Calcium in PDB 4dou: Crystal Structure of A Single-Chain Trimer of Human Adiponectin Globular Domain

The structure of Crystal Structure of A Single-Chain Trimer of Human Adiponectin Globular Domain, PDB code: 4dou was solved by X.Min, N.P.Walker, Z.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.00
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	48.310, 49.630, 50.460, 117.23, 101.68, 105.31
R / Rfree (%)	20 / 25.7

The structure of Crystal Structure of A Single-Chain Trimer of Human Adiponectin Globular Domain also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Calcium atom in the Crystal Structure of A Single-Chain Trimer of Human Adiponectin Globular Domain (pdb code 4dou). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of A Single-Chain Trimer of Human Adiponectin Globular Domain, PDB code: 4dou:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of A Single-Chain Trimer of Human Adiponectin Globular Domain


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 A Single-Chain Trimer of Human Adiponectin Globular Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:22.8 occ:1.00 O A:VAL476 2.3 27.1 1.0 OD1 A:ASP328 2.3 26.7 1.0 OD1 A:ASP336 2.3 27.1 1.0 O A:GLN329 2.4 29.7 1.0 OD1 A:ASP477 2.4 27.8 1.0 OD1 A:ASN475 2.5 30.2 1.0 C A:GLN329 3.4 30.7 1.0 N A:GLN329 3.4 29.3 1.0 CG A:ASP336 3.4 25.9 1.0 C A:VAL476 3.4 27.2 1.0 CG A:ASP328 3.5 24.4 1.0 CG A:ASN475 3.6 31.3 1.0 CG A:ASP477 3.6 27.0 1.0 O A:HOH1114 3.8 15.8 1.0 CA A:ASP477 3.8 25.7 1.0 CA A:GLN329 3.9 30.9 1.0 O A:HOH1113 3.9 17.1 1.0 N A:ASP477 4.1 26.2 1.0 CB A:ASP336 4.1 24.5 1.0 C A:ASP328 4.1 27.8 1.0 O A:HOH1166 4.2 25.2 1.0 CB A:GLN329 4.2 32.6 1.0 OD2 A:ASP328 4.2 21.3 1.0 O A:ASN475 4.3 28.6 1.0 ND2 A:ASN475 4.3 31.4 1.0 C A:ASN475 4.3 29.5 1.0 CB A:ASP477 4.4 25.9 1.0 OD2 A:ASP336 4.4 25.2 1.0 CA A:ASP328 4.5 26.5 1.0 N A:VAL476 4.6 28.9 1.0 OD2 A:ASP477 4.6 27.4 1.0 N A:TYR330 4.6 31.6 1.0 CB A:ASP328 4.6 24.4 1.0 CA A:VAL476 4.6 27.9 1.0 CB A:ASN475 4.8 31.6 1.0 CA A:ASN475 4.8 31.3 1.0 O A:ASP328 4.9 27.4 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of A Single-Chain Trimer of Human Adiponectin Globular Domain


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 A Single-Chain Trimer of Human Adiponectin Globular Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:25.6 occ:1.00 OD2 A:ASP477 2.2 27.4 1.0 O A:VAL194 2.3 26.8 1.0 OD1 A:ASP469 2.3 26.0 1.0 O A:GLN470 2.5 30.4 1.0 OD1 A:ASP195 2.5 27.6 1.0 OD1 A:ASN193 2.6 32.0 1.0 C A:VAL194 3.3 27.0 1.0 CG A:ASP477 3.4 27.0 1.0 C A:GLN470 3.5 31.2 1.0 CG A:ASP469 3.5 26.3 1.0 N A:GLN470 3.6 29.6 1.0 CG A:ASP195 3.7 27.1 1.0 CG A:ASN193 3.8 33.6 1.0 CA A:ASP195 3.9 25.1 1.0 CA A:GLN470 4.0 31.4 1.0 N A:ASP195 4.0 25.6 1.0 O A:ASN193 4.0 29.6 1.0 O A:HOH1136 4.1 12.8 1.0 CB A:ASP477 4.2 25.9 1.0 C A:ASP469 4.2 28.1 1.0 C A:ASN193 4.2 31.2 1.0 O A:HOH1202 4.2 18.6 1.0 OD2 A:ASP469 4.2 24.1 1.0 O A:HOH1166 4.3 25.2 1.0 CB A:GLN470 4.3 33.1 1.0 OD1 A:ASP477 4.3 27.8 1.0 N A:VAL194 4.4 30.4 1.0 CB A:ASP195 4.4 24.9 1.0 CA A:VAL194 4.5 28.2 1.0 CA A:ASP469 4.6 26.5 1.0 OD2 A:ASP195 4.6 29.4 1.0 ND2 A:ASN193 4.6 36.2 1.0 N A:TYR471 4.6 32.3 1.0 CB A:ASP469 4.6 25.0 1.0 CA A:ASN193 4.8 34.0 1.0 O A:ASP469 4.8 28.2 1.0 CB A:ASN193 4.9 34.3 1.0 CA A:TYR471 5.0 32.7 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of A Single-Chain Trimer of Human Adiponectin Globular Domain


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 A Single-Chain Trimer of Human Adiponectin Globular Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:27.8 occ:1.00 OD2 A:ASP336 2.2 25.2 1.0 OD2 A:ASP195 2.3 29.4 1.0 O A:VAL335 2.3 25.2 1.0 OD2 A:ASP187 2.4 26.6 1.0 OD1 A:ASN334 2.5 31.9 1.0 O A:GLN188 2.5 30.1 1.0 C A:VAL335 3.4 25.1 1.0 CG A:ASP336 3.4 25.9 1.0 CG A:ASP195 3.4 27.1 1.0 C A:GLN188 3.5 31.0 1.0 CG A:ASN334 3.6 32.1 1.0 CG A:ASP187 3.6 24.6 1.0 N A:GLN188 3.6 28.9 1.0 CA A:ASP336 3.7 24.1 1.0 O A:HOH1225 3.8 26.4 1.0 O A:HOH1153 3.8 15.1 1.0 N A:ASP336 3.9 24.4 1.0 CA A:GLN188 4.1 30.9 1.0 O A:ASN334 4.1 27.9 1.0 O A:HOH1166 4.1 25.2 1.0 CB A:ASP336 4.1 24.5 1.0 C A:ASN334 4.2 28.8 1.0 CB A:ASP195 4.2 24.9 1.0 ND2 A:ASN334 4.2 33.7 1.0 C A:ASP187 4.3 27.4 1.0 OD1 A:ASP187 4.3 23.7 1.0 OD1 A:ASP336 4.3 27.1 1.0 OD1 A:ASP195 4.3 27.6 1.0 N A:VAL335 4.4 27.4 1.0 CB A:GLN188 4.5 32.9 1.0 CA A:ASP187 4.6 25.6 1.0 CA A:VAL335 4.6 26.0 1.0 CB A:ASP187 4.7 24.1 1.0 CB A:ASN334 4.7 31.6 1.0 CA A:ASN334 4.7 30.9 1.0 N A:TYR189 4.7 32.4 1.0 C A:ASP336 4.9 23.1 1.0

X.Min, B.Lemon, J.Tang, Q.Liu, R.Zhang, N.Walker, Y.Li, Z.Wang. Crystal Structure of A Single-Chain Trimer of Human Adiponectin Globular Domain. Febs Lett. V. 586 912 2012.
ISSN: ISSN 0014-5793
PubMed: 22449980
DOI: 10.1016/J.FEBSLET.2012.02.024