Calcium in PDB 2ggz: Crystal Structure of Human Guanylate Cyclase Activating Protein-3

The structure of Crystal Structure of Human Guanylate Cyclase Activating Protein-3, PDB code: 2ggz was solved by R.Stephen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.43 / 3.00
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	88.190, 88.190, 71.020, 90.00, 90.00, 90.00
R / Rfree (%)	25.6 / 29

The binding sites of Calcium atom in the Crystal Structure of Human Guanylate Cyclase Activating Protein-3 (pdb code 2ggz). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Human Guanylate Cyclase Activating Protein-3, PDB code: 2ggz:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of Human Guanylate Cyclase Activating Protein-3


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 Human Guanylate Cyclase Activating Protein-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca500 b:56.4 occ:1.00 OD1 A:ASN66 2.1 46.6 1.0 OD1 A:ASP64 2.1 36.3 1.0 OE1 A:GLU75 2.3 44.0 1.0 OE2 A:GLU75 2.3 46.7 1.0 O A:PHE70 2.4 34.4 1.0 CD A:GLU75 2.6 44.3 1.0 OD1 A:ASP68 2.6 54.4 1.0 OD2 A:ASP68 2.8 52.8 1.0 CG A:ASP68 2.9 51.3 1.0 CG A:ASP64 3.3 39.0 1.0 CG A:ASN66 3.3 46.1 1.0 C A:PHE70 3.4 38.2 1.0 OD1 A:ASP72 3.6 48.1 1.0 CG A:GLU75 4.0 42.7 1.0 CB A:ASP64 4.0 40.5 1.0 ND2 A:ASN66 4.1 46.8 1.0 N A:PHE70 4.1 42.9 1.0 N A:ASP68 4.1 49.4 1.0 CA A:ASP64 4.1 41.6 1.0 CB A:ASP68 4.2 48.3 1.0 OD2 A:ASP64 4.3 38.6 1.0 CA A:PHE70 4.3 40.2 1.0 N A:VAL71 4.3 38.1 1.0 CA A:VAL71 4.3 40.1 1.0 N A:ASP72 4.3 43.9 1.0 N A:ASN66 4.4 45.7 1.0 C A:ASP64 4.4 41.1 1.0 CB A:ASN66 4.4 45.9 1.0 CG A:ASP72 4.5 47.4 1.0 C A:ASN66 4.6 46.6 1.0 CB A:PHE70 4.6 41.4 1.0 CA A:ASP68 4.6 47.4 1.0 N A:GLY69 4.7 47.0 1.0 O A:ASP64 4.7 40.0 1.0 CA A:ASN66 4.7 45.7 1.0 N A:LYS67 4.7 48.1 1.0 C A:VAL71 4.8 42.1 1.0 N A:THR65 4.8 42.3 1.0 O A:ASN66 4.9 48.2 1.0 C A:ASP68 4.9 47.1 1.0 CB A:GLU75 4.9 42.9 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of Human Guanylate Cyclase Activating Protein-3


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 Human Guanylate Cyclase Activating Protein-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:60.0 occ:1.00 OD1 A:ASN104 2.0 70.3 1.0 O A:SER106 2.3 65.6 1.0 OE2 A:GLU111 2.3 62.3 1.0 OE1 A:GLU111 2.4 63.5 1.0 OD1 A:ASP102 2.4 78.0 1.0 OD2 A:ASP100 2.7 61.6 1.0 CD A:GLU111 2.7 63.0 1.0 CG A:ASP102 2.9 77.8 1.0 OD2 A:ASP102 3.0 79.8 1.0 CG A:ASN104 3.0 69.5 1.0 C A:SER106 3.4 66.0 1.0 ND2 A:ASN104 3.6 69.8 1.0 CG A:ASP100 3.8 64.2 1.0 N A:ASN104 4.1 69.7 1.0 CG A:GLU111 4.1 63.8 1.0 CB A:ASN104 4.2 68.5 1.0 N A:ASP102 4.2 71.6 1.0 CB A:ASP102 4.3 75.4 1.0 CA A:ILE107 4.3 65.2 1.0 N A:ILE107 4.3 65.3 1.0 CA A:ASP100 4.3 66.8 1.0 N A:SER106 4.4 66.9 1.0 N A:ASP108 4.4 68.1 1.0 CA A:SER106 4.4 66.0 1.0 C A:ASP102 4.4 73.0 1.0 C A:ASP100 4.5 68.8 1.0 CA A:ASP102 4.5 73.0 1.0 N A:GLY103 4.6 72.2 1.0 CB A:ASP100 4.6 65.9 1.0 CA A:ASN104 4.6 69.4 1.0 OD1 A:ASP100 4.7 61.7 1.0 CB A:SER106 4.8 64.5 1.0 OG A:SER106 4.8 63.3 1.0 C A:ILE107 4.8 66.8 1.0 N A:ALA101 4.8 70.7 1.0 O A:ASP102 4.8 73.1 1.0 O A:ASP100 4.8 68.6 1.0 CG A:ASP108 4.9 71.8 1.0 C A:ASN104 5.0 69.6 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of Human Guanylate Cyclase Activating Protein-3


