Atomistry » Cadmium » PDB 4l8q-4qdp » 4o81
Atomistry »
  Cadmium »
    PDB 4l8q-4qdp »
      4o81 »

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

Go back to Cadmium Binding Sites List in 4o81
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

Go back to Cadmium Binding Sites List in 4o81
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

Go back to Cadmium Binding Sites List in 4o81
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

Go back to Cadmium Binding Sites List in 4o81
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

Go back to Cadmium Binding Sites List in 4o81
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

Go back to Cadmium Binding Sites List in 4o81
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

Go back to Cadmium Binding Sites List in 4o81
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

Go back to Cadmium Binding Sites List in 4o81
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

Go back to Cadmium Binding Sites List in 4o81
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

Go back to Cadmium Binding Sites List in 4o81
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: Fri Jul 19 17:44:36 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy