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Cadmium in PDB 4o81: Saicar Synthetase (Type-1) in Complex with Adp and Amp

Enzymatic activity of Saicar Synthetase (Type-1) in Complex with Adp and Amp

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

Protein crystallography data

The structure of Saicar Synthetase (Type-1) in Complex with Adp and Amp, PDB code: 4o81 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) 49.42 / 2.10
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 95.140, 95.140, 148.251, 90.00, 90.00, 120.00
R / Rfree (%) 21.3 / 25.5

Cadmium Binding Sites:

Pages:

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

Binding sites:

The binding sites of Cadmium atom in the Saicar Synthetase (Type-1) in Complex with Adp and Amp (pdb code 4o81). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 20 binding sites of Cadmium where determined in the Saicar Synthetase (Type-1) in Complex with Adp and Amp, PDB code: 4o81:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 20 in 4o81

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Cadmium binding site 1 out of 20 in the Saicar Synthetase (Type-1) in Complex with Adp and 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 and Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd301

b:24.0
occ:1.00
OD2 A:ASP162 2.2 21.3 1.0
OE2 A:GLU158 2.2 19.2 1.0
OE2 B:GLU158 2.3 25.5 1.0
OD1 B:ASP162 2.4 20.8 1.0
OD1 A:ASP162 2.5 19.4 1.0
OD2 B:ASP162 2.5 21.0 1.0
CG A:ASP162 2.7 20.2 1.0
CG B:ASP162 2.8 21.6 1.0
CD A:GLU158 3.1 19.9 1.0
CD B:GLU158 3.2 24.9 1.0
CG A:GLU158 3.3 20.9 1.0
CG B:GLU158 3.5 24.5 1.0
CE B:LYS161 4.0 24.0 1.0
NZ B:LYS161 4.0 23.9 1.0
CB A:ASP162 4.2 19.0 1.0
CE A:LYS161 4.2 25.1 1.0
CB B:ASP162 4.3 21.5 1.0
OE1 A:GLU158 4.3 21.0 1.0
NZ A:LYS161 4.4 26.3 1.0
OE1 B:GLU158 4.4 26.4 1.0
O A:HOH472 4.4 25.1 1.0
O A:GLU158 4.5 21.2 1.0
O B:HOH417 4.5 20.4 1.0
O B:GLU158 4.6 22.2 1.0
CB A:GLU158 4.7 20.8 1.0
CB B:GLU158 4.9 23.1 1.0

Cadmium binding site 2 out of 20 in 4o81

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Cadmium binding site 2 out of 20 in the Saicar Synthetase (Type-1) in Complex with Adp and 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 and Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd302

b:57.6
occ:1.00
NE2 A:HIS63 2.3 34.2 1.0
OE2 B:GLU111 2.3 53.7 1.0
CD B:GLU111 2.7 51.0 1.0
OE1 B:GLU111 2.7 55.3 1.0
CE1 A:HIS63 3.2 35.9 1.0
CD2 A:HIS63 3.4 32.8 1.0
O A:HOH436 3.6 37.2 1.0
CG B:GLU111 3.9 46.7 1.0
ND1 A:HIS63 4.4 35.8 1.0
CG A:HIS63 4.5 33.6 1.0
O B:HOH409 4.9 41.9 1.0

Cadmium binding site 3 out of 20 in 4o81

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Cadmium binding site 3 out of 20 in the Saicar Synthetase (Type-1) in Complex with Adp and 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 and Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd303

b:57.6
occ:0.95
OD2 A:ASP128 2.2 31.4 1.0
OE2 A:GLU89 2.7 46.2 1.0
CG A:ASP128 3.0 27.7 1.0
OD1 A:ASP128 3.1 26.5 1.0
N6 A:AMP309 3.2 30.9 0.8
CD A:GLU89 3.8 43.4 1.0
OD1 A:ASP124 4.1 46.3 1.0
CB A:ASP128 4.3 27.9 1.0
OE1 A:GLU89 4.3 48.8 1.0
C6 A:AMP309 4.5 35.0 0.8
CG A:LYS122 4.5 34.2 1.0
O A:HOH401 4.6 29.8 1.0
NZ A:LYS122 4.8 41.8 1.0
CE A:LYS122 4.8 36.2 1.0
CG A:GLU89 4.8 37.7 1.0

