Calcium in PDB 6kgf: Crystal Structure of CADOC0917(R16D)-CACOHA2 Complex at pH 8.2

The structure of Crystal Structure of CADOC0917(R16D)-CACOHA2 Complex at pH 8.2, PDB code: 6kgf 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)	47.17 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	41.650, 75.970, 120.330, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 24.9

The binding sites of Calcium atom in the Crystal Structure of CADOC0917(R16D)-CACOHA2 Complex at pH 8.2 (pdb code 6kgf). 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 8.2, PDB code: 6kgf:
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 8.2


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 8.2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca101 b:33.8 occ:1.00 OD1 D:ASP10 2.3 48.4 1.0 O D:VAL12 2.3 35.0 1.0 OD1 D:ASN8 2.4 39.8 1.0 OD1 D:ASP6 2.4 33.8 1.0 OD2 D:ASP17 2.4 36.2 1.0 O D:HOH204 2.5 62.9 1.0 OD1 D:ASP17 2.6 35.7 1.0 CG D:ASP17 2.8 35.8 1.0 HD21 D:ASN8 3.0 55.6 1.0 CG D:ASP10 3.1 50.2 1.0 CG D:ASN8 3.2 42.3 1.0 HA D:ASP6 3.2 45.4 1.0 CG D:ASP6 3.4 36.2 1.0 OD2 D:ASP10 3.4 51.4 1.0 H D:ASP10 3.4 53.1 1.0 ND2 D:ASN8 3.4 46.3 1.0 C D:VAL12 3.4 36.8 1.0 H D:VAL12 3.5 48.2 1.0 HG23 D:VAL12 3.6 52.8 1.0 HA D:VAL13 3.6 40.0 1.0 H D:ASN8 3.7 49.0 1.0 CA D:ASP6 4.0 37.8 1.0 CB D:ASP6 4.1 38.6 1.0 N D:VAL12 4.2 40.2 1.0 OD2 D:ASP6 4.2 37.7 1.0 H D:ASN14 4.2 47.9 1.0 H D:ASP9 4.2 46.8 1.0 N D:ASP10 4.2 44.2 1.0 HD22 D:ASN8 4.2 55.6 1.0 HB2 D:ASP6 4.3 46.3 1.0 H D:LEU7 4.3 47.5 1.0 N D:VAL13 4.3 34.0 1.0 CB D:ASP10 4.3 51.1 1.0 CB D:ASP17 4.3 32.3 1.0 HG22 D:VAL12 4.4 52.8 1.0 CA D:VAL12 4.4 39.1 1.0 CG2 D:VAL12 4.4 44.0 1.0 CA D:VAL13 4.4 33.4 1.0 N D:ASN8 4.4 40.9 1.0 H D:GLY11 4.4 56.4 1.0 OD1 D:ASN14 4.4 37.1 1.0 C D:ASP6 4.5 36.2 1.0 CB D:ASN8 4.5 43.0 1.0 HB3 D:ASP10 4.5 61.3 1.0 N D:LEU7 4.6 39.5 1.0 N D:ASP9 4.6 39.0 1.0 H D:ASP17 4.6 39.9 1.0 HB2 D:ASP17 4.7 38.7 1.0 CA D:ASP10 4.7 49.3 1.0 N D:GLY11 4.8 47.0 1.0 HB3 D:ASP17 4.8 38.7 1.0 HB2 D:ASP16 4.8 49.0 1.0 HG22 D:VAL13 4.8 41.2 1.0 N D:ASN14 4.8 39.9 1.0 CA D:ASN8 4.9 44.1 1.0 C D:ASN8 4.9 45.1 1.0 HB3 D:ASN8 4.9 51.6 1.0 C D:ASP10 5.0 47.0 1.0 N D:ASP17 5.0 33.2 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of CADOC0917(R16D)-CACOHA2 Complex at pH 8.2


