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Cadmium in PDB 3u54: Crystal Structure (Type-1) of Saicar Synthetase From Pyrococcus Horikoshii OT3

Enzymatic activity of Crystal Structure (Type-1) of Saicar Synthetase From Pyrococcus Horikoshii OT3

All present enzymatic activity of Crystal Structure (Type-1) of Saicar Synthetase From Pyrococcus Horikoshii OT3:
6.3.2.6;

Protein crystallography data

The structure of Crystal Structure (Type-1) of Saicar Synthetase From Pyrococcus Horikoshii OT3, PDB code: 3u54 was solved by K.Manjunath, S.P.Kanaujia, S.Kanagaraj, J.Jeyakanthan, K.Sekar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.26 / 2.35
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 95.420, 95.420, 148.631, 90.00, 90.00, 120.00
R / Rfree (%) 23.5 / 28.6

Cadmium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Cadmium atom in the Crystal Structure (Type-1) of Saicar Synthetase From Pyrococcus Horikoshii OT3 (pdb code 3u54). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 15 binding sites of Cadmium where determined in the Crystal Structure (Type-1) of Saicar Synthetase From Pyrococcus Horikoshii OT3, PDB code: 3u54:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 15 in 3u54

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Cadmium binding site 1 out of 15 in the Crystal Structure (Type-1) of Saicar Synthetase From Pyrococcus Horikoshii OT3


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure (Type-1) of Saicar Synthetase From Pyrococcus Horikoshii OT3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd400

b:20.1
occ:1.00
 OD2 A:ASP162 2.3 13.5 1.0
OE2 B:GLU158 2.3 21.6 1.0
OE2 A:GLU158 2.3 21.6 1.0
OD2 B:ASP162 2.4 12.6 1.0
OD1 B:ASP162 2.5 7.3 1.0
OD1 A:ASP162 2.6 8.1 1.0
CG A:ASP162 2.7 19.5 1.0
CG B:ASP162 2.7 19.4 1.0
CD B:GLU158 3.2 24.8 1.0
CD A:GLU158 3.3 24.9 1.0
CG B:GLU158 3.5 21.3 1.0
CG A:GLU158 3.5 20.9 1.0
NZ B:LYS161 3.8 13.6 1.0
CE B:LYS161 3.8 25.7 1.0
CE A:LYS161 4.1 26.2 1.0
CB A:ASP162 4.2 23.2 1.0
NZ A:LYS161 4.2 13.5 1.0
CB B:ASP162 4.2 22.8 1.0
OE1 B:GLU158 4.4 15.6 1.0
OE1 A:GLU158 4.4 15.2 1.0
O A:GLU158 4.5 19.5 1.0
O B:GLU158 4.5 19.6 1.0
CB A:GLU158 4.9 15.4 1.0
CB B:GLU158 4.9 15.5 1.0

Cadmium binding site 2 out of 15 in 3u54

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Cadmium binding site 2 out of 15 in the Crystal Structure (Type-1) of Saicar Synthetase From Pyrococcus Horikoshii OT3


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure (Type-1) of Saicar Synthetase From Pyrococcus Horikoshii OT3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd401

b:41.7
occ:0.50
 CD A:CD401 0.0 41.7 0.5
CD A:CD401 1.8 51.8 0.5
NE2 A:HIS63 2.6 33.5 1.0
CD2 A:HIS63 3.1 31.6 1.0
O A:HOH328 3.6 24.1 1.0
CE1 A:HIS63 3.8 36.4 1.0
CG B:GLU111 4.1 34.7 1.0
O A:HOH327 4.4 20.0 1.0
CG A:HIS63 4.4 31.5 1.0
ND1 A:HIS63 4.7 31.7 1.0
O B:LEU112 4.8 21.8 1.0

Cadmium binding site 3 out of 15 in 3u54

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Cadmium binding site 3 out of 15 in the Crystal Structure (Type-1) of Saicar Synthetase From Pyrococcus Horikoshii OT3