Cadmium binding site 4 out of 20 in 4o81

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Cadmium binding site 4 out of 20 in the Saicar Synthetase (Type-1) in Complex with Adp and 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 and Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd304

b:40.3
occ:0.50
CD A:CD304 0.0 40.3 0.5
CD A:CD304 1.3 40.5 0.5
ND1 A:HIS127 2.4 40.5 1.0
OD1 A:ASP35 2.5 47.8 1.0
O A:HOH401 2.6 29.8 1.0
OD2 A:ASP35 2.9 52.8 1.0
CG A:ASP35 3.0 51.0 1.0
CG A:HIS127 3.3 38.3 1.0
CE1 A:HIS127 3.4 41.9 1.0
CB A:HIS127 3.5 35.2 1.0
CA A:HIS127 3.7 32.3 1.0
O A:ASP124 3.7 40.3 1.0
CB A:ASP35 4.4 48.7 1.0
CD2 A:HIS127 4.4 40.4 1.0
NE2 A:HIS127 4.5 42.1 1.0
N A:HIS127 4.6 32.5 1.0
C A:HIS127 4.8 28.3 1.0
C A:ASP124 4.8 38.4 1.0

Cadmium binding site 5 out of 20 in 4o81

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Cadmium binding site 5 out of 20 in the Saicar Synthetase (Type-1) in Complex with Adp and 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 and Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd304

b:40.5
occ:0.50
CD A:CD304 0.0 40.5 0.5
CD A:CD304 1.3 40.3 0.5
ND1 A:HIS127 2.3 40.5 1.0
OD2 A:ASP35 2.6 52.8 1.0
OD1 A:ASP35 2.7 47.8 1.0
O A:HOH401 3.0 29.8 1.0
CG A:ASP35 3.0 51.0 1.0
CG A:HIS127 3.1 38.3 1.0
CB A:HIS127 3.2 35.2 1.0
CE1 A:HIS127 3.3 41.9 1.0
CA A:HIS127 3.9 32.3 1.0
CD2 A:HIS127 4.3 40.4 1.0
NE2 A:HIS127 4.4 42.1 1.0
CB A:ASP35 4.5 48.7 1.0
O A:ASP124 4.8 40.3 1.0
C A:HIS127 4.9 28.3 1.0
N A:HIS127 5.0 32.5 1.0

Cadmium binding site 6 out of 20 in 4o81

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Cadmium binding site 6 out of 20 in the Saicar Synthetase (Type-1) in Complex with Adp and 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 and Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd305

b:75.8
occ:0.50
N A:ASP124 4.3 36.9 1.0
OD2 A:ASP124 4.4 49.6 1.0
CB A:ASP124 4.5 42.5 1.0
CG A:ASP124 4.8 46.2 1.0
N A:GLU125 5.0 38.2 1.0
CA A:ASP124 5.0 39.4 1.0

Cadmium binding site 7 out of 20 in 4o81

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Cadmium binding site 7 out of 20 in the Saicar Synthetase (Type-1) in Complex with Adp and 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 and Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd306

b:39.5
occ:0.70
OE1 A:GLU89 2.3 48.8 1.0
N7 A:AMP309 2.4 34.1 0.8
O A:HOH463 2.5 33.1 1.0
C8 A:AMP309 3.2 34.4 0.8
CD A:GLU89 3.4 43.4 1.0
C5 A:AMP309 3.5 35.0 0.8
OE2 A:GLU89 3.8 46.2 1.0
N6 A:AMP309 4.0 30.9 0.8
OD2 A:ASP128 4.0 31.4 1.0
CB A:ASP128 4.1 27.9 1.0
C6 A:AMP309 4.3 35.0 0.8
CG A:ASP128 4.5 27.7 1.0
N9 A:AMP309 4.5 35.8 0.8
CG A:GLU89 4.7 37.7 1.0
C4 A:AMP309 4.7 34.9 0.8
CG A:TYR120 4.7 19.4 1.0
CB A:GLU89 4.8 31.3 1.0
CD1 A:TYR120 4.9 19.1 1.0
O A:ASP128 4.9 24.4 1.0
CB A:TYR120 5.0 19.2 1.0

