Cadmium in PDB 1ibs: Phosphoribosyldiphosphate Synthetase in Complex with Cadmium Ions

All present enzymatic activity of Phosphoribosyldiphosphate Synthetase in Complex with Cadmium Ions:
2.7.6.1;

The structure of Phosphoribosyldiphosphate Synthetase in Complex with Cadmium Ions, PDB code: 1ibs was solved by T.A.Eriksen, A.Kadziola, S.Larsen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.80
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	115.600, 115.600, 107.670, 90.00, 90.00, 120.00
R / Rfree (%)	20 / 27.3

The binding sites of Cadmium atom in the Phosphoribosyldiphosphate Synthetase in Complex with Cadmium Ions (pdb code 1ibs). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Phosphoribosyldiphosphate Synthetase in Complex with Cadmium Ions, PDB code: 1ibs:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in the Phosphoribosyldiphosphate Synthetase in Complex with Cadmium Ions


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Phosphoribosyldiphosphate Synthetase in Complex with Cadmium Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1005 b:25.4 occ:0.50 O3P A:ABM1009 1.8 58.0 1.0 NE2 A:HIS135 2.2 24.1 1.0 P A:ABM1009 2.8 59.9 1.0 CD2 A:HIS135 3.0 23.1 1.0 CE1 A:HIS135 3.2 22.4 1.0 O2P A:ABM1009 3.3 59.4 1.0 O5' A:ABM1009 3.4 59.3 1.0 C5' A:ABM1009 3.5 57.6 1.0 NH2 A:ARG104 3.9 40.4 1.0 OD1 A:ASP103 4.0 33.9 1.0 CG A:HIS135 4.2 22.5 1.0 NE A:ARG104 4.2 35.1 1.0 ND1 A:HIS135 4.2 22.0 1.0 OD2 A:ASP103 4.3 30.1 1.0 O A:ARG101 4.3 23.0 1.0 CM A:ABM1009 4.3 56.9 1.0 CZ A:ARG104 4.5 40.0 1.0 CG A:ASP103 4.6 31.8 1.0

Cadmium binding site 2 out of 4 in the Phosphoribosyldiphosphate Synthetase in Complex with Cadmium Ions


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Phosphoribosyldiphosphate Synthetase in Complex with Cadmium Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1006 b:30.8 occ:0.50 OD2 A:ASP174 2.3 45.9 1.0 OD1 A:ASP223 2.7 22.1 1.0 OD2 A:ASP223 2.8 15.6 1.0 CG A:ASP223 3.1 19.4 1.0 CG A:ASP174 3.1 41.5 1.0 O A:HOH1031 3.2 29.0 1.0 OD1 A:ASP174 3.3 41.9 1.0 CB A:ASP174 4.5 37.7 1.0 OD1 A:ASP224 4.5 25.7 1.0 CB A:ASP223 4.6 21.9 1.0

Cadmium binding site 3 out of 4 in the Phosphoribosyldiphosphate Synthetase in Complex with Cadmium Ions


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Phosphoribosyldiphosphate Synthetase in Complex with Cadmium Ions within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd1007 b:23.8 occ:0.60 O3P B:ABM1010 2.1 55.9 1.0 NE2 B:HIS135 2.3 28.1 1.0 P B:ABM1010 3.0 55.0 1.0 CD2 B:HIS135 3.2 23.1 1.0 O5' B:ABM1010 3.2 52.8 1.0 CM B:ABM1010 3.2 54.0 1.0 CE1 B:HIS135 3.3 24.0 1.0 C5' B:ABM1010 3.3 49.3 1.0 NH2 B:ARG104 3.9 42.8 1.0 OD1 B:ASP103 4.3 33.9 1.0 CG B:HIS135 4.4 21.3 1.0 ND1 B:HIS135 4.4 21.9 1.0 O2P B:ABM1010 4.5 52.8 1.0 O B:ARG101 4.6 22.3 1.0 NE B:ARG104 4.6 38.3 1.0 OD2 B:ASP103 4.6 33.8 1.0 CZ B:ARG104 4.7 41.0 1.0 C4' B:ABM1010 4.8 47.1 1.0 CG B:ASP103 4.8 32.1 1.0 CG B:ARG101 4.9 17.2 1.0

Cadmium binding site 4 out of 4 in the Phosphoribosyldiphosphate Synthetase in Complex with Cadmium Ions


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Phosphoribosyldiphosphate Synthetase in Complex with Cadmium Ions within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd1008 b:43.4 occ:0.75 OD2 B:ASP174 2.5 31.7 1.0 OD2 B:ASP223 2.8 29.1 1.0 OD1 B:ASP223 2.8 28.6 1.0 O B:HOH1033 3.0 22.1 1.0 CG B:ASP223 3.2 27.4 1.0 CG B:ASP174 3.4 28.3 1.0 OD1 B:ASP174 3.5 29.2 1.0 OD1 B:ASP224 4.3 13.5 1.0 CE1 B:HIS135 4.7 24.0 1.0 O B:HOH1029 4.7 20.0 1.0 CB B:ASP223 4.7 24.1 1.0 CB B:ASP174 4.7 27.7 1.0

T.A.Eriksen, A.Kadziola, S.Larsen. Binding of Cations in Bacillus Subtilis Phosphoribosyldiphosphate Synthetase and Their Role in Catalysis. Protein Sci. V. 11 271 2002.
ISSN: ISSN 0961-8368
PubMed: 11790837
DOI: 10.1110/PS.28502