Calcium in PDB 5wey: Joint X-Ray/Neutron Structure of Concanavalin A with ALPHA1-2 D- Mannobiose

The structure of Joint X-Ray/Neutron Structure of Concanavalin A with ALPHA1-2 D- Mannobiose, PDB code: 5wey was solved by A.Kovalevsky, O.O.Gerlits, R.J.Woods, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	N/A / 1.80
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	66.563, 86.618, 91.808, 90.00, 90.00, 90.00
R / Rfree (%)	24.7 / 28.5

The structure of Joint X-Ray/Neutron Structure of Concanavalin A with ALPHA1-2 D- Mannobiose also contains other interesting chemical elements:

Manganese

(Mn)

1 atom

The binding sites of Calcium atom in the Joint X-Ray/Neutron Structure of Concanavalin A with ALPHA1-2 D- Mannobiose (pdb code 5wey). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Joint X-Ray/Neutron Structure of Concanavalin A with ALPHA1-2 D- Mannobiose, PDB code: 5wey:

Calcium binding site 1 out of 1 in the Joint X-Ray/Neutron Structure of Concanavalin A with ALPHA1-2 D- Mannobiose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Joint X-Ray/Neutron Structure of Concanavalin A with ALPHA1-2 D- Mannobiose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:17.5 occ:1.00 O A:TYR12 2.4 15.9 1.0 O A:DOD456 2.4 17.3 1.0 OD2 A:ASP19 2.4 18.1 1.0 OD1 A:ASN14 2.4 16.8 1.0 OD1 A:ASP10 2.6 13.0 1.0 O A:DOD409 2.6 18.5 1.0 OD2 A:ASP10 2.6 10.3 1.0 D1 A:DOD409 2.8 17.7 1.0 CG A:ASP10 2.9 13.8 1.0 D1 A:DOD456 3.0 16.0 1.0 D2 A:DOD409 3.1 17.6 1.0 D2 A:DOD456 3.2 17.4 1.0 H A:ASN14 3.3 20.1 1.0 CG A:ASN14 3.5 21.2 1.0 CG A:ASP19 3.6 15.8 1.0 C A:TYR12 3.6 15.8 1.0 HB3 A:TYR12 3.7 16.6 1.0 HB2 A:ASN14 3.7 20.9 1.0 H A:TYR12 3.9 16.1 0.8 D A:TYR12 3.9 16.1 0.1 HA A:ARG228 4.0 18.0 1.0 N A:ASN14 4.0 21.0 1.0 HE1 A:HIS24 4.0 17.0 1.0 HB2 A:ARG228 4.0 20.4 1.0 OD1 A:ASP19 4.1 14.7 1.0 HA A:PRO13 4.1 21.2 1.0 CB A:ASN14 4.1 19.7 1.0 HD2 A:TYR12 4.2 18.6 1.0 MN A:MN301 4.2 17.5 1.0 CA A:TYR12 4.4 17.2 1.0 CB A:ASP10 4.4 14.1 1.0 N A:TYR12 4.5 16.2 1.0 CB A:TYR12 4.5 17.6 1.0 HD13 A:ILE17 4.5 25.9 1.0 O A:DOD454 4.6 19.5 1.0 O A:ASP208 4.6 13.5 1.0 N A:PRO13 4.6 18.7 1.0 CA A:PRO13 4.6 19.1 1.0 OD1 A:ASP208 4.6 14.6 1.0 ND2 A:ASN14 4.7 18.5 1.0 CA A:ASN14 4.7 20.7 1.0 C A:PRO13 4.7 21.5 1.0 CB A:ARG228 4.7 21.4 1.0 CB A:ASP19 4.8 17.1 1.0 HD13 A:LEU230 4.8 21.1 1.0 HD21 A:LEU230 4.8 21.2 1.0 HD22 A:ASN14 4.8 20.3 0.1 DD22 A:ASN14 4.8 20.3 0.9 O A:ARG228 4.8 17.8 1.0 HB3 A:ARG228 4.8 21.5 1.0 CE1 A:HIS24 4.8 19.2 1.0 CA A:ARG228 4.8 18.6 1.0 HB2 A:ASP19 4.9 16.6 1.0 HB3 A:ASP10 4.9 14.7 1.0 HB2 A:ASP10 4.9 13.7 1.0 HB3 A:ASP19 4.9 16.4 1.0 HA A:ASP10 4.9 14.8 1.0 HB3 A:ASP208 5.0 14.5 1.0

O.O.Gerlits, L.Coates, R.J.Woods, A.Kovalevsky. Mannobiose Binding Induces Changes in Hydrogen Bonding and Protonation States of Acidic Residues in Concanavalin A As Revealed By Neutron Crystallography. Biochemistry V. 56 4747 2017.
ISSN: ISSN 1520-4995
PubMed: 28846383
DOI: 10.1021/ACS.BIOCHEM.7B00654