Cadmium in PDB 4o82: Saicar Synthetase (Type-1) in Complex with Adp and Amp in Both Chains

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

The structure of Saicar Synthetase (Type-1) in Complex with Adp and Amp in Both Chains, PDB code: 4o82 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)	47.53 / 2.16
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	94.980, 94.980, 147.701, 90.00, 90.00, 120.00
R / Rfree (%)	23.3 / 27.3

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 23;

Binding sites:

The binding sites of Cadmium atom in the Saicar Synthetase (Type-1) in Complex with Adp and Amp in Both Chains (pdb code 4o82). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 23 binding sites of Cadmium where determined in the Saicar Synthetase (Type-1) in Complex with Adp and Amp in Both Chains, PDB code: 4o82:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 23 in the Saicar Synthetase (Type-1) in Complex with Adp and Amp in Both Chains


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 and Amp in Both Chains within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd301 b:27.1 occ:1.00 OD1 A:ASP162 2.2 22.6 1.0 OD2 B:ASP162 2.3 23.8 1.0 OE2 A:GLU158 2.4 21.8 1.0 OD1 B:ASP162 2.4 25.2 1.0 OD2 A:ASP162 2.4 20.5 1.0 OE2 B:GLU158 2.5 23.7 1.0 CG A:ASP162 2.7 21.9 1.0 CG B:ASP162 2.8 24.6 1.0 CD A:GLU158 3.2 22.7 1.0 CD B:GLU158 3.3 24.4 1.0 CG A:GLU158 3.3 22.4 1.0 CG B:GLU158 3.5 25.8 1.0 NZ B:LYS161 3.8 26.4 1.0 CE B:LYS161 3.9 27.4 1.0 CB A:ASP162 4.2 22.4 1.0 CE A:LYS161 4.2 24.3 1.0 NZ A:LYS161 4.2 25.3 1.0 CB B:ASP162 4.3 23.8 1.0 O B:GLU158 4.4 25.4 1.0 O A:GLU158 4.4 21.8 1.0 OE1 A:GLU158 4.4 24.7 1.0 O A:HOH452 4.5 32.8 1.0 O B:HOH501 4.5 37.0 1.0 OE1 B:GLU158 4.5 26.3 1.0 CB A:GLU158 4.7 21.5 1.0 CB B:GLU158 4.9 25.2 1.0

Cadmium binding site 2 out of 23 in the Saicar Synthetase (Type-1) in Complex with Adp and Amp in Both Chains


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 and Amp in Both Chains within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd302 b:54.1 occ:0.40 CD A:CD302 0.0 54.1 0.4 CD A:CD302 1.6 45.9 0.6 OE2 A:GLU89 2.3 50.0 1.0 OD2 A:ASP128 2.5 33.7 1.0 N6 A:AMP307 2.7 37.1 1.0 CG A:ASP128 3.2 30.9 1.0 OD1 A:ASP128 3.5 31.0 1.0 CD A:GLU89 3.6 47.7 1.0 C6 A:AMP307 3.9 40.2 1.0 NZ A:LYS122 4.1 42.8 1.0 CG A:GLU89 4.4 39.5 1.0 OE1 A:GLU89 4.4 50.5 1.0 CB A:ASP128 4.5 30.4 1.0 CD A:CD304 4.5 34.7 0.6 CG A:LYS122 4.7 41.0 1.0 N1 A:AMP307 4.8 39.8 1.0 CD A:CD306 4.8 51.2 0.5 C5 A:AMP307 4.8 41.6 1.0

Cadmium binding site 3 out of 23 in the Saicar Synthetase (Type-1) in Complex with Adp and Amp in Both Chains


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 and Amp in Both Chains within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd302 b:45.9 occ:0.60 CD A:CD302 0.0 45.9 0.6 CD A:CD302 1.6 54.1 0.4 OD2 A:ASP128 2.2 33.7 1.0 OD1 A:ASP128 2.8 31.0 1.0 CG A:ASP128 2.9 30.9 1.0 OE2 A:GLU89 3.7 50.0 1.0 N6 A:AMP307 4.1 37.1 1.0 CB A:ASP128 4.3 30.4 1.0 NZ A:LYS122 4.5 42.8 1.0 CG A:LYS122 4.6 41.0 1.0 CA A:ASP124 4.7 35.5 1.0 CD A:GLU89 4.8 47.7 1.0 N A:ASP124 4.8 34.6 1.0 N A:ASN123 4.8 33.6 1.0 CB A:ASP124 4.9 37.5 1.0

