Calcium in PDB 1i6t: Structure of Inorganic Pyrophosphatase

All present enzymatic activity of Structure of Inorganic Pyrophosphatase:
3.6.1.1;

The structure of Structure of Inorganic Pyrophosphatase, PDB code: 1i6t was solved by V.R.Samygina, A.N.Popov, V.S.Lamzin, S.M.Avaeva, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	12.00 / 1.20
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	109.356, 109.356, 75.582, 90.00, 90.00, 120.00
R / Rfree (%)	12.9 / 17

The structure of Structure of Inorganic Pyrophosphatase also contains other interesting chemical elements:

Chlorine	(Cl)	3 atoms
Sodium	(Na)	1 atom

The binding sites of Calcium atom in the Structure of Inorganic Pyrophosphatase (pdb code 1i6t). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structure of Inorganic Pyrophosphatase, PDB code: 1i6t:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Structure of Inorganic Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Inorganic Pyrophosphatase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:21.1 occ:0.80 OD1 A:ASP65 2.3 37.1 1.0 OD2 A:ASP70 2.4 22.8 1.0 O A:HOH437 2.4 22.0 0.5 O2 A:POP411 2.4 21.0 0.8 O A:HOH436 2.4 28.9 1.0 OD2 A:ASP102 2.5 28.1 1.0 OD1 A:ASP102 2.5 26.2 1.0 CG A:ASP102 2.9 26.4 1.0 OD1 A:ASP70 2.9 22.7 1.0 CG A:ASP70 3.0 20.6 1.0 O A:HOH412 3.3 18.5 0.2 CG A:ASP65 3.3 40.8 1.0 P1 A:POP411 3.6 21.1 0.8 CA A:CA303 3.8 24.7 0.8 CA A:CA302 3.8 23.2 0.8 OD2 A:ASP65 3.9 39.8 1.0 O1 A:POP411 3.9 23.2 0.8 O A:HOH427 4.2 23.6 1.0 NZ A:LYS104 4.3 25.4 1.0 O3 A:POP411 4.3 26.4 0.8 CB A:ASP102 4.4 27.9 1.0 CB A:ASP70 4.4 19.9 1.0 CB A:ASP65 4.5 38.7 1.0 OG A:SER63 4.6 32.6 0.5 O A:PRO68 4.7 24.2 1.0 CB A:ASP67 4.7 32.7 1.0 O A:HOH481 4.7 23.0 0.6 OH A:TYR55 4.8 24.3 1.0 O A:HOH426 4.8 23.9 1.0 O A:HOH492 4.8 34.6 1.0 O A:POP411 4.8 20.7 0.8

Calcium binding site 2 out of 4 in the Structure of Inorganic Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Inorganic Pyrophosphatase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:23.2 occ:0.80 O A:HOH435 2.3 27.2 1.0 O A:HOH418 2.3 24.5 1.0 O A:HOH436 2.3 28.9 1.0 OD1 A:ASP70 2.3 22.7 1.0 O A:HOH426 2.4 23.9 1.0 O1 A:POP411 2.4 23.2 0.8 O A:HOH412 3.0 18.5 0.2 CG A:ASP70 3.5 20.6 1.0 P1 A:POP411 3.6 21.1 0.8 CA A:CA301 3.8 21.1 0.8 O2 A:POP411 3.9 21.0 0.8 OH A:TYR55 4.0 24.3 1.0 OD2 A:ASP70 4.1 22.8 1.0 OE1 A:GLU20 4.1 19.5 1.0 O A:HOH494 4.2 35.5 1.0 O A:HOH429 4.2 26.8 1.0 NZ A:LYS29 4.2 23.8 1.0 CE2 A:TYR55 4.3 20.8 1.0 O A:PRO68 4.4 24.2 1.0 O A:HOH437 4.4 22.0 0.5 CZ A:TYR55 4.5 19.1 1.0 CB A:ASP70 4.5 19.9 1.0 O3 A:POP411 4.5 26.4 0.8 O A:POP411 4.6 20.7 0.8 OD2 A:ASP67 4.7 48.8 1.0 CB A:ASP67 4.7 32.7 1.0 O A:HOH417 4.8 21.6 1.0 CA A:ASP70 4.8 18.8 1.0 O A:GLY56 4.9 17.7 1.0