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 Human Guanylate Cyclase Activating Protein-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:70.7 occ:1.00 OD1 A:ASP146 2.2 78.3 1.0 OD1 A:ASP142 2.3 72.1 1.0 OE2 A:GLU153 2.4 73.2 1.0 O A:GLU148 2.5 70.3 1.0 OD2 A:ASP146 2.5 76.7 1.0 OE1 A:GLU153 2.5 76.0 1.0 CG A:ASP146 2.5 76.7 1.0 OD1 A:ASN144 2.7 74.5 1.0 CD A:GLU153 2.8 73.3 1.0 CG A:ASN144 3.4 75.4 1.0 CG A:ASP142 3.5 74.4 1.0 C A:GLU148 3.6 69.8 1.0 ND2 A:ASN144 3.7 76.3 1.0 N A:ASP146 3.8 73.5 1.0 CB A:ASP146 3.9 74.2 1.0 OD2 A:ASP142 4.1 74.7 1.0 N A:GLU148 4.2 72.3 1.0 N A:ASN144 4.3 74.2 1.0 CG A:GLU153 4.3 71.6 1.0 CA A:ASP146 4.3 72.8 1.0 N A:ASN145 4.4 72.4 1.0 CA A:GLU148 4.4 71.4 1.0 C A:ASN144 4.5 72.4 1.0 CG2 A:THR150 4.5 67.0 1.0 CA A:ASP142 4.5 75.3 1.0 CB A:ASN144 4.6 74.6 1.0 N A:LEU149 4.6 68.0 1.0 N A:GLY147 4.6 71.9 1.0 CB A:ASP142 4.6 74.1 1.0 C A:ASP142 4.6 75.8 1.0 CA A:ASN144 4.6 73.2 1.0 CA A:LEU149 4.6 67.0 1.0 N A:THR150 4.7 65.5 1.0 C A:ASP146 4.8 71.9 1.0 C A:ASN145 4.8 73.4 1.0 CB A:GLU148 4.8 72.4 1.0 N A:ILE143 4.8 75.6 1.0 CB B:ALA159 4.8 78.4 1.0 O A:ASN144 4.9 71.2 1.0 CA A:ASN145 4.9 73.5 1.0 O A:ASP142 5.0 76.9 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of Human Guanylate Cyclase Activating Protein-3


