Cadmium in PDB 4o83: Saicar Synthetase (Type-1) in Complex with Adp/Amp

All present enzymatic activity of Saicar Synthetase (Type-1) in Complex with Adp/Amp:
6.3.2.6;

The structure of Saicar Synthetase (Type-1) in Complex with Adp/Amp, PDB code: 4o83 was solved by K.Manjunath, J.Jeyakanthan, K.Sekar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.55 / 2.05
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	95.010, 95.010, 148.271, 90.00, 90.00, 120.00
R / Rfree (%)	22.3 / 26.4

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Cadmium atom in the Saicar Synthetase (Type-1) in Complex with Adp/Amp (pdb code 4o83). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 18 binding sites of Cadmium where determined in the Saicar Synthetase (Type-1) in Complex with Adp/Amp, PDB code: 4o83:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 18 in the Saicar Synthetase (Type-1) in Complex with Adp/Amp


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Saicar Synthetase (Type-1) in Complex with Adp/Amp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd301 b:21.2 occ:1.00 OD2 A:ASP162 2.2 20.0 1.0 OE2 A:GLU158 2.3 20.9 1.0 OE2 B:GLU158 2.3 22.1 1.0 OD1 B:ASP162 2.4 20.5 1.0 OD2 B:ASP162 2.4 19.6 1.0 OD1 A:ASP162 2.5 18.6 1.0 CG A:ASP162 2.7 20.3 1.0 CG B:ASP162 2.8 19.8 1.0 CD A:GLU158 3.2 21.2 1.0 CD B:GLU158 3.2 22.9 1.0 CG A:GLU158 3.4 20.2 1.0 CG B:GLU158 3.5 22.9 1.0 NZ B:LYS161 3.9 22.6 1.0 CE B:LYS161 4.0 22.4 1.0 CB A:ASP162 4.2 18.7 1.0 NZ A:LYS161 4.2 23.6 1.0 CE A:LYS161 4.3 22.3 1.0 CB B:ASP162 4.3 20.2 1.0 OE1 A:GLU158 4.4 22.4 1.0 O A:GLU158 4.4 19.4 1.0 OE1 B:GLU158 4.4 22.9 1.0 O B:GLU158 4.5 20.2 1.0 O A:HOH431 4.5 21.9 1.0 O B:HOH501 4.5 18.4 1.0 O A:HOH436 4.7 46.3 1.0 CB A:GLU158 4.7 19.9 1.0 CB B:GLU158 4.9 21.8 1.0

Cadmium binding site 2 out of 18 in the Saicar Synthetase (Type-1) in Complex with Adp/Amp


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Saicar Synthetase (Type-1) in Complex with Adp/Amp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd302 b:57.5 occ:1.00 NE2 A:HIS63 2.3 31.2 1.0 OE2 B:GLU111 2.3 47.7 1.0 CD B:GLU111 2.7 49.5 1.0 OE1 B:GLU111 2.8 55.5 1.0 CD2 A:HIS63 3.2 30.7 1.0 O A:HOH451 3.2 34.8 1.0 CE1 A:HIS63 3.3 31.6 1.0 CG B:GLU111 4.0 44.5 1.0 ND1 A:HIS63 4.4 32.3 1.0 CG A:HIS63 4.4 30.9 1.0

Cadmium binding site 3 out of 18 in the Saicar Synthetase (Type-1) in Complex with Adp/Amp


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Saicar Synthetase (Type-1) in Complex with Adp/Amp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd303 b:41.8 occ:0.55 CD A:CD303 0.0 41.8 0.6 CD A:CD303 0.2 44.3 0.5 OD2 A:ASP128 2.2 30.2 1.0 OE2 A:GLU89 2.3 27.4 0.5 OE2 A:GLU89 2.4 16.2 0.5 CG A:ASP128 3.0 28.0 1.0 CD A:GLU89 3.2 17.3 0.5 OD1 A:ASP128 3.2 27.5 1.0 CD A:GLU89 3.3 25.7 0.5 OE1 A:GLU89 3.4 16.4 0.5 OE1 A:GLU89 3.7 26.4 0.5 OD1 A:ASP124 4.2 44.1 1.0 NZ A:LYS122 4.3 31.2 1.0 CB A:ASP128 4.4 27.3 1.0 CG A:GLU89 4.5 24.6 0.5 CG A:GLU89 4.6 18.1 0.5 CG A:LYS122 4.8 30.9 1.0

