Calcium in PDB 1hdf: Evolution of the Eye Lens Beta-Gamma-Crystallin Domain Fold

The structure of Evolution of the Eye Lens Beta-Gamma-Crystallin Domain Fold, PDB code: 1hdf was solved by N.J.Clout, M.Kretschmar, R.Jaenicke, C.Slingsby, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20 / 2.35
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	41.350, 41.350, 213.640, 90.00, 90.00, 90.00
R / Rfree (%)	23.9 / n/a

The binding sites of Calcium atom in the Evolution of the Eye Lens Beta-Gamma-Crystallin Domain Fold (pdb code 1hdf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Evolution of the Eye Lens Beta-Gamma-Crystallin Domain Fold, PDB code: 1hdf:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Evolution of the Eye Lens Beta-Gamma-Crystallin Domain Fold


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Evolution of the Eye Lens Beta-Gamma-Crystallin Domain Fold within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1101 b:17.9 occ:1.00 O A:VAL46 2.2 14.1 1.0 OG A:SER48 2.3 13.7 1.0 O A:LYS19 2.3 12.3 1.0 OD1 A:ASP89 2.3 11.9 1.0 O A:HOH2070 2.5 9.0 1.0 O A:HOH2037 2.6 26.6 1.0 C A:VAL46 3.3 14.6 1.0 CG A:ASP89 3.4 13.8 1.0 C A:LYS19 3.5 12.6 1.0 CB A:SER48 3.5 13.1 1.0 OD2 A:ASP89 3.8 12.2 1.0 CA A:VAL46 3.9 14.6 1.0 N A:SER48 4.1 12.8 1.0 C A:VAL47 4.1 13.0 1.0 CG A:LYS19 4.2 11.4 1.0 N A:VAL47 4.3 13.9 1.0 CA A:LYS19 4.3 12.3 1.0 ND2 A:ASN88 4.3 15.1 1.0 CA A:SER48 4.3 12.7 1.0 O A:VAL47 4.3 13.5 1.0 CB A:VAL46 4.5 15.3 1.0 N A:HIS20 4.5 12.3 1.0 CA A:VAL47 4.6 12.9 1.0 CA A:HIS20 4.6 13.6 1.0 CD2 A:HIS20 4.6 15.2 1.0 CB A:ASP89 4.7 13.5 1.0 CB A:LYS19 4.9 12.1 1.0 CA A:ASP89 5.0 14.8 1.0 O A:HOH2016 5.0 7.1 1.0 N A:ASP89 5.0 14.3 1.0

Calcium binding site 2 out of 4 in the Evolution of the Eye Lens Beta-Gamma-Crystallin Domain Fold


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Evolution of the Eye Lens Beta-Gamma-Crystallin Domain Fold within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1102 b:24.8 occ:1.00 O A:LYS62 2.4 17.8 1.0 OG A:SER92 2.4 16.3 1.0 O A:ALA90 2.5 16.2 1.0 OD1 A:ASP45 2.5 18.5 1.0 O A:HOH2036 2.6 3.2 1.0 O A:HOH2041 2.7 27.0 1.0 O A:HOH2019 2.8 21.0 1.0 CG A:ASP45 3.4 17.4 1.0 C A:ALA90 3.4 16.0 1.0 OD2 A:ASP45 3.5 17.7 1.0 C A:LYS62 3.6 16.9 1.0 CB A:SER92 3.6 17.4 1.0 CA A:ALA90 3.9 15.2 1.0 CG A:LYS62 4.3 17.5 1.0 N A:SER92 4.3 17.7 1.0 C A:ILE91 4.3 17.5 1.0 OD1 A:ASP63 4.4 18.3 1.0 ND2 A:ASN44 4.4 15.6 1.0 N A:ILE91 4.5 16.4 1.0 CB A:ALA90 4.5 15.2 1.0 N A:ASP63 4.5 16.4 1.0 CA A:LYS62 4.5 15.9 1.0 CA A:ASP63 4.5 16.4 1.0 CA A:SER92 4.5 16.7 1.0 O A:ILE91 4.6 17.9 1.0 O A:HOH2069 4.6 25.9 1.0 CB A:ASP45 4.8 15.5 1.0 CA A:ILE91 4.8 16.8 1.0 OD1 A:ASN44 4.9 14.2 1.0

