Calcium in PDB 2d00: Subunit F of V-Type Atpase/Synthase

All present enzymatic activity of Subunit F of V-Type Atpase/Synthase:
3.6.3.14;

The structure of Subunit F of V-Type Atpase/Synthase, PDB code: 2d00 was solved by H.Makyio, R.Iino, C.Ikeda, H.Imamura, M.Tamakoshi, M.Iwata, D.Stock, R.A.Bernal, E.P.Carpenter, M.Yoshida, K.Yokoyama, S.Iwata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 2.20
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	81.705, 138.295, 66.096, 90.00, 90.00, 90.00
R / Rfree (%)	21.4 / 26.2

The binding sites of Calcium atom in the Subunit F of V-Type Atpase/Synthase (pdb code 2d00). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Subunit F of V-Type Atpase/Synthase, PDB code: 2d00:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Subunit F of V-Type Atpase/Synthase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Subunit F of V-Type Atpase/Synthase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1002 b:67.2 occ:1.00 O B:HOH1038 2.3 64.3 1.0 O E:HOH158 2.3 56.0 1.0 O E:GLY27 2.4 66.2 1.0 OD1 B:ASP72 2.4 60.9 1.0 O B:GLY70 2.4 60.6 1.0 C B:GLY70 3.5 61.7 1.0 C E:GLY27 3.5 65.5 1.0 CG B:ASP72 3.5 59.5 1.0 OE1 E:GLU33 3.9 66.6 1.0 OD2 B:ASP72 4.0 58.6 1.0 CA B:GLY70 4.1 60.7 1.0 O E:HOH152 4.2 57.9 1.0 N B:ASP72 4.2 59.8 1.0 CA E:GLY27 4.4 65.6 1.0 N E:GLY27 4.4 66.0 1.0 CA E:ALA28 4.4 64.2 1.0 N E:ALA28 4.4 64.5 1.0 C B:ARG71 4.5 61.7 1.0 N B:ARG71 4.6 61.2 1.0 CB B:ASP72 4.7 60.7 1.0 CA B:ASP72 4.7 61.1 1.0 O B:HOH1013 4.8 55.9 1.0 CD1 E:LEU37 4.8 64.7 1.0 CA B:ARG71 4.9 63.0 1.0 O B:ARG71 4.9 61.4 1.0

Calcium binding site 2 out of 4 in the Subunit F of V-Type Atpase/Synthase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Subunit F of V-Type Atpase/Synthase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1004 b:72.6 occ:1.00 O B:GLY27 2.5 66.5 1.0 O B:HOH1034 2.6 62.8 1.0 OD1 E:ASP72 2.8 52.9 1.0 OE2 B:GLU33 2.9 60.3 1.0 O E:GLY70 3.1 67.6 1.0 C B:GLY27 3.2 64.3 1.0 CG E:ASP72 3.8 57.2 1.0 CA B:GLY27 3.9 63.8 1.0 CD B:GLU33 4.0 62.5 1.0 N B:ALA28 4.1 66.8 1.0 N E:ASP72 4.1 62.2 1.0 N B:GLY27 4.2 62.7 1.0 C E:GLY70 4.2 67.6 1.0 OD2 E:ASP72 4.4 56.2 1.0 CA B:ALA28 4.4 66.1 1.0 CD1 B:LEU37 4.5 62.4 1.0 C E:ARG71 4.6 63.7 1.0 CA E:ASP72 4.7 59.9 1.0 O E:ARG71 4.8 63.6 1.0 OE1 B:GLU33 4.8 57.6 1.0 CG B:GLU33 4.9 64.1 1.0 CB E:ASP72 4.9 59.1 1.0

Calcium binding site 3 out of 4 in the Subunit F of V-Type Atpase/Synthase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Subunit F of V-Type Atpase/Synthase within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1003 b:53.9 occ:1.00 O C:GLY70 2.3 61.2 1.0 OD1 C:ASP72 2.5 67.5 1.0 O C:HOH1004 2.5 41.4 1.0 O C:HOH1041 2.6 64.0 1.0 O C:HOH1025 2.9 60.4 1.0 C C:GLY70 3.3 62.9 1.0 CG C:ASP72 3.5 63.2 1.0 CA C:GLY70 3.6 62.5 1.0 OD2 C:ASP72 4.0 58.8 1.0 N C:ASP72 4.1 63.6 1.0 N C:ARG71 4.5 62.5 1.0 C C:ARG71 4.5 64.3 1.0 CA C:ASP72 4.5 64.8 1.0 CB C:ASP72 4.6 63.4 1.0 OE2 C:GLU39 4.6 77.5 1.0 O C:HOH1008 4.7 50.4 1.0 O C:HOH1032 4.8 65.7 1.0 CA C:ARG71 4.9 64.6 1.0

Calcium binding site 4 out of 4 in the Subunit F of V-Type Atpase/Synthase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Subunit F of V-Type Atpase/Synthase within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1001 b:59.9 occ:1.00 O D:HOH1043 2.2 61.0 1.0 O D:GLY27 2.3 62.5 1.0 O A:HOH160 2.4 47.5 1.0 OD1 A:ASP72 2.5 69.2 1.0 OE2 D:GLU33 2.7 72.6 1.0 O A:GLY70 2.7 67.9 1.0 O D:HOH1042 3.1 73.5 1.0 C D:GLY27 3.3 61.6 1.0 CG A:ASP72 3.5 62.4 1.0 C A:GLY70 3.7 67.2 1.0 CD D:GLU33 3.8 71.9 1.0 OD2 A:ASP72 4.0 56.4 1.0 O D:HOH1004 4.0 53.0 1.0 CA D:GLY27 4.1 63.3 1.0 N D:GLY27 4.3 62.0 1.0 N D:ALA28 4.3 61.6 1.0 N A:ASP72 4.3 64.1 1.0 CA A:GLY70 4.4 68.5 1.0 CB A:ASP72 4.5 65.1 1.0 CA D:ALA28 4.5 61.0 1.0 C A:ARG71 4.6 65.2 1.0 CA A:ASP72 4.6 64.0 1.0 O A:HOH117 4.6 60.2 1.0 OE1 D:GLU33 4.7 73.5 1.0 CG D:GLU33 4.7 70.5 1.0 N A:ARG71 4.8 67.0 1.0 CD1 D:LEU37 4.9 70.0 1.0 CA A:ARG71 5.0 66.5 1.0

H.Makyio, R.Iino, C.Ikeda, H.Imamura, M.Tamakoshi, M.Iwata, D.Stock, R.A.Bernal, E.P.Carpenter, M.Yoshida, K.Yokoyama, S.Iwata. Structure of A Central Stalk Subunit F of Prokaryotic V-Type Atpase/Synthase From Thermus Thermophilus Embo J. V. 24 3974 2005.
ISSN: ISSN 0261-4189
PubMed: 16281059
DOI: 10.1038/SJ.EMBOJ.7600859