9 1.0 CA B:ASN8 4.9 23.2 1.0 C B:ASN8 4.9 24.3 1.0 N B:ASP17 4.9 12.8 1.0 HA B:ASP17 5.0 16.7 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of CADOC0917(R49D)-CACOHA2 Complex at pH 8.0


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of CADOC0917(R49D)-CACOHA2 Complex at pH 8.0 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca102 b:16.8 occ:1.00 OD1 B:ASP39 2.3 18.8 1.0 O B:ALA45 2.3 15.8 1.0 OD1 B:ASN41 2.4 19.3 1.0 OD1 B:ASP43 2.4 18.7 1.0 O B:HOH211 2.4 19.8 1.0 OD2 B:ASP50 2.4 15.1 1.0 OD1 B:ASP50 2.5 16.4 1.0 CG B:ASP50 2.8 17.2 1.0 CG B:ASN41 3.3 17.4 1.0 HD21 B:ASN41 3.3 34.3 1.0 CG B:ASP43 3.3 27.7 1.0 H B:ASP43 3.3 33.4 1.0 CG B:ASP39 3.4 18.2 1.0 HA B:ASP39 3.4 26.1 1.0 C B:ALA45 3.4 14.3 1.0 H B:ALA45 3.5 21.6 1.0 H B:ASN41 3.5 26.8 1.0 ND2 B:ASN41 3.6 28.6 1.0 HA B:VAL46 3.6 14.1 1.0 OD2 B:ASP43 3.7 26.9 1.0 H B:GLY42 4.0 29.1 1.0 CA B:ASP39 4.1 21.7 1.0 N B:ALA45 4.1 18.1 1.0 N B:ASP43 4.1 27.9 1.0 H B:ASN47 4.2 14.1 1.0 OD2 B:ASP39 4.2 22.0 1.0 CB B:ASP39 4.2 19.9 1.0 HB3 B:ALA45 4.2 23.4 1.0 CB B:ASP50 4.3 15.7 1.0 N B:ASN41 4.3 22.3 1.0 CA B:ALA45 4.3 15.1 1.0 N B:VAL46 4.4 12.1 1.0 H B:ILE40 4.4 29.0 1.0 C B:ASP39 4.4 24.7 1.0 H B:GLY44 4.4 26.6 1.0 N B:GLY42 4.4 24.3 1.0 CA B:VAL46 4.4 11.8 1.0 HD22 B:ASN41 4.4 34.3 1.0 HB2 B:ASP39 4.5 23.8 1.0 CB B:ASP43 4.5 28.9 1.0 N B:ILE40 4.6 24.2 1.0 CB B:ASN41 4.6 21.9 1.0 OD1 B:ASN47 4.6 14.3 1.0 H B:ASP50 4.6 18.2 1.0 HB2 B:ASP50 4.7 18.8 1.0 HB3 B:ASP43 4.7 34.6 1.0 HB3 B:ASP50 4.7 18.8 1.0 CA B:ASP43 4.7 27.5 1.0 N B:GLY44 4.7 22.1 1.0 CA B:ASN41 4.8 28.7 1.0 C B:ASN41 4.8 26.2 1.0 N B:ASN47 4.8 11.8 1.0 CB B:ALA45 4.8 19.6 1.0 HB2 B:ASP49 4.8 23.5 1.0 HA B:ASP50 4.9 17.0 1.0 C B:ASP43 4.9 27.8 1.0 N B:ASP50 4.9 15.2 1.0 HG22 B:VAL46 5.0 25.1 1.0 O B:ASP39 5.0 25.1 1.0 CA B:ASP50 5.0 14.2 1.0 HD21 B:ASN47 5.0 19.6 1.0

X.Yao, C.Chen, Y.Wang, S.Dong, Y.J.Liu, Y.Li, Z.Cui, W.Gong, S.Perrett, L.Yao, R.Lamed, E.A.Bayer, Q.Cui, Y.Feng. Discovery and Mechanism of A pH-Dependent Dual-Binding-Site Switch in the Interaction of A Pair of Protein Modules. Sci Adv V. 6 2020.
ISSN: ESSN 2375-2548
PubMed: 33097546
DOI: 10.1126/SCIADV.ABD7182