Calcium in PDB 6fie: Crystallographic Structure of Calcium Loaded Calbindin-D28K.

The structure of Crystallographic Structure of Calcium Loaded Calbindin-D28K., PDB code: 6fie was solved by J.W.Noble, R.Almalki, S.M.Roe, A.Wagner, R.Dumanc, J.R.Atack, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.90 / 1.51
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	84.617, 104.222, 29.614, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 23.6

The binding sites of Calcium atom in the Crystallographic Structure of Calcium Loaded Calbindin-D28K. (pdb code 6fie). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystallographic Structure of Calcium Loaded Calbindin-D28K., PDB code: 6fie:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystallographic Structure of Calcium Loaded Calbindin-D28K.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystallographic Structure of Calcium Loaded Calbindin-D28K. within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:19.9 occ:1.00 OD1 B:ASN203 2.3 23.1 1.0 OD1 B:ASP201 2.3 24.1 1.0 O B:TYR205 2.3 20.0 1.0 OD1 B:ASP199 2.4 21.6 1.0 O B:HOH442 2.4 23.4 1.0 OE2 B:GLU210 2.5 20.9 1.0 OE1 B:GLU210 2.6 24.6 1.0 CD B:GLU210 2.9 22.4 1.0 CG B:ASN203 3.2 21.7 1.0 H B:ASN203 3.3 23.9 1.0 CG B:ASP201 3.3 25.2 1.0 HD21 B:ASN203 3.4 27.8 1.0 CG B:ASP199 3.5 25.0 1.0 HA B:ASP199 3.5 15.9 1.0 H B:TYR205 3.5 20.1 1.0 HA B:ILE206 3.6 17.3 1.0 C B:TYR205 3.6 19.1 1.0 H B:ASP201 3.6 24.0 1.0 ND2 B:ASN203 3.7 27.2 1.0 OD2 B:ASP201 3.7 29.4 1.0 H B:ASP207 3.9 22.9 1.0 H B:GLY202 4.1 24.3 1.0 CA B:ASP199 4.2 19.9 1.0 N B:ASN203 4.3 24.3 1.0 OD2 B:ASP199 4.3 20.4 1.0 CB B:ASP199 4.3 21.5 1.0 N B:TYR205 4.4 19.1 1.0 CG B:GLU210 4.4 21.8 1.0 CA B:ILE206 4.4 18.1 1.0 H B:GLN200 4.4 18.6 1.0 N B:ILE206 4.4 18.1 1.0 H B:GLY204 4.4 21.4 1.0 N B:ASP201 4.5 24.2 1.0 CB B:ASN203 4.5 23.4 1.0 C B:ASP199 4.5 23.2 1.0 HB2 B:ASP199 4.6 20.4 1.0 CA B:TYR205 4.6 17.6 1.0 N B:GLY202 4.6 24.4 1.0 CD1 B:TYR205 4.6 23.1 1.0 CB B:ASP201 4.6 25.9 1.0 N B:ASP207 4.6 21.9 1.0 HD1 B:TYR205 4.6 21.2 1.0 N B:GLN200 4.7 21.6 1.0 OD2 B:ASP207 4.7 27.1 1.0 HD22 B:ASN203 4.7 27.7 1.0 CA B:ASN203 4.8 22.8 1.0 HG3 B:GLU210 4.8 21.2 1.0 HB3 B:ASP207 4.8 24.3 1.0 HB3 B:ASN203 4.8 24.7 1.0 CE1 B:TYR205 4.8 26.6 1.0 CA B:ASP201 4.8 23.3 1.0 HG12 B:ILE206 4.9 21.4 1.0 HG2 B:GLU210 4.9 19.8 1.0 N B:GLY204 4.9 22.0 1.0 CG B:ASP207 4.9 27.2 1.0 C B:ASP201 4.9 28.1 1.0 C B:ILE206 5.0 23.8 1.0 CG B:TYR205 5.0 21.6 1.0 HB2 B:GLU210 5.0 20.3 1.0