Cadmium binding site 4 out of 23 in the Saicar Synthetase (Type-1) in Complex with Adp and Amp in Both Chains


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 and Amp in Both Chains within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd303 b:46.6 occ:0.40 CD A:CD303 0.0 46.6 0.4 CD A:CD303 1.7 43.2 0.6 OD2 A:ASP35 2.6 50.5 1.0 ND1 A:HIS127 2.6 38.7 1.0 OD1 A:ASP35 3.2 45.1 1.0 CG A:HIS127 3.2 38.2 1.0 CG A:ASP35 3.2 49.6 1.0 CB A:HIS127 3.3 35.2 1.0 CE1 A:HIS127 3.6 40.2 1.0 CA A:HIS127 4.2 32.8 1.0 CD2 A:HIS127 4.4 41.3 1.0 NE2 A:HIS127 4.5 40.8 1.0 CB A:ASP35 4.7 50.9 1.0 O A:HIS127 4.9 30.0 1.0

Cadmium binding site 5 out of 23 in the Saicar Synthetase (Type-1) in Complex with Adp and Amp in Both Chains


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 and Amp in Both Chains within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd303 b:43.2 occ:0.60 CD A:CD303 0.0 43.2 0.6 CD A:CD303 1.7 46.6 0.4 ND1 A:HIS127 2.2 38.7 1.0 OD1 A:ASP35 2.4 45.1 1.0 OD2 A:ASP35 2.5 50.5 1.0 CG A:ASP35 2.7 49.6 1.0 CG A:HIS127 3.2 38.2 1.0 CE1 A:HIS127 3.2 40.2 1.0 CB A:HIS127 3.4 35.2 1.0 CA A:HIS127 3.8 32.8 1.0 O A:ASP124 4.0 43.0 1.0 CB A:ASP35 4.2 50.9 1.0 NE2 A:HIS127 4.4 40.8 1.0 CD2 A:HIS127 4.4 41.3 1.0 N A:HIS127 4.7 34.8 1.0 C A:HIS127 4.8 30.3 1.0

Cadmium binding site 6 out of 23 in the Saicar Synthetase (Type-1) in Complex with Adp and Amp in Both Chains


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 and Amp in Both Chains within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd304 b:34.7 occ:0.60 CD A:CD304 0.0 34.7 0.6 CD A:CD304 1.2 53.9 0.3 OE1 A:GLU89 2.2 50.5 1.0 N7 A:AMP307 2.4 41.5 1.0 CD A:GLU89 3.0 47.7 1.0 OE2 A:GLU89 3.1 50.0 1.0 C8 A:AMP307 3.3 41.8 1.0 C5 A:AMP307 3.5 41.6 1.0 O A:HOH449 3.8 32.3 1.0 N6 A:AMP307 3.9 37.1 1.0 OD2 A:ASP128 4.0 33.7 1.0 CB A:ASP128 4.1 30.4 1.0 C6 A:AMP307 4.2 40.2 1.0 CG A:GLU89 4.4 39.5 1.0 CG A:ASP128 4.4 30.9 1.0 N9 A:AMP307 4.5 42.1 1.0 CD A:CD302 4.5 54.1 0.4 C4 A:AMP307 4.7 42.5 1.0 CB A:GLU89 4.8 33.0 1.0 CG A:TYR120 4.8 24.3 1.0 CD1 A:TYR120 4.9 23.7 1.0 O A:ASP128 5.0 27.1 1.0

Cadmium binding site 7 out of 23 in the Saicar Synthetase (Type-1) in Complex with Adp and Amp in Both Chains


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 and Amp in Both Chains within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd304 b:53.9 occ:0.30 CD A:CD304 0.0 53.9 0.3 CD A:CD304 1.2 34.7 0.6 N7 A:AMP307 2.7 41.5 1.0 O A:HOH449 2.7 32.3 1.0 OE1 A:GLU89 2.8 50.5 1.0 C8 A:AMP307 3.0 41.8 1.0 CD A:GLU89 3.8 47.7 1.0 C5 A:AMP307 4.0 41.6 1.0 OE2 A:GLU89 4.1 50.0 1.0 O1P A:AMP307 4.2 35.0 1.0 N9 A:AMP307 4.4 42.1 1.0 CD1 A:TYR120 4.4 23.7 1.0 CG A:TYR120 4.4 24.3 1.0 CE1 A:TYR120 4.5 25.4 1.0 CD2 A:TYR120 4.6 24.9 1.0 CZ A:TYR120 4.6 23.0 1.0 CE2 A:TYR120 4.6 23.0 1.0 CB A:ASP128 4.8 30.4 1.0 CG2 A:VAL91 4.8 25.1 1.0 O5' A:AMP307 4.9 40.1 1.0 C4 A:AMP307 4.9 42.5 1.0 N6 A:AMP307 4.9 37.1 1.0 O3P A:AMP307 4.9 39.4 1.0 C6 A:AMP307 5.0 40.2 1.0 P A:AMP307 5.0 38.6 1.0

