Calcium in PDB 1vfp: Crystal Structure of the Sr CA2+-Atpase with Bound Amppcp

All present enzymatic activity of Crystal Structure of the Sr CA2+-Atpase with Bound Amppcp:
3.6.3.8;

The structure of Crystal Structure of the Sr CA2+-Atpase with Bound Amppcp, PDB code: 1vfp was solved by C.Toyoshima, T.Mizutani, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	90.920, 123.620, 151.820, 90.00, 107.21, 90.00
R / Rfree (%)	24.7 / 28.7

The structure of Crystal Structure of the Sr CA2+-Atpase with Bound Amppcp also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Calcium atom in the Crystal Structure of the Sr CA2+-Atpase with Bound Amppcp (pdb code 1vfp). 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 the Sr CA2+-Atpase with Bound Amppcp, PDB code: 1vfp:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of the Sr CA2+-Atpase with Bound Amppcp


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 Sr CA2+-Atpase with Bound Amppcp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca995 b:65.4 occ:1.00 OD2 A:ASP800 2.3 48.5 1.0 OD1 A:ASN796 2.4 59.5 1.0 O A:ILE307 2.4 58.5 1.0 OE2 A:GLU309 2.5 79.6 1.0 O A:VAL304 2.8 62.4 1.0 CD A:GLU309 2.9 79.6 1.0 OE1 A:GLU309 3.0 79.6 1.0 CG A:ASP800 3.2 48.5 1.0 O A:ALA305 3.3 70.2 1.0 C A:ALA305 3.4 70.2 1.0 CG A:ASN796 3.5 59.5 1.0 C A:ILE307 3.6 58.5 1.0 CB A:ASP800 3.6 48.5 1.0 ND2 A:ASN768 3.6 56.1 1.0 O A:HOH1014 3.7 42.6 1.0 CA A:ALA305 3.8 70.2 1.0 N A:ALA306 3.8 77.7 1.0 C A:ALA306 3.9 77.7 1.0 C A:VAL304 3.9 62.4 1.0 N A:ILE307 3.9 58.5 1.0 O A:ALA306 4.1 77.7 1.0 ND2 A:ASN796 4.1 59.5 1.0 CG A:GLU309 4.2 79.6 1.0 CA A:ALA306 4.3 77.7 1.0 CA A:ILE307 4.3 58.5 1.0 OD1 A:ASP800 4.3 48.5 1.0 N A:ALA305 4.3 70.2 1.0 N A:PRO308 4.5 97.2 1.0 CG A:ASN768 4.6 56.1 1.0 CB A:ASN796 4.7 59.5 1.0 N A:GLU309 4.7 77.0 1.0 OD1 A:ASN768 4.7 56.1 1.0 CA A:PRO308 4.8 97.2 1.0 CB A:ILE307 4.8 86.3 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of the Sr CA2+-Atpase with Bound Amppcp


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 Sr CA2+-Atpase with Bound Amppcp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca996 b:56.3 occ:1.00 OD1 A:ASP800 2.3 48.5 1.0 O A:HOH1013 2.4 56.4 1.0 OE2 A:GLU771 2.4 67.0 1.0 OG1 A:THR799 2.4 68.5 1.0 OE2 A:GLU908 2.5 44.1 1.0 OD1 A:ASN768 2.5 56.1 1.0 O A:HOH1014 2.7 42.6 1.0 OE1 A:GLU908 3.2 44.1 1.0 CD A:GLU908 3.2 44.1 1.0 CB A:THR799 3.3 68.5 1.0 CD A:GLU771 3.3 67.0 1.0 CG A:ASP800 3.4 48.5 1.0 CG A:ASN768 3.7 56.1 1.0 OE1 A:GLU771 3.9 67.0 1.0 OD2 A:ASP800 3.9 48.5 1.0 CB A:SER767 4.2 93.2 1.0 C A:THR799 4.2 52.2 1.0 N A:ASN768 4.3 60.7 1.0 CG2 A:THR799 4.3 68.5 1.0 N A:ASP800 4.3 44.2 1.0 CG A:GLU771 4.4 67.0 1.0 CA A:THR799 4.4 52.2 1.0 CA A:ASN768 4.4 60.7 1.0 O A:THR799 4.5 52.2 1.0 ND2 A:ASN768 4.6 56.1 1.0 CB A:ASP800 4.6 48.5 1.0 C A:SER767 4.6 91.3 1.0 O A:VAL795 4.7 87.3 1.0 CG A:GLU908 4.7 44.1 1.0 CB A:ASN768 4.7 56.1 1.0 O A:ALA305 4.7 70.2 1.0 CA A:ASP800 4.9 44.2 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of the Sr CA2+-Atpase with Bound Amppcp