Cadmium binding site 4 out of 18 in the Saicar Synthetase (Type-1) in Complex with Adp/Amp


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Saicar Synthetase (Type-1) in Complex with Adp/Amp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd303 b:44.3 occ:0.45 CD A:CD303 0.0 44.3 0.5 CD A:CD303 0.2 41.8 0.6 OE2 A:GLU89 2.2 16.2 0.5 OE2 A:GLU89 2.2 27.4 0.5 OD2 A:ASP128 2.3 30.2 1.0 CD A:GLU89 3.1 17.3 0.5 CG A:ASP128 3.1 28.0 1.0 CD A:GLU89 3.2 25.7 0.5 OD1 A:ASP128 3.3 27.5 1.0 OE1 A:GLU89 3.3 16.4 0.5 OE1 A:GLU89 3.5 26.4 0.5 NZ A:LYS122 4.1 31.2 1.0 OD1 A:ASP124 4.3 44.1 1.0 CG A:GLU89 4.4 24.6 0.5 CB A:ASP128 4.5 27.3 1.0 CG A:GLU89 4.5 18.1 0.5 CG A:LYS122 4.7 30.9 1.0

Cadmium binding site 5 out of 18 in the Saicar Synthetase (Type-1) in Complex with Adp/Amp


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Saicar Synthetase (Type-1) in Complex with Adp/Amp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd304 b:43.6 occ:0.50 CD A:CD304 0.0 43.6 0.5 CD A:CD304 1.4 36.1 0.5 ND1 A:HIS127 2.3 37.6 1.0 OD1 A:ASP35 2.5 40.2 1.0 OD2 A:ASP35 2.7 44.5 1.0 CG A:ASP35 2.9 43.1 1.0 CG A:HIS127 3.2 36.0 1.0 CE1 A:HIS127 3.2 38.3 1.0 CB A:HIS127 3.5 32.8 1.0 O A:ASP124 3.6 40.4 1.0 CA A:HIS127 3.7 31.7 1.0 CB A:ASP35 4.3 42.4 1.0 NE2 A:HIS127 4.3 38.5 1.0 CD2 A:HIS127 4.4 38.0 1.0 N A:HIS127 4.5 31.7 1.0 C A:ASP124 4.7 38.9 1.0 C A:HIS127 4.7 28.8 1.0

Cadmium binding site 6 out of 18 in the Saicar Synthetase (Type-1) in Complex with Adp/Amp


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Saicar Synthetase (Type-1) in Complex with Adp/Amp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd304 b:36.1 occ:0.50 CD A:CD304 0.0 36.1 0.5 CD A:CD304 1.4 43.6 0.5 ND1 A:HIS127 2.3 37.6 1.0 OD2 A:ASP35 2.5 44.5 1.0 OD1 A:ASP35 2.5 40.2 1.0 CG A:ASP35 2.9 43.1 1.0 CG A:HIS127 3.1 36.0 1.0 CB A:HIS127 3.3 32.8 1.0 CE1 A:HIS127 3.3 38.3 1.0 CA A:HIS127 4.0 31.7 1.0 CD2 A:HIS127 4.3 38.0 1.0 CB A:ASP35 4.4 42.4 1.0 NE2 A:HIS127 4.4 38.5 1.0 O A:ASP124 4.8 40.4 1.0 C A:HIS127 4.9 28.8 1.0 O A:HIS127 5.0 28.3 1.0

Cadmium binding site 7 out of 18 in the Saicar Synthetase (Type-1) in Complex with Adp/Amp