Calcium binding site 2 out of 4 in the Crystallographic Structure of Calcium Loaded Calbindin-D28K.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystallographic Structure of Calcium Loaded Calbindin-D28K. within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:18.4 occ:1.00 OE1 B:GLU119 2.3 22.5 1.0 OD1 B:ASP111 2.3 18.1 1.0 OD1 B:ASP113 2.4 19.7 1.0 OE1 B:GLU122 2.4 20.4 1.0 O B:PHE117 2.4 19.7 1.0 OG B:SER115 2.5 19.4 1.0 OE2 B:GLU122 2.5 19.2 1.0 CD B:GLU122 2.8 19.3 1.0 H B:SER115 3.0 18.2 1.0 HA B:ASP111 3.3 7.7 1.0 CD B:GLU119 3.3 29.6 1.0 CG B:ASP111 3.4 18.1 1.0 CG B:ASP113 3.4 22.6 1.0 H B:PHE117 3.5 18.8 1.0 H B:ASP113 3.5 16.9 1.0 H B:GLU119 3.5 21.5 1.0 OE2 B:GLU119 3.6 24.3 1.0 CB B:SER115 3.6 18.7 1.0 HA B:ILE118 3.6 16.4 1.0 C B:PHE117 3.6 21.2 1.0 HB3 B:SER115 3.6 16.9 1.0 OD2 B:ASP113 3.9 25.9 1.0 N B:SER115 4.0 18.6 1.0 CA B:ASP111 4.1 16.2 1.0 HD13 B:ILE118 4.2 20.9 1.0 CB B:ASP111 4.2 17.0 1.0 OD2 B:ASP111 4.2 20.8 1.0 CG B:GLU122 4.3 16.3 1.0 CA B:SER115 4.3 17.9 1.0 HB2 B:ASP111 4.3 16.1 1.0 N B:PHE117 4.3 18.9 1.0 N B:GLU119 4.4 18.5 1.0 HB2 B:PHE117 4.4 18.5 1.0 HB2 B:SER115 4.4 19.3 1.0 H B:GLY116 4.4 17.6 1.0 N B:ASP113 4.4 16.9 1.0 C B:ASP111 4.4 18.8 1.0 H B:HIS114 4.5 19.1 1.0 CA B:ILE118 4.5 17.9 1.0 HB2 B:GLU119 4.5 21.9 1.0 H B:THR112 4.5 18.3 1.0 N B:ILE118 4.5 17.6 1.0 CA B:PHE117 4.6 18.4 1.0 HG3 B:GLU122 4.6 15.2 1.0 CG B:GLU119 4.6 23.6 1.0 CB B:ASP113 4.6 18.6 1.0 N B:THR112 4.7 17.4 1.0 N B:HIS114 4.7 18.1 1.0 N B:GLY116 4.8 20.2 1.0 HG2 B:GLU122 4.8 17.4 1.0 HB2 B:GLU122 4.8 20.3 1.0 CA B:ASP113 4.9 16.9 1.0 C B:SER115 4.9 20.9 1.0 O B:HOH484 4.9 31.5 1.0 C B:ILE118 4.9 20.1 1.0 C B:ASP113 4.9 20.1 1.0 O B:HOH422 4.9 37.9 1.0 HB3 B:ASP113 4.9 16.9 1.0 CB B:GLU119 5.0 21.8 1.0 O B:ASP111 5.0 17.4 1.0

Calcium binding site 3 out of 4 in the Crystallographic Structure of Calcium Loaded Calbindin-D28K.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystallographic Structure of Calcium Loaded Calbindin-D28K. within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:24.4 occ:1.00 OD1 B:ASN157 2.3 25.7 1.0 OD1 B:ASP155 2.3 25.4 1.0 OD1 B:ASP159 2.3 30.5 1.0 O B:HOH439 2.3 29.0 1.0 O B:LYS161 2.3 23.2 1.0 OE1 B:GLU166 2.5 24.1 1.0 OE2 B:GLU166 2.6 29.7 1.0 CD B:GLU166 2.9 26.6 1.0 CG B:ASP159 3.2 33.7 1.0 H B:ASP159 3.3 27.1 1.0 CG B:ASN157 3.4 29.5 1.0 CG B:ASP155 3.4 24.2 1.0 H B:ASN157 3.4 29.4 1.0 HA B:LEU162 3.5 20.4 1.0 HA B:ASP155 3.5 25.0 1.0 H B:LYS161 3.5 19.4 1.0 C B:LYS161 3.5 24.1 1.0 OD2 B:ASP159 3.5 29.9 1.0 HD21 B:ASN157 3.7 27.8 1.0 H B:GLU163 3.8 26.9 1.0 HG2 B:GLU163 3.9 31.5 1.0 ND2 B:ASN157 4.0 28.0 1.0 HD23 B:LEU162 4.2 24.6 1.0 CA B:ASP155 4.2 23.7 1.0 N B:ASP159 4.2 28.1 1.0 OD2 B:ASP155 4.2 26.6 1.0 CA B:LEU162 4.3 19.4 1.0 CB B:ASP155 4.3 24.6 1.0 HG2 B:LYS161 4.3 25.3 1.0 N B:LEU162 4.3 20.1 1.0 N B:ASN157 4.4 28.8 1.0 H B:ASN158 4.4 28.0 1.0 CB B:ASP159 4.4 27.3 1.0 N B:LYS161 4.4 21.6 1.0 HG3 B:LYS161 4.4 19.9 1.0 N B:GLU163 4.4 24.1 1.0 CG B:GLU166 4.4 24.5 1.0 C B:ASP155 4.5 26.2 1.0 HB2 B:ASP155 4.5 22.8 1.0 H B:GLY160 4.6 26.2 1.0 CB B:ASN157 4.6 26.9 1.0 CA B:LYS161 4.6 21.9 1.0 HB3 B:ASP159 4.6 27.1 1.0 C B:LEU162 4.7 24.9 1.0 OE1 B:GLU163 4.7 31.8 1.0 N B:ASN158 4.7 27.2 1.0 H B:SER156 4.7 26.1 1.0 HB3 B:GLU163 4.7 23.4 1.0 CA B:ASP159 4.7 26.7 1.0 N B:SER156 4.7 26.1 1.0 CA B:ASN157 4.8 27.3 1.0 O B:HOH482 4.8 40.9 1.0 HG3 B:GLU166 4.8 23.3 1.0 CG B:LYS161 4.8 24.6 1.0 HB3 B:ASN157 4.9 26.3 1.0 CG B:GLU163 4.9 31.7 1.0 C B:ASN157 4.9 28.6 1.0 HG2 B:GLU166 4.9 25.2 1.0 O B:ASP155 4.9 27.5 1.0 HD22 B:ASN157 4.9 27.9 1.0 N B:GLY160 4.9 26.9 1.0 HB2 B:GLU166 5.0 27.2 1.0