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 the Sr CA2+-Atpase with Bound Amppcp within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca995 b:63.9 occ:1.00 OD1 B:ASN796 2.4 64.8 1.0 OD2 B:ASP800 2.4 58.7 1.0 O B:ILE307 2.5 89.1 1.0 OE2 B:GLU309 2.5 0.0 1.0 O B:VAL304 2.7 68.7 1.0 CD B:GLU309 3.0 0.0 1.0 OE1 B:GLU309 3.1 0.0 1.0 O B:ALA305 3.2 70.0 1.0 CG B:ASP800 3.3 58.7 1.0 C B:ALA305 3.3 70.0 1.0 CG B:ASN796 3.5 64.8 1.0 C B:ILE307 3.6 89.1 1.0 ND2 B:ASN768 3.6 77.0 1.0 CB B:ASP800 3.7 58.7 1.0 O B:HOH2014 3.7 69.7 1.0 CA B:ALA305 3.8 70.0 1.0 N B:ALA306 3.8 78.9 1.0 C B:VAL304 3.8 68.7 1.0 C B:ALA306 3.8 78.9 1.0 N B:ILE307 3.9 89.1 1.0 O B:ALA306 4.1 78.9 1.0 ND2 B:ASN796 4.1 64.8 1.0 CG B:GLU309 4.2 0.0 1.0 CA B:ALA306 4.2 78.9 1.0 N B:ALA305 4.3 70.0 1.0 CA B:ILE307 4.3 89.1 1.0 OD1 B:ASP800 4.3 58.7 1.0 N B:PRO308 4.6 91.2 1.0 CG B:ASN768 4.6 77.0 1.0 CB B:ASN796 4.7 64.8 1.0 OD1 B:ASN768 4.7 77.0 1.0 N B:GLU309 4.7 85.1 1.0 CA B:PRO308 4.8 91.2 1.0 CB B:ILE307 4.8 80.3 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of the Sr CA2+-Atpase with Bound Amppcp


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 the Sr CA2+-Atpase with Bound Amppcp within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca996 b:59.2 occ:1.00 OD1 B:ASP800 2.3 58.7 1.0 OE2 B:GLU771 2.4 76.5 1.0 O B:HOH2013 2.4 43.2 1.0 OG1 B:THR799 2.5 78.8 1.0 OD1 B:ASN768 2.5 77.0 1.0 OE2 B:GLU908 2.5 63.9 1.0 O B:HOH2014 2.6 69.7 1.0 OE1 B:GLU908 3.2 63.9 1.0 CD B:GLU908 3.2 63.9 1.0 CD B:GLU771 3.3 76.5 1.0 CB B:THR799 3.3 78.8 1.0 CG B:ASP800 3.4 58.7 1.0 CG B:ASN768 3.7 77.0 1.0 OE1 B:GLU771 3.8 76.5 1.0 OD2 B:ASP800 3.9 58.7 1.0 CB B:SER767 4.2 73.6 1.0 N B:ASN768 4.2 71.6 1.0 C B:THR799 4.3 64.0 1.0 CG2 B:THR799 4.3 78.8 1.0 CG B:GLU771 4.3 76.5 1.0 N B:ASP800 4.4 74.3 1.0 CA B:ASN768 4.4 71.6 1.0 CA B:THR799 4.4 64.0 1.0 O B:THR799 4.5 64.0 1.0 ND2 B:ASN768 4.5 77.0 1.0 C B:SER767 4.6 72.1 1.0 CB B:ASP800 4.6 58.7 1.0 CB B:ASN768 4.7 77.0 1.0 O B:VAL795 4.7 73.3 1.0 CG B:GLU908 4.7 63.9 1.0 O B:ALA305 4.7 70.0 1.0 CA B:ASP800 4.9 74.3 1.0

C.Toyoshima, T.Mizutani. Crystal Structure of the Calcium Pump with A Bound Atp Analogue. Nature V. 430 529 2004.
ISSN: ISSN 0028-0836
PubMed: 15229613
DOI: 10.1038/NATURE02680