Calcium in PDB 6ny8: Crystal Structure of Computationally Designed Protein XAA_GVDQ with Calcium

The structure of Crystal Structure of Computationally Designed Protein XAA_GVDQ with Calcium, PDB code: 6ny8 was solved by K.Y.Wei, M.J.Bick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	80.05 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	86.158, 49.602, 85.032, 90.00, 109.71, 90.00
R / Rfree (%)	28.8 / 30.4

The structure of Crystal Structure of Computationally Designed Protein XAA_GVDQ with Calcium also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Calcium atom in the Crystal Structure of Computationally Designed Protein XAA_GVDQ with Calcium (pdb code 6ny8). 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 Crystal Structure of Computationally Designed Protein XAA_GVDQ with Calcium, PDB code: 6ny8:

Calcium binding site 1 out of 1 in the Crystal Structure of Computationally Designed Protein XAA_GVDQ with Calcium


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 Computationally Designed Protein XAA_GVDQ with Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca102 b:72.5 occ:1.00 OD2 A:ASP75 2.8 67.2 1.0 OD1 B:ASP75 2.9 61.7 1.0 OD1 C:ASP75 3.1 69.2 1.0 HB2 A:ASP75 3.4 79.6 1.0 HB2 B:ASP75 3.5 83.9 1.0 HB3 A:ASP75 3.5 79.6 1.0 HB2 C:ASP75 3.5 81.3 1.0 HB3 B:ASP75 3.6 83.9 1.0 HG12 A:ILE72 3.6 79.8 1.0 HG12 B:ILE72 3.6 72.9 1.0 CG A:ASP75 3.6 69.6 1.0 HG12 C:ILE72 3.6 75.5 1.0 HB3 C:ASP75 3.7 81.3 1.0 CB A:ASP75 3.7 65.7 1.0 CG B:ASP75 3.7 74.2 1.0 HA A:ILE72 3.7 83.5 1.0 CB B:ASP75 3.8 69.3 1.0 HG23 A:ILE72 3.8 80.3 1.0 CG C:ASP75 3.8 69.5 1.0 HA B:ILE72 3.9 75.0 1.0 CB C:ASP75 3.9 67.1 1.0 HA C:ILE72 3.9 69.2 1.0 HG23 C:ILE72 4.2 75.9 1.0 HG23 B:ILE72 4.4 71.9 1.0 CG1 A:ILE72 4.5 65.8 1.0 CG1 B:ILE72 4.5 60.1 1.0 CG1 C:ILE72 4.6 62.3 1.0 CA A:ILE72 4.7 68.9 1.0 CG2 A:ILE72 4.7 66.3 1.0 HG13 B:ILE72 4.8 72.9 1.0 CA B:ILE72 4.8 61.8 1.0 CA C:ILE72 4.8 57.0 1.0 OD1 A:ASP75 4.8 72.9 1.0 OD2 B:ASP75 4.9 75.2 1.0 CB A:ILE72 4.9 66.3 1.0 HG13 C:ILE72 4.9 75.5 1.0 HG13 A:ILE72 4.9 79.8 1.0 OD2 C:ASP75 5.0 60.7 1.0

K.Y.Wei, D.Moschidi, M.J.Bick, S.Nerli, A.C.Mcshan, L.P.Carter, P.S.Huang, D.A.Fletcher, N.G.Sgourakis, S.E.Boyken, D.Baker. Computational Design of Closely Related Proteins That Adopt Two Well-Defined But Structurally Divergent Folds. Proc.Natl.Acad.Sci.Usa V. 117 7208 2020.
ISSN: ESSN 1091-6490
PubMed: 32188784
DOI: 10.1073/PNAS.1914808117