Calcium in PDB 6u66: Structure of the Trimeric Globular Domain of Adiponectin

The structure of Structure of the Trimeric Globular Domain of Adiponectin, PDB code: 6u66 was solved by R.Pascolutti, A.C.Kruse, S.C.Erlandson, D.J.Burri, S.Zheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.77 / 0.99
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	47.923, 49.635, 50.306, 116.83, 100.89, 104.92
R / Rfree (%)	16.5 / 19

The structure of Structure of the Trimeric Globular Domain of Adiponectin also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Calcium atom in the Structure of the Trimeric Globular Domain of Adiponectin (pdb code 6u66). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Structure of the Trimeric Globular Domain of Adiponectin, PDB code: 6u66:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Structure of the Trimeric Globular Domain of Adiponectin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the Trimeric Globular Domain of Adiponectin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:8.0 occ:1.00 OD1 A:ASP187 2.3 8.1 1.0 OD1 B:ASN193 2.3 9.8 1.0 OD2 A:ASP195 2.3 8.5 1.0 O A:GLN188 2.4 8.6 1.0 OD1 B:ASP195 2.4 8.6 1.0 O B:VAL194 2.4 7.5 1.0 HA B:ASP195 3.0 9.6 1.0 H A:GLN188 3.4 10.2 1.0 CG A:ASP195 3.5 8.0 1.0 C B:VAL194 3.5 7.4 1.0 CG B:ASN193 3.5 11.2 1.0 C A:GLN188 3.5 8.6 1.0 CG A:ASP187 3.5 7.7 1.0 CG B:ASP195 3.5 8.1 1.0 N A:GLN188 3.7 8.5 1.0 CA B:ASP195 3.8 8.0 1.0 HD21 B:ASN193 3.9 19.6 1.0 HB2 A:GLN188 4.0 11.4 1.0 O A:HOH417 4.0 7.7 1.0 O A:HOH435 4.1 9.7 1.0 N B:ASP195 4.1 7.6 1.0 HB3 A:ASP195 4.1 9.2 1.0 CA A:GLN188 4.1 8.2 1.0 HB2 A:ASP195 4.1 9.2 1.0 HA A:ASP187 4.1 9.0 1.0 O A:HOH536 4.1 10.2 1.0 ND2 B:ASN193 4.1 16.4 1.0 O B:ASN193 4.2 8.8 1.0 CB A:ASP195 4.2 7.7 1.0 C A:ASP187 4.2 8.2 1.0 OD2 A:ASP187 4.2 8.9 1.0 C B:ASN193 4.2 9.9 1.0 CB B:ASP195 4.3 8.1 1.0 HA A:TYR189 4.3 11.2 1.0 OD1 A:ASP195 4.4 8.3 1.0 HA B:ASN193 4.4 12.7 1.0 OD2 B:ASP195 4.5 8.3 1.0 CA A:ASP187 4.5 7.5 1.0 CB A:GLN188 4.5 9.5 1.0 CB A:ASP187 4.5 7.3 1.0 N B:VAL194 4.6 9.3 1.0 CB B:ASN193 4.6 10.4 1.0 N A:TYR189 4.6 8.5 1.0 CA B:VAL194 4.7 8.6 1.0 CA B:ASN193 4.7 10.6 1.0 HB3 B:ASP195 4.8 9.7 1.0 HB3 A:GLN188 4.9 11.4 1.0 H B:ASP195 4.9 9.1 1.0 HB3 A:ASP187 4.9 8.7 1.0 H B:GLN196 5.0 9.2 1.0 HB2 B:ASP195 5.0 9.7 1.0 HA A:GLN188 5.0 9.8 1.0 HG11 A:VAL166 5.0 11.5 1.0 O A:ASP187 5.0 8.4 1.0 HD22 B:ASN193 5.0 19.6 1.0 CA A:TYR189 5.0 9.4 1.0