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure (Type-1) of Saicar Synthetase From Pyrococcus Horikoshii OT3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd401

b:51.8
occ:0.50
 CD A:CD401 0.0 51.8 0.5
CD A:CD401 1.8 41.7 0.5
NE2 A:HIS63 2.9 33.5 1.0
O A:HOH301 3.5 27.4 1.0
O A:HOH327 3.6 20.0 1.0
CE1 A:HIS63 3.7 36.4 1.0
CD2 A:HIS63 3.9 31.6 1.0
CG B:GLU111 4.1 34.7 1.0
O A:HOH328 4.5 24.1 1.0
ND1 A:HIS63 4.9 31.7 1.0
O A:HOH384 4.9 21.8 1.0
CD1 A:LEU59 5.0 21.4 1.0

Cadmium binding site 4 out of 15 in 3u54

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Cadmium binding site 4 out of 15 in the Crystal Structure (Type-1) of Saicar Synthetase From Pyrococcus Horikoshii OT3


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure (Type-1) of Saicar Synthetase From Pyrococcus Horikoshii OT3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd402

b:39.6
occ:1.00
 OD2 A:ASP128 2.4 35.6 1.0
OE1 A:GLU89 2.5 42.4 1.0
OE2 A:GLU89 2.9 30.4 1.0
CD A:GLU89 3.0 30.6 1.0
CG A:ASP128 3.2 24.1 1.0
OD1 A:ASP128 3.3 23.0 1.0
O A:HOH373 4.1 31.9 1.0
OD1 A:ASP124 4.3 34.8 1.0
O A:HOH312 4.3 21.2 1.0
CG A:GLU89 4.4 24.6 1.0
CB A:ASP128 4.5 24.1 1.0
CG A:LYS122 4.5 23.6 1.0
CE A:LYS122 4.8 13.9 1.0

Cadmium binding site 5 out of 15 in 3u54

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Cadmium binding site 5 out of 15 in the Crystal Structure (Type-1) of Saicar Synthetase From Pyrococcus Horikoshii OT3


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure (Type-1) of Saicar Synthetase From Pyrococcus Horikoshii OT3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd403

b:54.8
occ:1.00
 ND1 A:HIS127 2.3 31.6 1.0
OD1 A:ASP35 2.5 29.9 1.0
OD2 A:ASP35 2.6 29.2 1.0
CG A:ASP35 2.8 28.4 1.0
CG A:HIS127 3.2 28.7 1.0
O A:HOH312 3.2 21.2 1.0
CE1 A:HIS127 3.3 33.3 1.0
CB A:HIS127 3.3 25.7 1.0
CA A:HIS127 3.7 26.2 1.0
O A:HOH340 3.8 34.7 1.0
O A:HOH374 3.9 28.0 1.0
O A:ASP124 4.0 28.0 1.0
CB A:ASP35 4.3 31.7 1.0
CD2 A:HIS127 4.3 34.1 1.0
O A:HOH375 4.4 30.9 1.0
NE2 A:HIS127 4.4 37.7 1.0
N A:HIS127 4.7 27.2 1.0
C A:HIS127 4.7 23.6 1.0

Cadmium binding site 6 out of 15 in 3u54

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Cadmium binding site 6 out of 15 in the Crystal Structure (Type-1) of Saicar Synthetase From Pyrococcus Horikoshii OT3


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Crystal Structure (Type-1) of Saicar Synthetase From Pyrococcus Horikoshii OT3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd404

b:73.8
occ:1.00
 OE2 A:GLU81 2.5 33.1 1.0
OD1 A:ASP181 3.0 25.8 1.0
CD A:GLU81 3.3 26.9 1.0
OE1 A:GLU81 3.4 31.8 1.0
CB A:ASP181 3.7 21.5 1.0
CG A:ASP181 3.8 24.4 1.0
O A:HOH371 4.4 23.8 1.0
CG2 A:VAL187 4.6 22.8 1.0
CG A:GLU81 4.7 24.2 1.0
OD2 A:ASP181 5.0 22.8 1.0

Cadmium binding site 7 out of 15 in 3u54

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Cadmium binding site 7 out of 15 in the Crystal Structure (Type-1) of Saicar Synthetase From Pyrococcus Horikoshii OT3