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 8.2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca102 b:28.9 occ:1.00 OD1 D:ASP43 2.3 31.6 1.0 O D:ALA45 2.3 46.5 1.0 OD1 D:ASP39 2.3 30.6 1.0 O D:HOH201 2.3 20.6 1.0 OD1 D:ASN41 2.4 36.0 1.0 OD2 D:ASP50 2.6 29.7 1.0 OD1 D:ASP50 2.6 26.8 1.0 CG D:ASP50 2.9 29.4 1.0 CG D:ASP43 3.1 35.2 1.0 CG D:ASN41 3.3 38.7 1.0 H D:ASP43 3.3 52.1 1.0 HD21 D:ASN41 3.3 46.7 1.0 OD2 D:ASP43 3.4 33.2 1.0 HA D:ASP39 3.4 41.2 1.0 H D:ALA45 3.4 50.6 1.0 C D:ALA45 3.4 42.8 1.0 CG D:ASP39 3.5 33.8 1.0 H D:ASN41 3.6 50.6 1.0 ND2 D:ASN41 3.7 38.9 1.0 HA D:VAL46 3.8 48.2 1.0 N D:ALA45 4.1 42.2 1.0 H D:ILE40 4.1 43.1 1.0 N D:ASP43 4.1 43.4 1.0 CA D:ASP39 4.2 34.3 1.0 OD2 D:ASP39 4.3 34.1 1.0 H D:ASN47 4.3 37.5 1.0 CA D:ALA45 4.3 42.5 1.0 CB D:ASP43 4.3 40.9 1.0 HB3 D:ALA45 4.3 51.5 1.0 H D:GLY42 4.3 47.4 1.0 CB D:ASP39 4.3 35.7 1.0 H D:GLY44 4.4 55.8 1.0 N D:VAL46 4.4 41.8 1.0 N D:ASN41 4.4 42.2 1.0 CB D:ASP50 4.4 28.5 1.0 N D:ILE40 4.5 35.9 1.0 HD22 D:ASN41 4.5 46.7 1.0 CA D:VAL46 4.5 40.2 1.0 HB3 D:ASP43 4.5 49.1 1.0 OD1 D:ASN47 4.6 36.4 1.0 C D:ASP39 4.6 35.2 1.0 N D:GLY42 4.6 39.5 1.0 HB2 D:ASP39 4.6 42.8 1.0 CB D:ASN41 4.6 40.2 1.0 CA D:ASP43 4.6 44.3 1.0 N D:GLY44 4.7 46.5 1.0 H D:ASP50 4.8 35.0 1.0 HB2 D:ASP50 4.8 34.2 1.0 C D:ASN41 4.8 43.4 1.0 CA D:ASN41 4.8 42.6 1.0 C D:ASP43 4.8 45.8 1.0 CB D:ALA45 4.9 42.9 1.0 HB3 D:ASP50 4.9 34.2 1.0 N D:ASN47 4.9 31.3 1.0 HA D:ASP50 4.9 34.5 1.0 HB3 D:ARG49 5.0 36.0 1.0 HG22 D:VAL46 5.0 54.9 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of CADOC0917(R16D)-CACOHA2 Complex at pH 8.2


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 8.2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca101 b:36.4 occ:1.00 OD1 B:ASN8 2.3 46.9 1.0 O B:VAL12 2.3 46.7 1.0 OD2 B:ASP17 2.4 42.2 1.0 OD1 B:ASP6 2.4 36.9 1.0 OD1 B:ASP10 2.4 45.0 1.0 O B:HOH202 2.5 36.7 1.0 OD1 B:ASP17 2.6 39.4 1.0 CG B:ASP17 2.8 38.6 1.0 HD21 B:ASN8 3.1 57.8 1.0 CG B:ASN8 3.2 47.2 1.0 HA B:ASP6 3.2 39.9 1.0 CG B:ASP10 3.2 47.5 1.0 H B:ASP10 3.4 59.9 1.0 CG B:ASP6 3.4 36.0 1.0 ND2 B:ASN8 3.5 48.2 1.0 OD2 B:ASP10 3.6 48.6 1.0 C B:VAL12 3.6 47.8 1.0 H B:VAL12 3.6 60.6 1.0 H B:ASN8 3.7 46.1 1.0 HA B:VAL13 3.7 46.0 1.0 HG13 B:VAL12 3.8 71.3 1.0 CA B:ASP6 3.9 33.2 1.0 H B:ASN14 4.1 43.9 1.0 HG12 B:VAL12 4.1 71.3 1.0 CB B:ASP6 4.1 33.1 1.0 H B:ASP9 4.1 57.3 1.0 N B:ASP10 4.2 49.9 1.0 H B:LEU7 4.3 43.4 1.0 HD22 B:ASN8 4.3 57.8 1.0 HB2 B:ASP6 4.3 39.8 1.0 CB B:ASP17 4.3 35.5 1.0 C B:ASP6 4.3 34.5 1.0 OD2 B:ASP6 4.3 39.0 1.0 N B:VAL12 4.3 50.5 1.0 N B:ASN8 4.4 38.5 1.0 CB B:ASP10 4.4 50.1 1.0 N B:VAL13 4.4 43.0 1.0 CG1 B:VAL12 4.4 59.4 1.0 N B:LEU7 4.5 36.2 1.0 CA B:VAL13 4.5 38.4 1.0 N B:ASP9 4.5 47.8 1.0 HB3 B:ASP10 4.5 60.1 1.0 CB B:ASN8 4.5 47.1 1.0 CA B:VAL12 4.5 51.4 1.0 H B:ASP17 4.6 49.2 1.0 HB2 B:ASP17 4.7 42.5 1.0 H B:GLY11 4.7 59.1 1.0 OD1 B:ASN14 4.7 39.2 1.0 CA B:ASP10 4.8 50.3 1.0 N B:ASN14 4.8 36.6 1.0 CA B:ASN8 4.8 43.6 1.0 HB3 B:ASP17 4.8 42.5 1.0 C B:ASN8 4.8 46.5 1.0 HB2 B:ASP16 4.9 61.8 1.0 HA B:ASP9 4.9 61.0 1.0 N B:ASP17 4.9 41.0 1.0 HG22 B:VAL13 4.9 37.8 1.0 HA B:ASP17 4.9 41.6 1.0 HB3 B:ASN8 4.9 56.6 1.0 O B:ASP6 5.0 34.2 1.0 N B:GLY11 5.0 49.3 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of CADOC0917(R16D)-CACOHA2 Complex at pH 8.2


