Calcium in PDB 6kge: Crystal Structure of CADOC0917(R16D)-CACOHA2 Complex at pH 5.5

The structure of Crystal Structure of CADOC0917(R16D)-CACOHA2 Complex at pH 5.5, PDB code: 6kge 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)	35.75 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	42.990, 76.030, 121.000, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 23.7

The binding sites of Calcium atom in the Crystal Structure of CADOC0917(R16D)-CACOHA2 Complex at pH 5.5 (pdb code 6kge). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of CADOC0917(R16D)-CACOHA2 Complex at pH 5.5, PDB code: 6kge:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of CADOC0917(R16D)-CACOHA2 Complex at pH 5.5


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(R16D)-CACOHA2 Complex at pH 5.5 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca101 b:30.5 occ:1.00 OD1 D:ASN8 2.2 22.7 1.0 O D:HOH213 2.2 23.0 1.0 OD1 D:ASP6 2.3 20.4 1.0 O D:VAL12 2.3 24.8 1.0 OD1 D:ASP10 2.5 24.5 1.0 OD2 D:ASP17 2.5 19.0 1.0 OD1 D:ASP17 2.6 19.4 1.0 CG D:ASP17 2.9 22.3 1.0 CG D:ASN8 3.2 25.3 1.0 HD21 D:ASN8 3.2 35.7 1.0 CG D:ASP10 3.2 30.3 1.0 CG D:ASP6 3.4 22.6 1.0 HA D:ASP6 3.4 29.0 1.0 H D:ASP10 3.5 40.1 1.0 OD2 D:ASP10 3.5 33.8 1.0 H D:ASN8 3.5 33.8 1.0 ND2 D:ASN8 3.5 29.7 1.0 C D:VAL12 3.5 28.0 1.0 H D:VAL12 3.6 36.4 1.0 HA D:VAL13 3.7 26.6 1.0 HG13 D:VAL12 3.8 38.4 1.0 H D:ASN14 4.1 33.7 1.0 OD2 D:ASP6 4.1 30.2 1.0 CA D:ASP6 4.1 24.1 1.0 H D:ASP9 4.2 52.4 1.0 H D:LEU7 4.2 45.6 1.0 N D:VAL12 4.3 30.3 1.0 CB D:ASP6 4.3 24.6 1.0 N D:ASP10 4.3 33.3 1.0 N D:ASN8 4.3 28.1 1.0 HD22 D:ASN8 4.4 35.7 1.0 CB D:ASP17 4.4 16.3 1.0 HG12 D:VAL12 4.4 38.4 1.0 OD1 D:ASN14 4.4 26.2 1.0 N D:VAL13 4.4 28.2 1.0 CB D:ASP10 4.4 37.5 1.0 CB D:ASN8 4.5 24.7 1.0 CA D:VAL12 4.5 28.6 1.0 HB2 D:ASP6 4.5 29.6 1.0 H D:GLY11 4.5 44.3 1.0 CA D:VAL13 4.5 22.1 1.0 CG1 D:VAL12 4.5 31.9 1.0 N D:LEU7 4.5 37.9 1.0 C D:ASP6 4.5 26.1 1.0 N D:ASP9 4.6 43.6 1.0 HB3 D:ASP10 4.6 45.1 1.0 HB2 D:ASP16 4.7 41.6 1.0 H D:ASP17 4.7 21.0 1.0 HB2 D:ASP17 4.7 19.6 1.0 CA D:ASN8 4.8 25.8 1.0 N D:ASN14 4.8 28.0 1.0 CA D:ASP10 4.8 36.9 1.0 C D:ASN8 4.8 27.5 1.0 HB3 D:ASP17 4.8 19.6 1.0 N D:GLY11 4.9 36.9 1.0 HB3 D:ASN8 4.9 29.3 1.0 N D:ASP17 5.0 17.8 1.0 HA D:ASP17 5.0 26.7 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of CADOC0917(R16D)-CACOHA2 Complex at pH 5.5


