Calcium in PDB 3enr: Zinc-Calcium Concanavalin A at pH 6.15

The structure of Zinc-Calcium Concanavalin A at pH 6.15, PDB code: 3enr was solved by J.Bouckaert, R.Loris, L.Wyns, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.40
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	60.130, 96.460, 87.420, 90.00, 90.00, 90.00
R / Rfree (%)	21.5 / 28.3

The structure of Zinc-Calcium Concanavalin A at pH 6.15 also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Calcium atom in the Zinc-Calcium Concanavalin A at pH 6.15 (pdb code 3enr). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Zinc-Calcium Concanavalin A at pH 6.15, PDB code: 3enr:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Zinc-Calcium Concanavalin A at pH 6.15


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Zinc-Calcium Concanavalin A at pH 6.15 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:76.2 occ:1.00 OD2 A:ASP19 2.6 41.6 1.0 OD2 A:ASP10 2.6 37.5 1.0 OD1 A:ASP10 2.6 50.7 1.0 CG A:ASP10 2.9 47.1 1.0 OD1 A:ASN14 3.2 77.9 1.0 O A:TYR12 3.3 53.0 1.0 CG A:ASP19 3.5 57.9 1.0 OD1 A:ASP19 3.7 66.4 1.0 O A:ARG228 3.8 67.7 1.0 CG A:ASN14 4.0 74.8 1.0 ZN A:ZN1001 4.3 62.0 1.0 CB A:ASP10 4.4 41.4 1.0 CA A:ARG228 4.5 61.0 1.0 C A:TYR12 4.5 65.7 1.0 CB A:ASN14 4.5 73.4 1.0 CB A:ARG228 4.6 64.9 1.0 C A:ARG228 4.6 63.9 1.0 OD2 A:ASP208 4.7 81.1 1.0 CD1 A:ILE17 4.7 68.0 1.0 N A:ASN14 4.8 72.2 1.0 CB A:ASP19 4.8 60.1 1.0 ND2 A:ASN14 4.9 72.0 1.0 O A:ASP208 4.9 65.4 1.0 CE1 A:HIS24 5.0 44.0 1.0 NE2 A:HIS24 5.0 36.0 1.0

Calcium binding site 2 out of 2 in the Zinc-Calcium Concanavalin A at pH 6.15


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Zinc-Calcium Concanavalin A at pH 6.15 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1004 b:54.2 occ:1.00 O B:TYR12 2.4 55.1 1.0 OD1 B:ASP10 2.4 43.0 1.0 O B:HOH1040 2.6 31.1 1.0 OD2 B:ASP19 2.7 52.0 1.0 OD1 B:ASN14 2.8 66.2 1.0 OD2 B:ASP10 3.1 25.9 1.0 CG B:ASP10 3.1 33.8 1.0 CG B:ASN14 3.5 67.8 1.0 C B:TYR12 3.5 64.3 1.0 CG B:ASP19 3.8 58.6 1.0 OD2 B:ASP208 4.0 78.0 1.0 ND2 B:ASN14 4.1 74.8 1.0 CA B:TYR12 4.3 65.1 1.0 CB B:ASN14 4.3 68.2 1.0 CB B:TYR12 4.3 70.6 1.0 N B:ASN14 4.3 66.6 1.0 OD1 B:ASP19 4.3 66.8 1.0 N B:TYR12 4.4 63.5 1.0 O B:ARG228 4.5 57.8 1.0 O B:ASP208 4.5 57.1 1.0 N B:PRO13 4.6 65.3 1.0 CA B:ARG228 4.6 58.9 1.0 CB B:ASP10 4.6 44.5 1.0 CB B:ARG228 4.6 64.3 1.0 ZN B:ZN1002 4.7 47.4 1.0 CA B:PRO13 4.8 64.1 1.0 CB B:ASP208 4.8 63.8 1.0 C B:PRO13 4.9 63.5 1.0 CG B:ASP208 4.9 72.9 1.0 CD2 B:TYR12 5.0 83.9 1.0 CA B:ASN14 5.0 68.1 1.0 CB B:ASP19 5.0 59.1 1.0

J.Bouckaert, R.Loris, L.Wyns. Zinc/Calcium- and Cadmium/Cadmium-Substituted Concanavalin A: Interplay of Metal Binding, pH and Molecular Packing. Acta Crystallogr.,Sect.D V. 56 1569 2000.
ISSN: ISSN 0907-4449
PubMed: 11092923
DOI: 10.1107/S0907444900013342