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Crystal Structure (Type-1) of Saicar Synthetase From Pyrococcus Horikoshii OT3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd405

b:67.3
occ:1.00
 O A:HOH321 3.5 34.1 1.0
O A:HOH349 4.0 28.7 1.0
OE2 A:GLU125 4.1 36.4 1.0
OD2 A:ASP124 4.3 40.2 1.0
CG A:GLU125 4.3 31.0 1.0
CB A:ASP124 4.4 27.1 1.0
N A:ASP124 4.5 27.0 1.0
CG A:ASP124 4.7 31.9 1.0
CD A:GLU125 4.8 34.3 1.0
N A:GLU125 4.9 27.5 1.0

Cadmium binding site 8 out of 15 in 3u54

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Cadmium binding site 8 out of 15 in the Crystal Structure (Type-1) of Saicar Synthetase From Pyrococcus Horikoshii OT3


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Crystal Structure (Type-1) of Saicar Synthetase From Pyrococcus Horikoshii OT3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd401

b:41.7
occ:0.50
 CD B:CD401 0.0 41.7 0.5
CD B:CD401 1.1 70.7 0.5
O5 A:BU1410 2.7 27.6 1.0
NE2 B:HIS63 2.7 33.1 1.0
OE2 A:GLU111 3.3 64.2 1.0
O B:HOH353 3.3 25.2 1.0
O B:HOH372 3.5 27.6 1.0
CD2 B:HIS63 3.6 31.1 1.0
CE1 B:HIS63 3.7 36.2 1.0
C1 A:BU1410 4.0 25.1 1.0
CD A:GLU111 4.3 62.5 1.0
C2 A:BU1410 4.4 22.6 1.0
OE1 A:GLU111 4.6 67.8 1.0
CG B:HIS63 4.8 31.4 1.0
ND1 B:HIS63 4.8 31.5 1.0

Cadmium binding site 9 out of 15 in 3u54

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Cadmium binding site 9 out of 15 in the Crystal Structure (Type-1) of Saicar Synthetase From Pyrococcus Horikoshii OT3


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Crystal Structure (Type-1) of Saicar Synthetase From Pyrococcus Horikoshii OT3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd401

b:70.7
occ:0.50
 CD B:CD401 0.0 70.7 0.5
CD B:CD401 1.1 41.7 0.5
OE2 A:GLU111 2.8 64.2 1.0
NE2 B:HIS63 3.1 33.1 1.0
O5 A:BU1410 3.2 27.6 1.0
O B:HOH353 3.5 25.2 1.0
CD A:GLU111 3.8 62.5 1.0
OE1 A:GLU111 3.9 67.8 1.0
CE1 B:HIS63 4.0 36.2 1.0
CD2 B:HIS63 4.1 31.1 1.0
O B:HOH372 4.3 27.6 1.0
C1 A:BU1410 4.5 25.1 1.0
C2 A:BU1410 4.6 22.6 1.0
O B:HOH316 4.9 36.2 1.0

Cadmium binding site 10 out of 15 in 3u54

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Cadmium binding site 10 out of 15 in the Crystal Structure (Type-1) of Saicar Synthetase From Pyrococcus Horikoshii OT3


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Crystal Structure (Type-1) of Saicar Synthetase From Pyrococcus Horikoshii OT3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd402

b:38.5
occ:1.00
 O B:HOH351 2.3 19.9 1.0
OE1 B:GLU89 2.6 42.4 1.0
OD2 B:ASP128 2.7 35.5 1.0
O B:HOH302 2.8 18.3 1.0
OE2 B:GLU89 2.9 30.3 1.0
CD B:GLU89 3.1 31.0 1.0
CG B:ASP128 3.4 23.9 1.0
OD1 B:ASP128 3.4 23.1 1.0
OD1 B:ASP124 4.5 35.4 1.0
CG B:GLU89 4.5 24.9 1.0
CG B:LYS122 4.6 23.3 1.0
CB B:ASP128 4.8 24.1 1.0
CE B:LYS122 4.8 14.1 1.0

Reference:

K.Manjunath, S.P.Kanaujia, S.Kanagaraj, J.Jeyakanthan, K.Sekar. Structure of Saicar Synthetase From Pyrococcus Horikoshii OT3: Insights Into Thermal Stability Int.J.Biol.Macromol. V. 53 7 2013.
ISSN: ISSN 0141-8130
PubMed: 23137517
DOI: 10.1016/J.IJBIOMAC.2012.10.028
Page generated: Fri Jul 19 16:33:50 2024

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