Calcium binding site 3 out of 4 in the Evolution of the Eye Lens Beta-Gamma-Crystallin Domain Fold


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Evolution of the Eye Lens Beta-Gamma-Crystallin Domain Fold within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1101 b:18.4 occ:1.00 OG B:SER92 2.1 11.1 1.0 O B:ALA90 2.2 12.3 1.0 O B:LYS62 2.3 12.6 1.0 OD1 B:ASP45 2.4 17.3 1.0 O B:HOH2026 2.6 8.9 1.0 O B:HOH2030 2.7 2.8 1.0 C B:ALA90 3.3 12.9 1.0 CB B:SER92 3.4 9.4 1.0 CG B:ASP45 3.4 16.2 1.0 C B:LYS62 3.5 11.7 1.0 OD2 B:ASP45 3.6 15.4 1.0 CA B:ALA90 3.9 13.3 1.0 C B:ILE91 4.0 11.8 1.0 N B:SER92 4.0 11.3 1.0 ND2 B:ASN44 4.1 10.5 1.0 O B:HOH2031 4.2 12.7 1.0 O B:ILE91 4.2 11.4 1.0 CA B:SER92 4.3 10.2 1.0 N B:ILE91 4.3 13.0 1.0 O B:HOH2008 4.3 12.4 1.0 CG B:LYS62 4.4 15.5 1.0 CA B:LYS62 4.4 11.7 1.0 N B:ASP63 4.4 11.8 1.0 CA B:ASP63 4.4 12.6 1.0 CB B:ALA90 4.5 11.7 1.0 CA B:ILE91 4.5 13.1 1.0 OD1 B:ASP63 4.5 15.8 1.0 O B:HOH2050 4.6 18.6 1.0 CB B:ASP45 4.8 15.9 1.0 OD1 B:ASN44 4.9 12.3 1.0 CG B:ASN44 4.9 12.2 1.0

Calcium binding site 4 out of 4 in the Evolution of the Eye Lens Beta-Gamma-Crystallin Domain Fold


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Evolution of the Eye Lens Beta-Gamma-Crystallin Domain Fold within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1102 b:29.0 occ:1.00 OG B:SER48 2.0 16.9 1.0 O B:HOH2049 2.2 17.9 1.0 OD1 B:ASP89 2.3 23.0 1.0 O B:LYS19 2.3 20.5 1.0 O B:VAL46 2.4 12.9 1.0 O B:HOH2029 2.7 16.2 1.0 CG B:ASP89 3.3 22.2 1.0 CB B:SER48 3.3 15.3 1.0 C B:VAL46 3.4 13.6 1.0 C B:LYS19 3.5 20.3 1.0 OD2 B:ASP89 3.6 23.9 1.0 N B:SER48 3.9 14.6 1.0 ND2 B:ASN88 4.0 14.2 1.0 C B:VAL47 4.0 13.7 1.0 CA B:SER48 4.1 14.0 1.0 CA B:VAL46 4.2 13.8 1.0 O B:VAL47 4.3 12.8 1.0 CG B:LYS19 4.4 20.1 1.0 CA B:LYS19 4.4 19.5 1.0 N B:VAL47 4.4 13.3 1.0 N B:HIS20 4.5 20.6 1.0 CA B:HIS20 4.5 21.4 1.0 CA B:VAL47 4.6 13.3 1.0 CB B:ASP89 4.6 19.8 1.0 CB B:VAL46 4.7 14.8 1.0 CD2 B:HIS20 4.8 23.8 1.0 N B:ASP89 4.8 16.7 1.0 CG B:ASN88 4.8 17.5 1.0 CA B:ASP89 4.9 17.3 1.0 OD1 B:ASN88 4.9 16.2 1.0 CB B:LYS19 5.0 20.5 1.0

N.J.Clout, M.Kretschmar, R.Jaenicke, C.Slingsby. Crystal Structure of the Calcium-Loaded Spherulin 3A Dimer Sheds Light on the Evolution of the Eye Lens Betagamma-Crystallin Domain Fold Structure V. 9 115 2001.
ISSN: ISSN 0969-2126
PubMed: 11250196
DOI: 10.1016/S0969-2126(01)00573-1