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Cadmium in PDB 4o84: Saicar Synthetase (Type-1) in Complex with Gmp

Enzymatic activity of Saicar Synthetase (Type-1) in Complex with Gmp

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

Protein crystallography data

The structure of Saicar Synthetase (Type-1) in Complex with Gmp, PDB code: 4o84 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) 54.98 / 2.09
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 94.810, 94.810, 148.051, 90.00, 90.00, 120.00
R / Rfree (%) 21.9 / 26.9

Cadmium Binding Sites:

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 Gmp (pdb code 4o84). 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 Gmp, PDB code: 4o84:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 18 in 4o84

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


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 Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd301

b:19.7
occ:1.00
OE2 B:GLU158 2.2 16.0 1.0
OE2 A:GLU158 2.2 15.1 1.0
OD2 A:ASP162 2.2 14.2 1.0
OD1 B:ASP162 2.5 15.4 1.0
OD2 B:ASP162 2.5 15.1 1.0
OD1 A:ASP162 2.5 12.9 1.0
CG A:ASP162 2.7 14.0 1.0
CG B:ASP162 2.8 15.7 1.0
CD A:GLU158 3.2 16.1 1.0
CD B:GLU158 3.2 17.1 1.0
CG A:GLU158 3.4 16.2 1.0
CG B:GLU158 3.5 17.7 1.0
CE B:LYS161 4.0 20.2 1.0
NZ B:LYS161 4.0 20.0 1.0
CB A:ASP162 4.1 14.5 1.0
CE A:LYS161 4.2 20.2 1.0
NZ A:LYS161 4.2 21.8 1.0
CB B:ASP162 4.3 16.4 1.0
OE1 B:GLU158 4.3 16.4 1.0
OE1 A:GLU158 4.3 17.0 1.0
O A:HOH434 4.4 18.9 1.0
O A:GLU158 4.5 16.0 1.0
O B:GLU158 4.6 17.5 1.0
O B:HOH519 4.6 17.4 1.0
CB A:GLU158 4.8 16.3 1.0
CB B:GLU158 4.9 17.2 1.0

Cadmium binding site 2 out of 18 in 4o84

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


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 Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd302

b:45.5
occ:1.00
NE2 A:HIS63 2.2 29.0 1.0
OE2 B:GLU111 2.5 45.6 1.0
OE1 B:GLU111 2.7 53.2 1.0
CD B:GLU111 2.8 46.3 1.0
CD2 A:HIS63 3.2 27.3 1.0
CE1 A:HIS63 3.2 28.4 1.0
CG B:GLU111 4.0 40.7 1.0
ND1 A:HIS63 4.3 29.1 1.0
CG A:HIS63 4.3 28.4 1.0
CG2 A:ILE159 4.9 18.1 1.0

Cadmium binding site 3 out of 18 in 4o84

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


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 Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd303

b:41.7
occ:0.50
CD A:CD303 0.0 41.7 0.5
CD A:CD303 1.3 42.4 0.5
OD2 A:ASP128 2.3 29.3 1.0
OD1 A:ASP128 3.0 26.2 1.0
CG A:ASP128 3.0 26.8 1.0
OE2 A:GLU89 3.3 34.9 1.0
OD1 A:ASP124 3.5 34.0 1.0
O6 A:5GP308 3.8 35.8 1.0
CD A:GLU89 4.2 31.8 1.0
CB A:ASP128 4.5 25.4 1.0
CG A:LYS122 4.5 31.6 1.0
OE1 A:GLU89 4.6 35.5 1.0
CE A:LYS122 4.6 31.6 1.0
CG A:ASP124 4.7 35.7 1.0
CD A:CD307 4.7 67.8 0.3

Cadmium binding site 4 out of 18 in 4o84

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


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 Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd303

b:42.4
occ:0.50
CD A:CD303 0.0 42.4 0.5
CD A:CD303 1.3 41.7 0.5
OD2 A:ASP128 2.2 29.3 1.0
OE2 A:GLU89 2.3 34.9 1.0
O6 A:5GP308 2.8 35.8 1.0
CG A:ASP128 3.2 26.8 1.0
CD A:GLU89 3.2 31.8 1.0
OD1 A:ASP128 3.5 26.2 1.0
OE1 A:GLU89 3.6 35.5 1.0
CD A:CD307 3.8 67.8 0.3
C6 A:5GP308 3.9 36.5 1.0
CB A:ASP128 4.5 25.4 1.0
CG A:GLU89 4.5 28.5 1.0
CE A:LYS122 4.5 31.6 1.0
CD A:CD307 4.5 37.9 0.6
CG A:LYS122 4.6 31.6 1.0
N1 A:5GP308 4.7 36.2 1.0
C5 A:5GP308 4.8 35.9 1.0
OD1 A:ASP124 4.8 34.0 1.0