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Saicar Synthetase (Type-1) in Complex with Adp/Amp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd305 b:59.5 occ:0.50 O A:HOH445 3.1 44.2 1.0 OE2 A:GLU125 4.3 69.1 1.0 N A:ASP124 4.5 36.7 1.0 OD2 A:ASP124 4.6 48.3 1.0 CB A:ASP124 4.7 41.9 1.0 N A:GLU125 4.9 40.9 1.0 O A:HOH429 4.9 30.9 1.0 OD1 A:ASN123 5.0 35.7 1.0

Cadmium binding site 8 out of 18 in the Saicar Synthetase (Type-1) in Complex with Adp/Amp


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Saicar Synthetase (Type-1) in Complex with Adp/Amp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd306 b:47.4 occ:0.60 OE1 A:GLU226 2.4 45.1 1.0 OE2 A:GLU226 2.8 45.0 1.0 CD A:GLU226 3.0 42.4 1.0 OE1 A:GLU229 4.0 44.4 1.0 CG A:GLU226 4.5 39.7 1.0 CD A:GLU229 4.6 46.0 1.0 NE A:ARG230 4.6 33.8 1.0 CG A:ARG230 4.8 34.8 1.0 CG A:GLU229 4.9 42.1 1.0

Cadmium binding site 9 out of 18 in the Saicar Synthetase (Type-1) in Complex with Adp/Amp


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Saicar Synthetase (Type-1) in Complex with Adp/Amp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd307 b:54.4 occ:0.40 CD A:CD307 0.0 54.4 0.4 CD A:CD307 2.0 41.4 0.6 O A:HOH440 2.2 22.6 1.0 NZ A:LYS13 2.3 36.3 1.0 OD2 A:ASP190 2.6 25.3 1.0 OD1 A:ASP190 2.8 23.9 1.0 O5' A:AMP310 3.0 54.0 0.9 O2P A:AMP310 3.0 59.0 0.9 CG A:ASP190 3.1 23.1 1.0 CE A:LYS13 3.4 34.0 1.0 P A:AMP310 3.5 61.8 0.9 O1P A:AMP310 3.9 58.8 0.9 OE2 A:GLU191 4.0 28.6 1.0 O A:HOH435 4.1 31.7 1.0 C5' A:AMP310 4.1 43.9 0.9 NZ A:LYS175 4.1 24.1 1.0 OE2 A:GLU177 4.2 23.3 1.0 C3' A:AMP310 4.3 38.1 0.9 CB A:ASP190 4.6 23.2 1.0 C2' A:AMP310 4.6 36.8 0.9 CD A:LYS13 4.7 37.2 1.0 CD A:GLU177 4.8 23.1 1.0 C4' A:AMP310 4.9 39.9 0.9 O3P A:AMP310 4.9 59.6 0.9 CD A:GLU191 5.0 27.5 1.0

Cadmium binding site 10 out of 18 in the Saicar Synthetase (Type-1) in Complex with Adp/Amp


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Saicar Synthetase (Type-1) in Complex with Adp/Amp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd307 b:41.4 occ:0.60 CD A:CD307 0.0 41.4 0.6 CD A:CD307 2.0 54.4 0.4 O A:HOH440 2.7 22.6 1.0 O2P A:AMP310 2.8 59.0 0.9 O A:HOH435 2.9 31.7 1.0 O1P A:AMP310 3.0 58.8 0.9 P A:AMP310 3.3 61.8 0.9 O5' A:AMP310 3.5 54.0 0.9 NZ A:LYS13 3.8 36.3 1.0 NZ A:LYS122 4.3 31.2 1.0 OE2 A:GLU177 4.4 23.3 1.0 OD2 A:ASP190 4.4 25.3 1.0 OD1 A:ASP190 4.5 23.9 1.0 NZ A:LYS175 4.6 24.1 1.0 O3P A:AMP310 4.8 59.6 0.9 C3' A:AMP310 4.8 38.1 0.9 CG A:ASP190 4.9 23.1 1.0 C5' A:AMP310 4.9 43.9 0.9

K.Manjunath, J.Jeyakanthan, K.Sekar. Saicar Synthetase (Type-1) in Complex with Adp/Amp To Be Published.