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(R16D)-CACOHA2 Complex at pH 5.5 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca102 b:15.1 occ:1.00 O D:ALA45 2.2 37.2 1.0 O D:HOH208 2.3 25.3 1.0 OD1 D:ASN41 2.3 37.9 1.0 OD1 D:ASP43 2.3 36.5 1.0 OD1 D:ASP50 2.4 19.1 1.0 OD2 D:ASP50 2.4 18.1 1.0 OD1 D:ASP39 2.5 31.4 1.0 CG D:ASP50 2.8 18.5 1.0 CG D:ASP43 3.2 43.8 1.0 H D:ASP43 3.3 52.5 1.0 CG D:ASN41 3.4 39.9 1.0 H D:ALA45 3.4 42.1 1.0 C D:ALA45 3.4 22.3 1.0 HD21 D:ASN41 3.4 51.6 1.0 HA D:ASP39 3.5 34.7 1.0 OD2 D:ASP43 3.6 35.2 1.0 CG D:ASP39 3.6 34.4 1.0 HA D:VAL46 3.7 23.8 1.0 H D:ASN41 3.7 40.2 1.0 ND2 D:ASN41 3.8 43.0 1.0 N D:ALA45 4.1 35.0 1.0 H D:GLY42 4.1 53.2 1.0 N D:ASP43 4.2 43.7 1.0 H D:ASN47 4.2 33.6 1.0 CA D:ASP39 4.2 28.8 1.0 CB D:ASP50 4.2 14.9 1.0 HB3 D:ALA45 4.3 31.4 1.0 CA D:ALA45 4.3 33.0 1.0 N D:VAL46 4.3 28.3 1.0 CB D:ASP43 4.4 37.2 1.0 OD2 D:ASP39 4.4 39.8 1.0 H D:GLY44 4.4 44.0 1.0 H D:ILE40 4.4 23.2 1.0 CA D:VAL46 4.4 19.9 1.0 CB D:ASP39 4.4 26.9 1.0 N D:ASN41 4.5 33.4 1.0 OD1 D:ASN47 4.5 20.5 1.0 H D:ASP50 4.5 22.4 1.0 N D:GLY42 4.5 44.3 1.0 C D:ASP39 4.5 17.0 1.0 HB3 D:ASP43 4.6 44.7 1.0 N D:ILE40 4.6 19.3 1.0 HD22 D:ASN41 4.6 51.6 1.0 CB D:ASN41 4.7 26.1 1.0 HB2 D:ASP50 4.7 17.6 1.0 HB3 D:ASP50 4.7 17.6 1.0 CA D:ASP43 4.7 42.4 1.0 HB2 D:ASP39 4.7 32.4 1.0 N D:GLY44 4.8 36.6 1.0 HA D:ASP50 4.8 24.0 1.0 HB3 D:ARG49 4.8 24.5 1.0 CB D:ALA45 4.8 26.5 1.0 N D:ASN47 4.8 28.0 1.0 N D:ASP50 4.9 18.6 1.0 HD21 D:ASN47 4.9 35.5 1.0 HG22 D:VAL46 4.9 33.0 1.0 CA D:ASN41 4.9 21.8 1.0 C D:ASN41 4.9 21.2 1.0 CA D:ASP50 4.9 19.9 1.0 C D:ASP43 4.9 37.1 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of CADOC0917(R16D)-CACOHA2 Complex at pH 5.5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of CADOC0917(R16D)-CACOHA2 Complex at pH 5.5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca101 b:42.9 occ:1.00 O B:ALA45 2.1 40.6 1.0 O B:HOH208 2.3 20.3 1.0 OD1 B:ASP39 2.3 25.3 1.0 OD1 B:ASN41 2.4 26.0 1.0 OD2 B:ASP50 2.4 27.1 1.0 OD1 B:ASP43 2.5 33.1 1.0 OD1 B:ASP50 2.5 27.4 1.0 CG B:ASP50 2.8 23.9 1.0 CG B:ASP43 3.1 37.4 1.0 CG B:ASN41 3.4 25.0 1.0 HD21 B:ASN41 3.4 50.1 1.0 H B:ASP43 3.4 39.6 1.0 OD2 B:ASP43 3.4 44.2 1.0 C B:ALA45 3.4 25.6 1.0 H B:ALA45 3.4 33.6 1.0 HA B:ASP39 3.5 39.9 1.0 CG B:ASP39 3.5 26.2 1.0 HA B:VAL46 3.6 30.6 1.0 H B:ASN41 3.7 49.5 1.0 ND2 B:ASN41 3.7 41.7 1.0 N B:ALA45 4.1 28.0 1.0 H B:ASN47 4.2 29.7 1.0 N B:ASP43 4.2 33.0 1.0 CA B:ASP39 4.2 33.2 1.0 OD2 B:ASP39 4.2 26.8 1.0 H B:ILE40 4.3 42.3 1.0 H B:GLY42 4.3 34.4 1.0 N B:VAL46 4.3 22.9 1.0 CB B:ASP50 