Cadmium binding site 8 out of 20 in 4o81

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Cadmium binding site 8 out of 20 in the Saicar Synthetase (Type-1) in Complex with Adp and 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 and Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd307

b:38.6
occ:0.60
CD A:CD307 0.0 38.6 0.6
CD A:CD307 2.1 38.8 0.4
O3P A:AMP308 2.3 56.3 0.8
O A:HOH468 2.6 24.2 1.0
O A:HOH438 2.8 27.1 1.0
CD A:CD311 3.0 42.7 0.5
P A:AMP308 3.4 51.4 0.8
O5' A:AMP308 3.4 45.9 0.8
NZ A:LYS13 4.0 41.1 1.0
O1P A:AMP308 4.0 50.9 0.8
OD2 A:ASP190 4.3 26.8 1.0
OE2 A:GLU177 4.4 24.9 1.0
NZ A:LYS122 4.4 41.8 1.0
OD1 A:ASP190 4.4 26.8 1.0
NZ A:LYS175 4.5 27.4 1.0
O2P A:AMP308 4.6 53.1 0.8
C3' A:AMP308 4.7 31.2 0.8
CG A:ASP190 4.8 25.1 1.0
C5' A:AMP308 4.8 35.5 0.8
CE A:LYS122 4.9 36.2 1.0
N1 A:AMP309 4.9 35.8 0.8

Cadmium binding site 9 out of 20 in 4o81

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Cadmium binding site 9 out of 20 in the Saicar Synthetase (Type-1) in Complex with Adp and 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 and Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd307

b:38.8
occ:0.40
CD A:CD307 0.0 38.8 0.4
CD A:CD307 2.1 38.6 0.6
NZ A:LYS13 2.3 41.1 1.0
OD2 A:ASP190 2.4 26.8 1.0
O A:HOH468 2.5 24.2 1.0
OD1 A:ASP190 2.7 26.8 1.0
CG A:ASP190 2.9 25.1 1.0
O5' A:AMP308 3.0 45.9 0.8
O3P A:AMP308 3.4 56.3 0.8
CE A:LYS13 3.4 42.0 1.0
P A:AMP308 3.7 51.4 0.8
O1P A:AMP308 4.0 50.9 0.8
OE2 A:GLU191 4.0 30.4 1.0
C5' A:AMP308 4.1 35.5 0.8
NZ A:LYS175 4.1 27.4 1.0
O A:HOH438 4.2 27.1 1.0
OE2 A:GLU177 4.3 24.9 1.0
C3' A:AMP308 4.3 31.2 0.8
CB A:ASP190 4.4 23.2 1.0
CD A:CD311 4.5 42.7 0.5
C2' A:AMP308 4.6 29.6 0.8
CD A:LYS13 4.7 42.5 1.0
C4' A:AMP308 4.8 32.4 0.8
CD A:GLU177 4.9 25.4 1.0
CG A:GLU191 4.9 27.1 1.0
CD A:GLU191 4.9 29.0 1.0
OE1 A:GLU177 5.0 25.9 1.0

Cadmium binding site 10 out of 20 in 4o81

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Cadmium binding site 10 out of 20 in the Saicar Synthetase (Type-1) in Complex with Adp and 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 and Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd311

b:42.7
occ:0.45
N1 A:AMP309 2.4 35.8 0.8
O A:HOH438 2.5 27.1 1.0
O A:HOH468 2.9 24.2 1.0
CD A:CD307 3.0 38.6 0.6
C2 A:AMP309 3.2 36.0 0.8
C6 A:AMP309 3.4 35.0 0.8
N6 A:AMP309 3.5 30.9 0.8
O3P A:AMP308 4.5 56.3 0.8
CD A:CD307 4.5 38.8 0.4
N3 A:AMP309 4.6 35.8 0.8
C5 A:AMP309 4.7 35.0 0.8
NZ A:LYS175 4.8 27.4 1.0
CE A:LYS175 4.9 26.0 1.0

Reference:

K.Manjunath, J.Jeyakanthan, K.Sekar. Saicar Synthetase (Type-1) in Complex with Adp and Amp To Be Published.
Page generated: Sat Dec 12 08:25:23 2020

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