Calcium in PDB 1i40: 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: 1i40 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 / 1.10
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	109.520, 109.520, 75.080, 90.00, 90.00, 120.00
R / Rfree (%)	11.7 / 15.3

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 1i40). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Structure of Inorganic Pyrophosphatase, PDB code: 1i40:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 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:Ca302 b:19.5 occ:0.70 OD1 A:ASP102 1.5 28.4 0.3 O A:HOH310 2.1 25.1 1.0 O A:HOH330 2.2 28.3 1.0 OD1 A:ASP102 2.3 20.9 0.7 OD1 A:ASP65 2.4 36.2 1.0 OD2 A:ASP70 2.4 23.8 1.0 O A:HOH464 2.5 31.4 1.0 O A:HOH323 2.6 18.2 1.0 CG A:ASP102 2.6 26.0 0.3 OD2 A:ASP102 3.1 26.9 0.3 CG A:ASP102 3.4 22.8 0.7 CG A:ASP65 3.4 27.9 1.0 CG A:ASP70 3.4 17.3 1.0 OD2 A:ASP65 3.7 25.6 1.0 OD2 A:ASP102 3.9 25.6 0.7 CB A:ASP102 3.9 22.9 0.3 OG A:SER63 4.0 21.6 0.3 O A:ALA103 4.1 18.5 1.0 OD1 A:ASP70 4.1 20.1 1.0 O A:HOH329 4.2 35.4 1.0 NZ A:LYS104 4.2 22.6 1.0 O A:HOH395 4.3 30.0 1.0 O A:HOH383 4.3 37.3 0.8 CA A:ASP102 4.4 21.7 0.3 CB A:ASP70 4.4 14.5 1.0 C A:ASP102 4.4 15.1 0.3 N A:ALA103 4.5 16.7 1.0 O A:PRO68 4.6 16.5 1.0 CB A:ASP102 4.6 19.3 0.7 O A:ASP102 4.7 20.2 0.3 N A:ASP70 4.7 12.8 1.0 CB A:ASP65 4.7 24.1 1.0 O A:HOH382 4.8 20.6 0.5 CA A:ASP102 4.9 20.0 0.7

Calcium binding site 2 out of 5 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:Ca303 b:18.4 occ:0.50 O A:HOH506 2.0 32.6 0.7 O A:HOH389 2.3 33.2 0.5 O A:HOH332 2.5 21.3 0.5 O A:ASN24 2.6 21.4 1.0 O A:HOH507 2.6 15.0 0.3 O A:HOH470 2.9 50.6 1.0 O A:HOH359 3.2 41.4 0.5 OD1 A:ASN24 3.3 35.1 0.6 C A:ASN24 3.5 16.0 1.0 CG A:ASN24 3.8 26.9 0.6 ND2 A:ASN24 4.2 35.5 0.6 O A:HOH572 4.2 44.0 1.0 N A:ALA25 4.2 13.2 1.0 CA A:ALA25 4.3 12.8 1.0 C A:ALA25 4.3 12.2 1.0 CA A:ASN24 4.4 21.0 1.0 O A:HOH554 4.5 24.0 0.3 O A:ALA25 4.5 16.1 1.0 CB A:ASN24 4.6 27.9 0.6 CB A:ASN24 4.6 26.4 0.4 OD1 A:ASP26 4.7 24.0 1.0 N A:ASP26 4.8 12.8 1.0

Calcium binding site 3 out of 5 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:Ca304 b:22.7 occ:0.60 O A:HOH377 1.9 42.4 1.0 O A:HOH322 2.1 22.9 1.0 O A:HOH329 2.2 35.4 1.0 O A:HOH509 2.3 18.0 0.4 O A:HOH315 2.4 20.2 0.6 O A:HOH508 2.5 28.3 0.6 OD1 A:ASP70 2.6 20.1 1.0 O A:HOH539 2.7 27.1 0.6 CG A:ASP70 3.8 17.3 1.0 O A:HOH394 4.1 16.2 0.5 OD2 A:ASP70 4.3 23.8 1.0 OE1 A:GLU20 4.4 15.3 1.0 O A:HOH310 4.4 25.1 1.0 O A:PRO68 4.5 16.5 1.0 OH A:TYR55 4.5 18.0 1.0 OE2 A:GLU31 4.6 43.8 0.5 CB A:ASP67 4.7 25.5 1.0 O A:HOH314 4.8 33.9 1.0 CB A:TYR57 4.8 11.8 1.0 CB A:ASP70 4.9 14.5 1.0 OE2 A:GLU20 4.9 13.9 1.0 CE2 A:TYR55 5.0 15.0 1.0

Calcium binding site 4 out of 5 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:Ca305 b:20.2 occ:0.70 O A:HOH452 1.8 21.7 0.6 O A:VAL150 2.3 21.6 1.0 OE2 A:GLU139 2.3 30.3 1.0 O A:HOH503 2.4 24.4 0.5 O A:HOH531 2.4 31.2 0.6 O A:GLU139 2.5 15.7 1.0 O A:HOH347 2.5 22.7 0.8 O A:HOH396 2.7 20.7 1.0 CD A:GLU139 3.3 19.3 1.0 C A:VAL150 3.6 19.4 1.0 C A:GLU139 3.6 13.5 1.0 CE A:LYS151 3.8 53.5 0.7 CG A:GLU139 3.9 18.7 1.0 OD1 A:ASP143 4.0 15.6 1.0 CA A:GLU139 4.1 13.9 1.0 N A:VAL150 4.2 20.3 1.0 O A:HOH493 4.2 37.2 0.6 OE1 A:GLU139 4.3 21.4 1.0 O A:HOH335 4.4 15.4 1.0 CA A:VAL150 4.4 19.4 1.0 N A:LYS151 4.5 20.4 1.0 CA A:LYS151 4.6 20.8 1.0 CB A:GLU139 4.6 15.2 1.0 NZ A:LYS151 4.6 29.5 0.7 N A:HIS140 4.8 12.8 1.0 CG A:LYS151 4.8 32.9 0.3 CB A:VAL150 4.8 19.9 1.0 CG A:LYS151 4.9 36.4 0.7 CD A:LYS151 4.9 51.3 0.7 O A:HOH342 5.0 16.2 1.0

Calcium binding site 5 out of 5 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 5 of Structure of Inorganic Pyrophosphatase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca306 b:23.3 occ:0.20 OD2 A:ASP97 2.2 35.6 1.0 O A:HOH383 2.3 37.3 0.8 OD2 A:ASP102 2.8 26.9 0.3 OD2 A:ASP102 2.9 25.6 0.7 CG A:ASP97 3.3 23.9 1.0 O A:HOH482 3.4 25.5 0.7 CG A:ASP102 3.5 26.0 0.3 CB A:ASP102 3.7 22.9 0.3 CG A:ASP102 3.8 22.8 0.7 OD1 A:ASP97 4.0 25.3 1.0 O A:HOH310 4.2 25.1 1.0 O A:HOH448 4.2 32.9 1.0 CB A:ASP97 4.3 23.5 1.0 OD1 A:ASP102 4.4 28.4 0.3 CB A:ASP102 4.5 19.3 0.7 O A:HOH368 4.5 24.6 0.9 OD1 A:ASP102 4.5 20.9 0.7 O A:HOH481 4.6 42.9 1.0 NZ A:LYS104 4.7 22.6 1.0 NZ A:LYS142 4.8 27.1 0.7 OD1 A:ASP65 4.8 36.2 1.0 OE2 A:GLU98 5.0 34.4 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