Cadmium binding site 8 out of 23 in the Saicar Synthetase (Type-1) in Complex with Adp and Amp in Both Chains


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 and Amp in Both Chains within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd305 b:37.7 occ:0.70 CD A:CD305 0.0 37.7 0.7 CD A:CD305 2.2 42.6 0.3 O2A A:ADP308 2.4 35.1 0.7 O1B A:ADP308 2.4 37.9 0.7 O A:HOH446 2.7 28.6 1.0 CD A:CD306 3.1 51.2 0.5 O3A A:ADP308 3.3 38.7 0.7 PA A:ADP308 3.4 36.1 0.7 PB A:ADP308 3.4 38.5 0.7 NZ A:LYS13 4.0 39.8 1.0 NZ A:LYS122 4.2 42.8 1.0 OE2 A:GLU177 4.2 26.7 1.0 O3B A:ADP308 4.3 38.2 0.7 O5' A:ADP308 4.3 36.1 0.7 OD1 A:ASP190 4.3 27.6 1.0 NZ A:LYS175 4.4 28.6 1.0 OD2 A:ASP190 4.4 28.3 1.0 O2B A:ADP308 4.6 39.0 0.7 C3' A:ADP308 4.6 28.8 0.7 C5' A:ADP308 4.6 30.4 0.7 O1A A:ADP308 4.6 36.5 0.7 CG A:ASP190 4.8 26.2 1.0 N1 A:AMP307 5.0 39.8 1.0

Cadmium binding site 9 out of 23 in the Saicar Synthetase (Type-1) in Complex with Adp and Amp in Both Chains


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 and Amp in Both Chains within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd305 b:42.6 occ:0.30 CD A:CD305 0.0 42.6 0.3 CD A:CD305 2.2 37.7 0.7 O2A A:ADP308 2.3 35.1 0.7 NZ A:LYS13 2.3 39.8 1.0 OD1 A:ASP190 2.4 27.6 1.0 OD2 A:ASP190 2.5 28.3 1.0 CG A:ASP190 2.8 26.2 1.0 CE A:LYS13 3.5 39.9 1.0 PA A:ADP308 3.7 36.1 0.7 OE2 A:GLU191 3.9 37.5 1.0 NZ A:LYS175 4.0 28.6 1.0 C5' A:ADP308 4.0 30.4 0.7 OE2 A:GLU177 4.1 26.7 1.0 O A:HOH446 4.2 28.6 1.0 CB A:ASP190 4.2 27.3 1.0 O5' A:ADP308 4.3 36.1 0.7 O1B A:ADP308 4.4 37.9 0.7 C3' A:ADP308 4.5 28.8 0.7 O3A A:ADP308 4.5 38.7 0.7 CD A:GLU177 4.7 25.0 1.0 CD A:CD306 4.7 51.2 0.5 C2' A:ADP308 4.7 27.9 0.7 CD A:LYS13 4.8 41.7 1.0 CG A:GLU191 4.8 34.3 1.0 CD A:GLU191 4.8 35.5 1.0 OE1 A:GLU177 4.8 23.5 1.0 O1A A:ADP308 4.8 36.5 0.7 C4' A:ADP308 4.9 29.0 0.7

Cadmium binding site 10 out of 23 in the Saicar Synthetase (Type-1) in Complex with Adp and Amp in Both Chains


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 and Amp in Both Chains within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd306 b:51.2 occ:0.50 N1 A:AMP307 2.4 39.8 1.0 O A:HOH446 2.4 28.6 1.0 CD A:CD305 3.1 37.7 0.7 C2 A:AMP307 3.3 39.5 1.0 C6 A:AMP307 3.3 40.2 1.0 N6 A:AMP307 3.4 37.1 1.0 O1B A:ADP308 4.4 37.9 0.7 N3 A:AMP307 4.6 42.6 1.0 CD A:CD305 4.7 42.6 0.3 C5 A:AMP307 4.7 41.6 1.0 NZ A:LYS175 4.7 28.6 1.0 CD A:CD302 4.8 54.1 0.4 O2A A:ADP308 5.0 35.1 0.7

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