Calcium binding site 4 out of 4 in the Crystallographic Structure of Calcium Loaded Calbindin-D28K.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystallographic Structure of Calcium Loaded Calbindin-D28K. within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca304 b:25.9 occ:0.52 OD1 B:ASP24 2.2 36.5 1.0 OD1 B:ASP26 2.3 45.4 1.0 O B:TYR30 2.3 44.9 0.7 O B:TYR30 2.3 45.5 0.3 OE1 B:GLU35 2.4 41.4 1.0 OG B:SER28 2.5 44.9 1.0 OE2 B:GLU35 2.7 45.4 1.0 CD B:GLU35 2.9 53.5 1.0 H B:SER28 3.2 37.0 1.0 CG B:ASP26 3.3 48.3 1.0 H B:TYR30 3.4 42.2 0.3 HA B:ASP24 3.4 38.5 1.0 H B:TYR30 3.4 41.3 0.7 CG B:ASP24 3.5 38.6 1.0 C B:TYR30 3.5 45.8 0.3 C B:TYR30 3.5 45.0 0.7 OD2 B:ASP26 3.6 48.8 1.0 HA B:LEU31 3.6 42.3 1.0 H B:ASP26 3.6 43.4 1.0 CB B:SER28 3.7 42.4 1.0 HB3 B:SER28 3.8 43.5 1.0 N B:SER28 4.1 37.6 1.0 H B:GLU32 4.1 44.2 1.0 HG2 B:GLU32 4.2 52.2 1.0 O B:HOH423 4.2 43.7 1.0 CA B:ASP24 4.2 38.6 1.0 N B:TYR30 4.2 41.9 0.3 O B:HOH500 4.3 49.0 1.0 N B:TYR30 4.3 40.6 0.7 OD2 B:ASP24 4.3 38.0 1.0 CG B:GLU35 4.4 46.0 1.0 CB B:ASP24 4.4 39.9 1.0 N B:LEU31 4.4 41.6 1.0 CA B:LEU31 4.4 42.1 1.0 CA B:SER28 4.4 38.0 1.0 H B:GLY29 4.5 41.4 1.0 CA B:TYR30 4.5 41.9 0.3 HB2 B:SER28 4.5 42.6 1.0 CA B:TYR30 4.5 39.9 0.7 N B:ASP26 4.5 43.5 1.0 H B:GLY27 4.5 39.5 1.0 H B:ALA25 4.5 43.8 1.0 CB B:ASP26 4.6 44.4 1.0 C B:ASP24 4.6 44.6 1.0 HB2 B:ASP24 4.7 40.1 1.0 HB2 B:TYR30 4.7 40.1 0.7 N B:ALA25 4.8 43.9 1.0 HB2 B:GLU35 4.8 43.1 1.0 N B:GLY29 4.8 40.8 1.0 N B:GLY27 4.8 39.1 1.0 HG3 B:GLU35 4.8 45.8 1.0 HB2 B:TYR30 4.8 43.4 0.3 N B:GLU32 4.8 44.5 1.0 HG2 B:GLU35 4.9 45.6 1.0 C B:SER28 4.9 42.1 1.0 CA B:ASP26 4.9 42.8 1.0 HB3 B:GLU35 5.0 43.7 1.0 OE2 B:GLU32 5.0 68.0 1.0

J.W.Noble, R.Almalki, S.M.Roe, A.Wagner, R.Duman, J.R.Atack. The X-Ray Structure of Human Calbindin-D28K: An Improved Model. Acta Crystallogr D Struct V. 74 1008 2018BIOL.
ISSN: ISSN 2059-7983
PubMed: 30289411
DOI: 10.1107/S2059798318011610