Calcium in PDB 6ou1: Crystal Structure of the Computationally-Derived 21-Variant of the Myocilin Olfactomedin Domain

The structure of Crystal Structure of the Computationally-Derived 21-Variant of the Myocilin Olfactomedin Domain, PDB code: 6ou1 was solved by S.E.Hill, M.S.Kwon, R.L.Lieberman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.71 / 1.88
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	43.357, 66.889, 80.999, 90.00, 95.19, 90.00
R / Rfree (%)	16.8 / 19.5

The structure of Crystal Structure of the Computationally-Derived 21-Variant of the Myocilin Olfactomedin Domain also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Calcium atom in the Crystal Structure of the Computationally-Derived 21-Variant of the Myocilin Olfactomedin Domain (pdb code 6ou1). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of the Computationally-Derived 21-Variant of the Myocilin Olfactomedin Domain, PDB code: 6ou1:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of the Computationally-Derived 21-Variant of the Myocilin Olfactomedin 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 the Computationally-Derived 21-Variant of the Myocilin Olfactomedin Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:7.6 occ:1.00 OD2 A:ASP380 2.3 10.2 1.0 O A:ILE477 2.3 15.4 1.0 O A:ALA429 2.3 16.8 1.0 OD1 A:ASN428 2.4 16.8 1.0 OD1 A:ASP478 2.4 23.7 1.0 O A:HOH744 2.4 17.4 1.0 O A:HOH760 2.5 18.0 1.0 OD1 A:ASP380 3.0 18.2 1.0 CG A:ASP380 3.0 17.2 1.0 H A:ALA429 3.3 17.4 1.0 C A:ILE477 3.5 19.3 1.0 HA A:ASP478 3.5 22.0 1.0 CG A:ASN428 3.5 15.8 1.0 C A:ALA429 3.5 17.2 1.0 CG A:ASP478 3.6 19.7 1.0 H A:ILE477 3.7 22.5 1.0 HB3 A:PHE430 3.8 23.9 1.0 HD21 A:ASN428 3.9 20.4 1.0 HH A:TYR371 4.0 23.0 1.0 NA A:NA602 4.0 16.1 1.0 HA A:PHE430 4.1 21.0 1.0 N A:ALA429 4.1 14.4 1.0 ND2 A:ASN428 4.2 16.9 1.0 CA A:ASP478 4.2 18.3 1.0 N A:ASP478 4.2 16.5 1.0 HB A:ILE477 4.3 19.7 1.0 HE2 A:TYR371 4.3 19.3 1.0 N A:ILE477 4.4 18.7 1.0 HD12 A:ILE391 4.4 23.2 1.0 CA A:ALA429 4.5 14.7 1.0 CA A:ILE477 4.5 18.0 1.0 OD2 A:ASP478 4.5 21.9 1.0 N A:PHE430 4.5 18.3 1.0 CB A:ASP380 4.5 15.1 1.0 O A:HOH794 4.5 20.3 1.0 CB A:ASP478 4.5 16.8 1.0 O A:HOH820 4.6 19.8 1.0 CA A:PHE430 4.6 17.4 1.0 OH A:TYR371 4.6 19.1 1.0 O A:HOH724 4.6 17.8 1.0 HB3 A:ASN428 4.6 18.2 1.0 CB A:PHE430 4.6 19.8 1.0 CB A:ASN428 4.7 15.1 1.0 HB3 A:ASP380 4.8 18.2 1.0 HB2 A:ASP380 4.8 18.2 1.0 O A:LEU381 4.8 19.2 1.0 HD2 A:PHE430 4.8 25.8 1.0 HB3 A:ALA429 4.9 18.3 1.0 CE2 A:TYR371 4.9 16.1 1.0 CB A:ILE477 4.9 16.4 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of the Computationally-Derived 21-Variant of the Myocilin Olfactomedin 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 the Computationally-Derived 21-Variant of the Myocilin Olfactomedin Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca601 b:49.7 occ:1.00 O B:HOH701 2.4 21.8 1.0 O B:ILE477 2.5 32.4 1.0 OD2 B:ASP380 2.6 24.5 1.0 O B:HOH772 2.6 28.9 1.0 OD1 B:ASP380 2.9 24.6 1.0 OD1 B:ASN428 2.9 31.0 1.0 CG B:ASP380 3.1 26.7 1.0 O B:ALA429 3.1 19.2 1.0 OD1 B:ASP478 3.1 29.7 1.0 H B:ILE477 3.6 36.5 1.0 C B:ILE477 3.7 33.9 1.0 NA B:NA602 3.8 34.4 1.0 CG B:ASP478 3.8 35.3 1.0 HD21 B:ASN428 3.9 51.2 1.0 H B:ALA429 3.9 22.6 1.0 CG B:ASN428 3.9 35.0 1.0 HA B:ASP478 3.9 36.0 1.0 OD2 B:ASP478 4.2 36.2 1.0 ND2 B:ASN428 4.3 42.6 1.0 C B:ALA429 4.3 25.1 1.0 N B:ILE477 4.3 30.3 1.0 HB B:ILE477 4.4 42.8 1.0 HB3 B:PHE430 4.4 30.7 1.0 O B:LEU381 4.4 17.9 1.0 HH B:TYR371 4.5 24.4 1.0 N B:ASP478 4.6 30.5 1.0 CB B:ASP380 4.6 21.9 1.0 CA B:ASP478 4.6 29.9 1.0 CA B:ILE477 4.6 32.6 1.0 O B:HOH769 4.6 24.4 1.0 HE2 B:TYR371 4.7 27.0 1.0 HA B:PHE430 4.7 28.4 1.0 N B:ALA429 4.7 18.8 1.0 HD12 B:ILE391 4.8 31.5 1.0 CB B:ASP478 4.8 30.6 1.0 HB2 B:ASP380 4.9 26.4 1.0 HB3 B:ASP380 5.0 26.4 1.0 HG2 B:MET476 5.0 40.7 1.0 HB2 B:ALA382 5.0 24.9 1.0 HA B:MET476 5.0 37.6 1.0

S.E.Hill, M.S.Kwon, M.D.Martin, A.Suntharalingam, A.Hazel, C.A.Dickey, J.C.Gumbart, R.L.Lieberman. Calcium-Depleted Variants of the Myocilin Olfactomedin Domain Reveal A Stable Alternative Conformation with An Unwound Helix To Be Published.