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 Human Guanylate Cyclase Activating Protein-3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:50.6 occ:1.00 OD1 B:ASP68 2.0 57.6 1.0 OE2 B:GLU75 2.2 43.4 1.0 O B:PHE70 2.3 44.9 1.0 OD1 B:ASP64 2.3 41.5 1.0 OD1 B:ASN66 2.4 44.2 1.0 OE1 B:GLU75 2.4 44.2 1.0 CD B:GLU75 2.6 43.6 1.0 CG B:ASP68 2.9 54.5 1.0 C B:PHE70 3.2 44.0 1.0 OD2 B:ASP68 3.2 55.2 1.0 CG B:ASP64 3.4 45.2 1.0 CG B:ASN66 3.5 41.7 1.0 OD1 B:ASP72 3.8 47.9 1.0 N B:VAL71 4.0 42.5 1.0 ND2 B:ASN66 4.0 40.0 1.0 CG B:GLU75 4.0 41.3 1.0 N B:PHE70 4.0 45.3 1.0 CA B:PHE70 4.1 44.4 1.0 OD2 B:ASP64 4.1 46.9 1.0 CA B:VAL71 4.1 42.0 1.0 CB B:ASP68 4.2 51.2 1.0 N B:ASP72 4.2 42.5 1.0 N B:ASP68 4.2 48.7 1.0 CB B:ASP64 4.3 43.2 1.0 CA B:ASP64 4.4 43.7 1.0 CG B:ASP72 4.4 47.2 1.0 CB B:PHE70 4.4 44.6 1.0 CB B:ASN66 4.6 41.2 1.0 N B:ASN66 4.6 42.4 1.0 CA B:ASP68 4.6 49.0 1.0 C B:VAL71 4.7 42.5 1.0 C B:ASP64 4.7 43.9 1.0 CB B:GLU75 4.8 41.3 1.0 N B:GLY69 4.9 47.8 1.0 C B:ASN66 4.9 43.3 1.0 C B:ASP68 4.9 48.0 1.0 N B:LYS67 5.0 45.1 1.0 CA B:ASN66 5.0 41.9 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of Human Guanylate Cyclase Activating Protein-3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Human Guanylate Cyclase Activating Protein-3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca504 b:76.4 occ:1.00 OE2 B:GLU111 2.3 72.3 1.0 OE1 B:GLU111 2.3 72.9 1.0 ND2 B:ASN104 2.5 74.3 1.0 CD B:GLU111 2.6 73.5 1.0 OD2 B:ASP100 2.7 78.9 1.0 OD2 B:ASP102 2.7 86.7 1.0 OD1 B:ASN104 2.8 75.5 1.0 OD1 B:ASP102 2.8 84.5 1.0 CG B:ASN104 2.9 74.9 1.0 O B:SER106 3.0 78.2 1.0 CG B:ASP102 3.0 84.1 1.0 C B:SER106 3.7 77.8 1.0 CG B:ASP100 3.7 78.1 1.0 CA B:ASP100 3.9 75.5 1.0 CA B:ILE107 4.0 80.3 1.0 N B:ASP108 4.1 84.2 1.0 CG B:GLU111 4.1 74.5 1.0 N B:ILE107 4.1 78.7 1.0 CB B:ASN104 4.2 74.4 1.0 N B:ALA101 4.2 77.0 1.0 C B:ASP100 4.2 76.3 1.0 CB B:ASP100 4.3 76.5 1.0 N B:ASP102 4.3 78.2 1.0 N B:ASN104 4.4 75.4 1.0 CB B:ASP102 4.4 81.3 1.0 N B:SER106 4.4 76.0 1.0 C B:ILE107 4.5 82.3 1.0 N B:GLY103 4.7 77.6 1.0 CA B:SER106 4.7 77.0 1.0 OD1 B:ASP100 4.8 78.2 1.0 CA B:ASP102 4.8 79.1 1.0 CA B:ASN104 4.8 75.0 1.0 CG B:ASP108 4.9 86.3 1.0 CB B:ASP108 4.9 85.7 1.0 CB B:GLU111 4.9 78.3 1.0 OD1 B:ASP108 4.9 86.6 1.0 N B:GLY105 4.9 75.1 1.0 O B:ASP100 5.0 76.2 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of Human Guanylate Cyclase Activating Protein-3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Human Guanylate Cyclase Activating Protein-3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca505 b:90.3 occ:1.00 OD1 B:ASP146 2.4 0.9 1.0 OE1 B:GLU153 2.4 85.5 1.0 O B:GLU148 2.6 92.4 1.0 OE2 B:GLU153 2.7 86.9 1.0 OD1 B:ASP142 2.8 0.3 1.0 CD B:GLU153 2.8 85.4 1.0 CG B:ASP146 3.2 0.9 1.0 OD2 B:ASP146 3.2 0.6 1.0 OD1 B:ASN144 3.3 0.4 1.0 C B:GLU148 3.4 92.2 1.0 ND2 B:ASN144 3.7 0.1 1.0 CG B:ASN144 3.9 0.0 1.0 CG B:ASP142 3.9 0.4 1.0 CA B:LEU149 3.9 85.1 1.0 N B:THR150 3.9 82.2 1.0 N B:LEU149 4.0 88.8 1.0 CB B:GLU148 4.3 96.3 1.0 CG B:GLU153 4.3 83.8 1.0 CG2 B:THR150 4.3 81.8 1.0 CA B:GLU148 4.3 94.7 1.0 C B:LEU149 4.4 83.6 1.0 OD2 B:ASP142 4.4 0.3 1.0 OG1 B:THR150 4.5 80.1 1.0 N B:ASP146 4.6 0.0 1.0 CB B:ASP146 4.6 0.2 1.0 N B:GLU148 4.7 97.4 1.0 CB B:GLU153 4.8 81.0 1.0 CD1 B:LEU149 4.8 80.8 1.0 CB B:THR150 4.8 81.5 1.0 CB B:ASP142 4.9 0.8 1.0 CA B:ASP142 4.9 0.3 1.0 CA B:THR150 5.0 81.3 1.0

R.Stephen, K.Palczewski, M.C.Sousa. The Crystal Structure of GCAP3 Suggests Molecular Mechanism of Gcap-Linked Cone Dystrophies. J.Mol.Biol. V. 359 266 2006.
ISSN: ISSN 0022-2836
PubMed: 16626734
DOI: 10.1016/J.JMB.2006.03.042