Cadmium binding site 5 out of 18 in 4o84

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


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 Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd304

b:37.1
occ:0.65
CD A:CD304 0.0 37.1 0.7
CD A:CD304 1.7 46.8 0.3
ND1 A:HIS127 2.2 31.4 1.0
OD1 A:ASP35 2.5 44.7 1.0
OD2 A:ASP35 2.6 50.5 1.0
CG A:ASP35 2.9 47.7 1.0
CG A:HIS127 3.1 31.8 1.0
CE1 A:HIS127 3.3 32.5 1.0
CB A:HIS127 3.3 29.2 1.0
CA A:HIS127 3.7 28.2 1.0
O A:ASP124 4.1 34.0 1.0
CD2 A:HIS127 4.3 33.4 1.0
CB A:ASP35 4.3 46.6 1.0
NE2 A:HIS127 4.4 32.1 1.0
N A:HIS127 4.6 28.4 1.0
C A:HIS127 4.7 26.2 1.0

Cadmium binding site 6 out of 18 in 4o84

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


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 Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd304

b:46.8
occ:0.35
CD A:CD304 0.0 46.8 0.3
CD A:CD304 1.7 37.1 0.7
ND1 A:HIS127 2.6 31.4 1.0
OD2 A:ASP35 2.8 50.5 1.0
OD1 A:ASP35 3.1 44.7 1.0
CG A:HIS127 3.2 31.8 1.0
CG A:ASP35 3.3 47.7 1.0
CB A:HIS127 3.4 29.2 1.0
CE1 A:HIS127 3.6 32.5 1.0
CA A:HIS127 4.3 28.2 1.0
CD2 A:HIS127 4.4 33.4 1.0
NE2 A:HIS127 4.5 32.1 1.0
CB A:ASP35 4.8 46.6 1.0
O A:HIS127 5.0 25.5 1.0

Cadmium binding site 7 out of 18 in 4o84

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


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 Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd305

b:67.3
occ:0.60
OD2 A:ASP124 4.2 38.8 1.0
N A:ASP124 4.5 32.8 1.0
CB A:ASP124 4.7 35.5 1.0
CG A:ASP124 4.8 35.7 1.0

Cadmium binding site 8 out of 18 in 4o84

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


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 Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd306

b:49.1
occ:0.50
OE2 A:GLU226 2.6 45.5 1.0
OE1 A:GLU226 2.8 42.7 1.0
CD A:GLU226 3.0 42.7 1.0
CD A:GLU229 4.3 44.0 1.0
OE1 A:GLU229 4.4 47.2 1.0
OE2 A:GLU229 4.4 46.8 1.0
CG A:GLU226 4.5 37.4 1.0
CG A:ARG230 4.6 32.3 1.0
NE A:ARG230 4.6 33.0 1.0
O A:HOH453 4.8 50.4 1.0
CG A:GLU229 4.8 41.6 1.0

Cadmium binding site 9 out of 18 in 4o84

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


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 Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd307

b:37.9
occ:0.60
CD A:CD307 0.0 37.9 0.6
CD A:CD307 1.1 67.8 0.3
N7 A:5GP308 2.3 34.6 1.0
OE1 A:GLU89 2.3 35.5 1.0
C8 A:5GP308 3.2 34.4 1.0
C5 A:5GP308 3.4 35.9 1.0
CD A:GLU89 3.5 31.8 1.0
OD2 A:ASP128 3.7 29.3 1.0
O6 A:5GP308 3.8 35.8 1.0
CB A:ASP128 4.0 25.4 1.0
OE2 A:GLU89 4.1 34.9 1.0
C6 A:5GP308 4.1 36.5 1.0
CG A:ASP128 4.3 26.8 1.0
N9 A:5GP308 4.4 35.3 1.0
CD A:CD303 4.5 42.4 0.5
C4 A:5GP308 4.6 35.8 1.0
CG A:GLU89 4.7 28.5 1.0
CB A:GLU89 4.8 24.8 1.0
CG A:TYR120 4.8 18.8 1.0
CD1 A:TYR120 4.9 19.4 1.0
O A:ASP128 4.9 20.5 1.0

Cadmium binding site 10 out of 18 in 4o84

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


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 Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd307

b:67.8
occ:0.30
CD A:CD307 0.0 67.8 0.3
CD A:CD307 1.1 37.9 0.6
N7 A:5GP308 2.5 34.6 1.0
OE1 A:GLU89 2.7 35.5 1.0
OD2 A:ASP128 3.0 29.3 1.0
O6 A:5GP308 3.1 35.8 1.0
C5 A:5GP308 3.3 35.9 1.0
C8 A:5GP308 3.7 34.4 1.0
CD A:GLU89 3.7 31.8 1.0
C6 A:5GP308 3.7 36.5 1.0
CB A:ASP128 3.7 25.4 1.0
CG A:ASP128 3.7 26.8 1.0
CD A:CD303 3.8 42.4 0.5
OE2 A:GLU89 3.9 34.9 1.0
C4 A:5GP308 4.6 35.8 1.0
CD A:CD303 4.7 41.7 0.5
N9 A:5GP308 4.7 35.3 1.0
OD1 A:ASP128 4.9 26.2 1.0

Reference:

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

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