Calcium in PDB 5k8q: Crystal Structure of Calcium-Loaded Calmodulin in Complex with STRA6 CAMBP2-Site Peptide.

The structure of Crystal Structure of Calcium-Loaded Calmodulin in Complex with STRA6 CAMBP2-Site Peptide., PDB code: 5k8q was solved by S.D.Stowe, O.B.Clarke, M.C.Cavalier, R.Godoy-Ruiz, F.Mancia, D.J.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.37 / 1.74
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	156.510, 37.230, 35.730, 90.00, 94.35, 90.00
R / Rfree (%)	22.7 / 26.7

The binding sites of Calcium atom in the Crystal Structure of Calcium-Loaded Calmodulin in Complex with STRA6 CAMBP2-Site Peptide. (pdb code 5k8q). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Calcium-Loaded Calmodulin in Complex with STRA6 CAMBP2-Site Peptide., PDB code: 5k8q:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Calcium-Loaded Calmodulin in Complex with STRA6 CAMBP2-Site Peptide.


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 Calcium-Loaded Calmodulin in Complex with STRA6 CAMBP2-Site Peptide. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:20.2 occ:1.00 OD1 A:ASP129 2.2 27.9 1.0 O A:GLN135 2.3 19.4 1.0 OD2 A:ASP133 2.3 20.2 1.0 O A:HOH307 2.4 22.2 1.0 OD2 A:ASP131 2.4 27.4 1.0 OE2 A:GLU140 2.4 15.1 1.0 OE1 A:GLU140 2.5 23.1 1.0 CD A:GLU140 2.8 16.3 1.0 CG A:ASP131 3.1 23.5 1.0 CG A:ASP133 3.2 30.7 1.0 OD1 A:ASP131 3.4 28.0 1.0 CG A:ASP129 3.4 25.9 1.0 C A:GLN135 3.4 12.8 1.0 OD1 A:ASP133 3.6 21.6 1.0 CA A:ASP129 4.1 19.8 1.0 N A:ASP133 4.1 26.5 1.0 CB A:ASP129 4.2 23.9 1.0 N A:GLN135 4.2 20.9 1.0 N A:ASP131 4.2 30.5 1.0 N A:VAL136 4.2 12.5 1.0 OD2 A:ASP129 4.3 24.9 1.0 CA A:VAL136 4.3 15.3 1.0 CB A:ASP133 4.3 24.2 1.0 CG A:GLU140 4.3 23.8 1.0 N A:ASN137 4.3 13.5 1.0 CB A:ASP131 4.4 24.4 1.0 CA A:GLN135 4.4 20.2 1.0 C A:ASP129 4.4 23.3 1.0 N A:ILE130 4.5 28.0 1.0 N A:GLY132 4.5 30.6 1.0 CA A:ASP133 4.7 27.8 1.0 CA A:ASP131 4.7 27.0 1.0 C A:VAL136 4.8 16.2 1.0 C A:ASP131 4.8 30.9 1.0 N A:GLY134 4.8 21.6 1.0 CG A:ASN137 4.9 25.9 1.0 ND2 A:ASN137 4.9 20.2 1.0 C A:ASP133 4.9 20.5 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Calcium-Loaded Calmodulin in Complex with STRA6 CAMBP2-Site Peptide.