Calcium binding site 3 out of 4 in the Structure of Inorganic Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Inorganic Pyrophosphatase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:24.7 occ:0.80 OD2 A:ASP97 2.2 32.4 1.0 O5 A:POP411 2.4 21.9 0.8 OD2 A:ASP102 2.4 28.1 1.0 O2 A:POP411 2.5 21.0 0.8 O A:HOH524 2.5 39.2 0.8 O A:HOH481 2.6 23.0 0.6 CG A:ASP97 3.3 31.1 1.0 P1 A:POP411 3.4 21.1 0.8 CG A:ASP102 3.6 26.4 1.0 P2 A:POP411 3.6 20.0 0.8 O A:HOH412 3.7 18.5 0.2 O A:POP411 3.7 20.7 0.8 CA A:CA301 3.8 21.1 0.8 O3 A:POP411 3.8 26.4 0.8 OD1 A:ASP97 3.9 34.2 1.0 NZ A:LYS142 4.0 26.5 1.0 O A:HOH482 4.0 23.9 0.4 OD1 A:ASP65 4.2 37.1 1.0 CB A:ASP102 4.3 27.9 1.0 OD1 A:ASP102 4.5 26.2 1.0 O6 A:POP411 4.5 24.6 0.8 NZ A:LYS104 4.5 25.4 1.0 CB A:ASP97 4.6 32.7 1.0 OE2 A:GLU98 4.7 37.1 1.0 O4 A:POP411 4.7 20.6 0.8 O1 A:POP411 4.9 23.2 0.8 OD2 A:ASP70 4.9 22.8 1.0 O A:HOH436 4.9 28.9 1.0 OH A:TYR141 5.0 22.7 1.0

Calcium binding site 4 out of 4 in the Structure of Inorganic Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Inorganic Pyrophosphatase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:16.4 occ:0.50 O A:ASN24 2.3 17.2 1.0 O A:HOH420 2.4 19.8 1.0 O A:HOH573 2.4 23.0 0.5 O A:HOH471 2.4 17.3 1.0 O A:HOH439 2.4 30.0 1.0 C A:ASN24 3.5 16.4 1.0 ND2 A:ASN24 3.8 21.4 0.5 O A:HOH509 3.9 18.0 0.5 CG A:ASN24 4.0 17.8 0.5 CA A:ALA25 4.1 15.5 1.0 O A:HOH421 4.2 19.1 1.0 O A:HOH496 4.2 35.1 0.5 N A:ALA25 4.2 16.7 1.0 OD1 A:ASN24 4.2 19.5 0.5 O A:HOH585 4.3 38.6 0.5 O A:HOH433 4.3 20.7 1.0 O A:HOH555 4.3 42.0 1.0 O A:HOH574 4.5 18.9 0.5 CB A:ASN24 4.5 17.1 1.0 C A:ALA25 4.5 14.6 1.0 CA A:ASN24 4.6 16.0 1.0 O A:HOH443 4.8 32.9 1.0 N A:ASP26 4.9 14.9 1.0 OD1 A:ASP26 5.0 19.5 1.0

V.R.Samygina, A.N.Popov, E.V.Rodina, N.N.Vorobyeva, V.S.Lamzin, K.M.Polyakov, S.A.Kurilova, T.I.Nazarova, S.M.Avaeva. The Structures of Escherichia Coli Inorganic Pyrophosphatase Complexed with Ca(2+) or Capp(I) at Atomic Resolution and Their Mechanistic Implications. J.Mol.Biol. V. 314 633 2001.
ISSN: ISSN 0022-2836
PubMed: 11846572
DOI: 10.1006/JMBI.2001.5149