4.3 22.1 1.0 CA B:ALA45 4.3 30.6 1.0 HB3 B:ALA45 4.3 38.8 1.0 CA B:VAL46 4.4 25.5 1.0 CB B:ASP43 4.4 32.3 1.0 N B:ASN41 4.4 41.2 1.0 CB B:ASP39 4.4 38.6 1.0 N B:ILE40 4.5 35.2 1.0 C B:ASP39 4.5 25.0 1.0 HD22 B:ASN41 4.6 50.1 1.0 H B:ASP50 4.6 32.8 1.0 N B:GLY42 4.6 28.6 1.0 HB3 B:ASP43 4.6 38.8 1.0 H B:GLY44 4.6 38.6 1.0 OD1 B:ASN47 4.7 23.5 1.0 HB3 B:ARG49 4.7 42.1 1.0 CB B:ASN41 4.7 32.3 1.0 HB2 B:ASP50 4.7 26.6 1.0 HG22 B:VAL46 4.7 40.8 1.0 CA B:ASP43 4.7 33.7 1.0 HB3 B:ASP50 4.8 26.6 1.0 HB2 B:ASP39 4.8 46.4 1.0 HD21 B:ASN47 4.8 37.2 1.0 N B:ASN47 4.8 24.7 1.0 HA B:ASP50 4.9 26.1 1.0 CB B:ALA45 4.9 32.2 1.0 N B:GLY44 4.9 32.1 1.0 CA B:ASN41 4.9 34.4 1.0 N B:ASP50 4.9 27.2 1.0 C B:ASN41 4.9 37.8 1.0 C B:ASP43 4.9 33.9 1.0 CA B:ASP50 5.0 22.0 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of CADOC0917(R16D)-CACOHA2 Complex at pH 5.5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of CADOC0917(R16D)-CACOHA2 Complex at pH 5.5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca102 b:21.6 occ:1.00 O B:VAL12 2.3 24.0 1.0 OD1 B:ASN8 2.3 31.9 1.0 OD1 B:ASP10 2.4 42.6 1.0 OD1 B:ASP17 2.4 24.0 1.0 OD1 B:ASP6 2.4 27.4 1.0 OD2 B:ASP17 2.5 19.6 1.0 O B:HOH202 2.6 16.5 1.0 CG B:ASP17 2.8 18.4 1.0 HD21 B:ASN8 3.1 52.9 1.0 CG B:ASP10 3.1 26.3 1.0 CG B:ASN8 3.2 32.2 1.0 HA B:ASP6 3.3 26.7 1.0 OD2 B:ASP10 3.4 29.2 1.0 H B:ASN8 3.5 29.3 1.0 C B:VAL12 3.5 21.0 1.0 ND2 B:ASN8 3.5 44.0 1.0 CG B:ASP6 3.5 26.9 1.0 H B:VAL12 3.6 35.6 1.0 H B:ASP10 3.6 30.1 1.0 HA B:VAL13 3.6 36.5 1.0 CA B:ASP6 4.0 22.2 1.0 H B:ASN14 4.0 32.9 1.0 H B:LEU7 4.0 30.9 1.0 CB B:ASP6 4.2 23.3 1.0 N B:VAL12 4.3 29.6 1.0 CB B:ASP17 4.3 27.5 1.0 N B:ASN8 4.3 24.4 1.0 HB B:VAL12 4.3 39.0 1.0 HD22 B:ASN8 4.3 52.9 1.0 HB2 B:ASP6 4.3 28.0 1.0 C B:ASP6 4.3 23.4 1.0 N B:LEU7 4.4 25.6 1.0 N B:VAL13 4.4 26.0 1.0 OD1 B:ASN14 4.4 26.4 1.0 N B:ASP10 4.4 25.4 1.0 CA B:VAL13 4.4 30.4 1.0 CA B:VAL12 4.4 22.7 1.0 H B:ASP9 4.4 47.4 1.0 OD2 B:ASP6 4.5 20.4 1.0 CB B:ASP10 4.5 28.6 1.0 CB B:ASN8 4.5 38.3 1.0 H B:ASP17 4.6 25.4 1.0 HB3 B:ASP10 4.7 33.9 1.0 N B:ASN14 4.7 27.3 1.0 HB3 B:ASP17 4.7 33.1 1.0 HB2 B:ASP17 4.7 33.1 1.0 N B:ASP9 4.7 39.4 1.0 H B:GLY11 4.8 35.1 1.0 HB2 B:ASP16 4.8 34.8 1.0 CA B:ASN8 4.8 24.2 1.0 CA B:ASP10 4.9 38.8 1.0 N B:ASP17 4.9 21.5 1.0 CB B:VAL12 4.9 32.4 1.0 CG B:ASN14 4.9 31.3 1.0 HD21 B:ASN14 4.9 42.1 1.0 HA B:ASP17 4.9 22.3 1.0 C B:ASN8 4.9 32.7 1.0 HG22 B:VAL13 5.0 29.1 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