Calcium in PDB 6dhy: Crystallogrpahic Tetramer of Zn-Bound RIDC1 Variant Bearing Two Disulfide Bonded Cysteines

The structure of Crystallogrpahic Tetramer of Zn-Bound RIDC1 Variant Bearing Two Disulfide Bonded Cysteines, PDB code: 6dhy was solved by F.A.Tezcan, L.A.Churchfield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.84 / 2.22
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	52.510, 52.510, 255.670, 90.00, 90.00, 120.00
R / Rfree (%)	22.9 / 25.8

The structure of Crystallogrpahic Tetramer of Zn-Bound RIDC1 Variant Bearing Two Disulfide Bonded Cysteines also contains other interesting chemical elements:

Iron	(Fe)	4 atoms
Zinc	(Zn)	10 atoms

The binding sites of Calcium atom in the Crystallogrpahic Tetramer of Zn-Bound RIDC1 Variant Bearing Two Disulfide Bonded Cysteines (pdb code 6dhy). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystallogrpahic Tetramer of Zn-Bound RIDC1 Variant Bearing Two Disulfide Bonded Cysteines, PDB code: 6dhy:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystallogrpahic Tetramer of Zn-Bound RIDC1 Variant Bearing Two Disulfide Bonded Cysteines


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystallogrpahic Tetramer of Zn-Bound RIDC1 Variant Bearing Two Disulfide Bonded Cysteines within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:39.7 occ:1.00 OD2 A:ASP2 2.5 32.9 1.0 CG A:ASP2 3.3 35.1 1.0 OD1 A:ASP2 3.4 36.0 1.0 OD1 A:ASP5 3.9 27.9 1.0 OD2 A:ASP5 3.9 28.0 1.0 CG A:ASP5 4.1 28.8 1.0 OE2 A:GLU4 4.5 37.7 1.0 CB A:GLU4 4.8 34.7 1.0 CB A:ASP2 4.8 34.7 1.0 N A:ASP5 5.0 29.4 1.0

Calcium binding site 2 out of 3 in the Crystallogrpahic Tetramer of Zn-Bound RIDC1 Variant Bearing Two Disulfide Bonded Cysteines


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystallogrpahic Tetramer of Zn-Bound RIDC1 Variant Bearing Two Disulfide Bonded Cysteines within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca202 b:49.6 occ:1.00 O1A C:HEM201 2.1 34.6 1.0 OE1 C:GLU4 3.0 36.9 1.0 CGA C:HEM201 3.3 33.2 1.0 CD C:GLU4 3.6 36.3 1.0 CBA C:HEM201 4.0 32.3 1.0 OE2 C:GLU4 4.1 37.1 1.0 O2A C:HEM201 4.2 34.4 1.0 O C:HOH308 4.5 21.0 1.0 CG C:GLU4 4.5 35.2 1.0 CAA C:HEM201 4.6 29.9 1.0

Calcium binding site 3 out of 3 in the Crystallogrpahic Tetramer of Zn-Bound RIDC1 Variant Bearing Two Disulfide Bonded Cysteines


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystallogrpahic Tetramer of Zn-Bound RIDC1 Variant Bearing Two Disulfide Bonded Cysteines within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca203 b:34.3 occ:1.00 OD2 C:ASP5 2.9 37.9 1.0 ZN C:ZN206 3.7 42.9 1.0 CG C:ASP5 4.1 37.1 1.0 CB C:ASP5 4.8 35.4 1.0 ZN C:ZN207 4.9 40.7 1.0

L.A.Churchfield, R.G.Alberstein, L.M.Williamson, F.A.Tezcan. Determining the Structural and Energetic Basis of Allostery in A De Novo Designed Metalloprotein Assembly. J. Am. Chem. Soc. V. 140 10043 2018.
ISSN: ESSN 1520-5126
PubMed: 29996654
DOI: 10.1021/JACS.8B05812