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 Calcium-Loaded Calmodulin in Complex with STRA6 CAMBP2-Site Peptide. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:18.1 occ:1.00 OD2 A:ASP93 2.2 26.1 1.0 O A:TYR99 2.2 19.9 1.0 OD1 A:ASP95 2.4 31.0 1.0 OD1 A:ASN97 2.4 22.2 1.0 O A:HOH368 2.4 24.3 1.0 OE2 A:GLU104 2.5 24.7 1.0 OE1 A:GLU104 2.5 29.6 1.0 CD A:GLU104 2.9 22.4 1.0 CG A:ASN97 3.3 18.8 1.0 CG A:ASP93 3.4 22.4 1.0 C A:TYR99 3.4 26.9 1.0 CG A:ASP95 3.5 36.5 1.0 ND2 A:ASN97 3.9 19.7 1.0 OD2 A:ASP95 4.0 33.5 1.0 N A:TYR99 4.1 22.2 1.0 OD1 A:ASP93 4.2 25.6 1.0 CA A:ASP93 4.2 23.1 1.0 CB A:ASP93 4.2 15.5 1.0 CA A:TYR99 4.3 26.6 1.0 N A:ASN97 4.3 20.8 1.0 CG A:GLU104 4.4 18.4 1.0 N A:ASP95 4.4 28.9 1.0 N A:ILE100 4.4 20.2 1.0 O A:HOH381 4.4 40.7 1.0 CB A:ASN97 4.5 19.1 1.0 CA A:ILE100 4.5 18.3 1.0 C A:ASP93 4.5 25.8 1.0 N A:LYS94 4.6 26.0 0.6 N A:GLY96 4.6 25.9 1.0 N A:LYS94 4.6 26.4 0.4 N A:SER101 4.6 14.9 1.0 CB A:TYR99 4.6 19.2 1.0 CB A:ASP95 4.7 27.4 1.0 OE1 A:GLN135 4.7 25.7 1.0 CA A:ASN97 4.8 23.8 1.0 CA A:ASP95 4.8 23.6 1.0 C A:ASP95 4.9 25.4 1.0 N A:GLY98 4.9 21.8 1.0 OG A:SER101 5.0 14.8 1.0 C A:ILE100 5.0 12.6 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Calcium-Loaded Calmodulin in Complex with STRA6 CAMBP2-Site Peptide.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Calcium-Loaded Calmodulin in Complex with STRA6 CAMBP2-Site Peptide. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:20.6 occ:1.00 O A:THR62 2.3 19.6 1.0 OD2 A:ASP56 2.3 25.8 1.0 OE2 A:GLU67 2.3 25.5 1.0 OD1 A:ASP58 2.4 32.6 1.0 OD1 A:ASN60 2.4 27.5 1.0 O A:HOH315 2.4 39.5 1.0 OE1 A:GLU67 2.6 21.6 1.0 O A:HOH346 2.6 36.3 0.7 CD A:GLU67 2.8 21.7 1.0 CG A:ASP58 3.4 32.4 1.0 CG A:ASN60 3.4 27.1 1.0 C A:THR62 3.5 23.3 1.0 CG A:ASP56 3.5 25.7 1.0 OD2 A:ASP58 3.7 28.4 1.0 ND2 A:ASN60 3.8 19.1 1.0 OD1 A:ASP56 4.3 33.5 1.0 N A:THR62 4.3 29.7 1.0 CG A:GLU67 4.3 15.7 1.0 N A:ILE63 4.3 20.5 1.0 N A:ASP58 4.4 24.4 1.0 CA A:ILE63 4.4 23.0 1.0 OG1 A:THR62 4.4 22.5 1.0 CA A:ASP56 4.4 23.7 1.0 N A:ASN60 4.4 26.7 1.0 N A:ASP64 4.5 15.8 1.0 CA A:THR62 4.5 25.8 1.0 N A:ALA57 4.5 25.1 1.0 CB A:ASP56 4.5 25.9 1.0 CB A:ASP58 4.7 27.4 1.0 CB A:ASN60 4.7 32.8 1.0 N A:GLY59 4.8 40.7 1.0 OD1 A:ASP64 4.8 36.4 1.0 C A:ASP56 4.8 19.0 1.0 C5 A:IMD205 4.8 35.7 1.0 C A:ILE63 4.9 16.9 1.0 CG A:ASP64 4.9 28.7 1.0 CA A:ASP58 4.9 31.0 1.0 N A:GLY61 4.9 26.9 1.0 CA A:ASN60 5.0 28.3 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Calcium-Loaded Calmodulin in Complex with STRA6 CAMBP2-Site Peptide.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Calcium-Loaded Calmodulin in Complex with STRA6 CAMBP2-Site Peptide. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca204 b:20.9 occ:1.00 OD2 A:ASP20 2.3 22.7 1.0 O A:THR26 2.3 30.9 1.0 OD1 A:ASP22 2.3 24.4 1.0 OE1 A:GLU31 2.3 30.1 1.0 OD1 A:ASP24 2.4 31.7 1.0 O A:HOH350 2.4 18.8 1.0 OE2 A:GLU31 2.5 23.6 1.0 CD A:GLU31 2.7 26.4 1.0 CG A:ASP22 3.3 28.7 1.0 CG A:ASP24 3.3 28.7 1.0 CG A:ASP20 3.4 24.8 1.0 C A:THR26 3.5 26.3 1.0 OD2 A:ASP22 3.6 37.2 1.0 OD2 A:ASP24 3.8 34.4 1.0 OG1 A:THR26 4.0 40.8 1.0 CA A:ASP20 4.1 23.5 1.0 N A:THR26 4.2 23.4 1.0 CB A:ASP20 4.2 17.9 1.0 CG A:GLU31 4.3 19.9 1.0 OD1 A:ASP20 4.3 24.2 1.0 CA A:THR26 4.4 21.5 1.0 N A:ASP24 4.4 32.3 1.0 N A:ILE27 4.4 17.7 1.0 CB A:ASP24 4.5 24.7 1.0 CA A:ILE27 4.5 18.5 1.0 C A:ASP20 4.6 31.0 1.0 N A:ASP22 4.6 35.1 1.0 CB A:ASP22 4.7 28.8 1.0 CG2 A:THR28 4.7 26.9 1.0 O A:HOH318 4.8 25.4 1.0 CB A:THR26 4.8 27.0 1.0 N A:GLY23 4.8 39.6 1.0 N A:THR28 4.9 17.4 1.0 CA A:ASP24 4.9 27.8 1.0 N A:LYS21 4.9 33.7 1.0 N A:GLY25 4.9 30.7 1.0 CA A:ASP22 5.0 34.1 1.0

Y.Chen, O.B.Clarke, J.Kim, S.Stowe, Y.K.Kim, Z.Assur, M.Cavalier, R.Godoy-Ruiz, D.C.Von Alpen, C.Manzini, W.S.Blaner, J.Frank, L.Quadro, D.J.Weber, L.Shapiro, W.A.Hendrickson, F.Mancia. Structure of the STRA6 Receptor For Retinol Uptake. Science V. 353 2016.
ISSN: ESSN 1095-9203
PubMed: 27563101
DOI: 10.1126/SCIENCE.AAD8266