Calcium binding site 2 out of 3 in the Structure of the Trimeric Globular Domain of Adiponectin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the Trimeric Globular Domain of Adiponectin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:8.2 occ:1.00 OD1 B:ASP187 2.3 8.6 1.0 OD1 C:ASN193 2.3 9.9 1.0 OD2 B:ASP195 2.3 8.3 1.0 OD1 C:ASP195 2.4 8.4 1.0 O C:VAL194 2.4 8.1 1.0 O B:GLN188 2.4 8.8 1.0 HA C:ASP195 3.0 9.6 1.0 H B:GLN188 3.4 9.8 1.0 C C:VAL194 3.4 8.5 1.0 CG B:ASP195 3.5 8.1 1.0 C B:GLN188 3.5 9.1 1.0 CG C:ASN193 3.5 10.8 1.0 CG C:ASP195 3.5 7.6 1.0 CG B:ASP187 3.5 7.5 1.0 N B:GLN188 3.6 8.1 1.0 HB3 B:GLN188 3.8 8.9 0.2 CA C:ASP195 3.8 8.0 1.0 HD21 C:ASN193 3.9 19.4 1.0 HB2 B:GLN188 3.9 13.8 0.8 O B:HOH427 4.0 10.6 1.0 O B:HOH411 4.0 7.5 1.0 N C:ASP195 4.0 8.2 1.0 CA B:GLN188 4.0 8.5 0.2 HB2 B:ASP195 4.0 9.7 1.0 CA B:GLN188 4.0 9.9 0.8 HB3 B:ASP195 4.1 9.7 1.0 O A:HOH536 4.1 10.2 1.0 HA B:ASP187 4.1 9.6 1.0 CB B:ASP195 4.1 8.1 1.0 ND2 C:ASN193 4.1 16.2 1.0 O C:ASN193 4.2 9.4 1.0 C B:ASP187 4.2 7.5 1.0 OD2 B:ASP187 4.2 9.1 1.0 C C:ASN193 4.3 8.8 1.0 CB C:ASP195 4.3 7.5 1.0 HA B:TYR189 4.3 12.6 1.0 OD1 B:ASP195 4.3 8.6 1.0 CB B:GLN188 4.4 7.4 0.2 HA C:ASN193 4.4 12.3 1.0 CB B:GLN188 4.4 11.5 0.8 OD2 C:ASP195 4.4 7.8 1.0 CA B:ASP187 4.5 8.0 1.0 N C:VAL194 4.5 9.1 1.0 HB3 B:GLN188 4.6 13.8 0.8 CB B:ASP187 4.6 7.4 1.0 N B:TYR189 4.6 9.3 1.0 CA C:VAL194 4.6 8.8 1.0 CB C:ASN193 4.6 10.6 1.0 CA C:ASN193 4.7 10.2 1.0 HB3 C:ASP195 4.8 8.9 1.0 H C:ASP195 4.9 9.8 1.0 HB2 B:GLN188 4.9 8.9 0.2 HB2 C:ASP195 4.9 8.9 1.0 H C:GLN196 4.9 9.2 1.0 HA B:GLN188 4.9 10.2 1.0 HB3 B:ASP187 5.0 8.9 1.0 HG11 B:VAL166 5.0 10.2 1.0 O B:ASP187 5.0 9.0 1.0 CA B:TYR189 5.0 10.5 1.0 HD22 C:ASN193 5.0 19.4 1.0 HB3 C:ASN193 5.0 12.7 1.0

Calcium binding site 3 out of 3 in the Structure of the Trimeric Globular Domain of Adiponectin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the Trimeric Globular Domain of Adiponectin within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca301 b:7.9 occ:1.00 OD1 C:ASP187 2.3 8.3 1.0 OD1 A:ASN193 2.3 9.5 1.0 OD2 C:ASP195 2.3 7.8 1.0 O C:GLN188 2.3 8.9 1.0 OD1 A:ASP195 2.4 8.3 1.0 O A:VAL194 2.4 8.0 1.0 HA A:ASP195 3.0 9.9 1.0 H C:GLN188 3.4 10.4 1.0 C C:GLN188 3.4 9.0 1.0 CG C:ASP195 3.5 7.6 1.0 C A:VAL194 3.5 7.3 1.0 CG A:ASN193 3.5 10.0 1.0 CG C:ASP187 3.5 7.9 1.0 CG A:ASP195 3.5 8.0 1.0 N C:GLN188 3.6 8.6 1.0 CA A:ASP195 3.8 8.2 1.0 HD21 A:ASN193 3.9 17.0 1.0 HB2 C:GLN188 3.9 11.4 1.0 O C:HOH409 4.0 7.9 1.0 O C:HOH440 4.0 10.6 1.0 CA C:GLN188 4.0 8.8 1.0 N A:ASP195 4.0 8.2 1.0 HA C:ASP187 4.1 10.1 1.0 O A:HOH536 4.1 10.2 1.0 HB2 C:ASP195 4.1 8.9 1.0 HB3 C:ASP195 4.1 8.9 1.0 ND2 A:ASN193 4.1 14.2 1.0 O A:ASN193 4.2 8.7 1.0 CB C:ASP195 4.2 7.5 1.0 C C:ASP187 4.2 8.7 1.0 OD2 C:ASP187 4.2 8.3 1.0 CB A:ASP195 4.3 7.7 1.0 C A:ASN193 4.3 8.8 1.0 HA A:ASN193 4.3 10.9 1.0 OD1 C:ASP195 4.4 8.4 1.0 HA C:TYR189 4.4 11.8 1.0 OD2 A:ASP195 4.5 8.5 1.0 CA C:ASP187 4.5 8.4 1.0 CB C:GLN188 4.5 9.5 1.0 CB C:ASP187 4.5 7.8 1.0 N A:VAL194 4.6 8.8 1.0 N C:TYR189 4.6 9.2 1.0 CB A:ASN193 4.7 9.2 1.0 CA A:VAL194 4.7 8.1 1.0 CA A:ASN193 4.7 9.1 1.0 HB3 A:ASP195 4.8 9.2 1.0 HB3 C:GLN188 4.8 11.4 1.0 H A:ASP195 4.9 9.8 1.0 HB2 A:ASP195 4.9 9.2 1.0 HA C:GLN188 4.9 10.6 1.0 O C:ASP187 4.9 9.2 1.0 HB3 C:ASP187 4.9 9.4 1.0 HD22 A:ASN193 4.9 17.0 1.0 HG11 C:VAL166 5.0 11.2 1.0 H A:GLN196 5.0 9.2 1.0

R.Pascolutti, S.C.Erlandson, D.J.Burri, S.Zheng, A.C.Kruse. Mapping and Engineering the Interaction Between Adiponectin and T-Cadherin. J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X
PubMed: 31915248
DOI: 10.1074/JBC.RA119.010970