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 8.2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca102 b:32.1 occ:1.00 O B:ALA45 2.2 38.7 1.0 OD1 B:ASN41 2.3 40.9 1.0 OD1 B:ASP39 2.3 34.0 1.0 OD2 B:ASP50 2.4 36.0 1.0 OD1 B:ASP43 2.5 38.5 1.0 OD1 B:ASP50 2.6 34.6 1.0 O B:HOH201 2.7 21.2 1.0 CG B:ASP50 2.8 37.9 1.0 HD21 B:ASN41 3.1 49.5 1.0 CG B:ASN41 3.2 41.8 1.0 CG B:ASP43 3.2 38.0 1.0 HA B:ASP39 3.4 45.5 1.0 OD2 B:ASP43 3.4 39.4 1.0 H B:ALA45 3.4 47.8 1.0 C B:ALA45 3.4 38.5 1.0 H B:ASP43 3.4 47.4 1.0 CG B:ASP39 3.5 36.6 1.0 ND2 B:ASN41 3.5 41.2 1.0 H B:ASN41 3.6 45.4 1.0 HA B:VAL46 3.6 48.0 1.0 N B:ALA45 4.1 39.8 1.0 CA B:ASP39 4.1 37.9 1.0 H B:GLY42 4.2 63.4 1.0 H B:ILE40 4.2 41.9 1.0 H B:ASN47 4.2 38.9 1.0 OD2 B:ASP39 4.3 38.3 1.0 N B:ASP43 4.3 39.5 1.0 CB B:ASP50 4.3 39.3 1.0 H B:GLY44 4.3 43.7 1.0 CA B:ALA45 4.3 39.1 1.0 HD22 B:ASN41 4.3 49.5 1.0 N B:VAL46 4.3 38.8 1.0 CB B:ASP39 4.3 39.4 1.0 N B:ASN41 4.4 37.8 1.0 HB3 B:ALA45 4.4 48.9 1.0 CA B:VAL46 4.4 40.0 1.0 CB B:ASP43 4.5 36.8 1.0 OD1 B:ASN47 4.5 40.9 1.0 C B:ASP39 4.5 38.2 1.0 CB B:ASN41 4.5 41.6 1.0 N B:ILE40 4.5 34.9 1.0 N B:GLY42 4.6 52.8 1.0 H B:ASP50 4.6 51.1 1.0 HB2 B:ASP50 4.7 47.1 1.0 HB2 B:ASP39 4.7 47.3 1.0 HB3 B:ASP43 4.7 44.1 1.0 HB3 B:ARG49 4.7 56.7 1.0 HG22 B:VAL46 4.8 45.7 1.0 N B:GLY44 4.8 36.5 1.0 HB3 B:ASP50 4.8 47.1 1.0 CA B:ASN41 4.8 40.1 1.0 CA B:ASP43 4.8 39.2 1.0 C B:ASN41 4.8 41.3 1.0 HD21 B:ASN47 4.8 47.8 1.0 N B:ASN47 4.9 32.4 1.0 HA B:ASP50 4.9 47.8 1.0 CB B:ALA45 4.9 40.8 1.0 N B:ASP50 4.9 42.6 1.0 O B:HOH205 5.0 34.6 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