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Bromine in PDB 3klc: Crystal Structure of Hyperthermophilic Nitrilase

Enzymatic activity of Crystal Structure of Hyperthermophilic Nitrilase

All present enzymatic activity of Crystal Structure of Hyperthermophilic Nitrilase:
3.5.1.6;

Protein crystallography data

The structure of Crystal Structure of Hyperthermophilic Nitrilase, PDB code: 3klc was solved by J.Raczynska, C.Vorgias, G.Antranikian, W.Rypniewski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.69 / 1.76
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 59.283, 59.283, 129.196, 90.00, 90.00, 90.00
R / Rfree (%) 15.5 / 19.2

Other elements in 3klc:

The structure of Crystal Structure of Hyperthermophilic Nitrilase also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Bromine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Bromine atom in the Crystal Structure of Hyperthermophilic Nitrilase (pdb code 3klc). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 14 binding sites of Bromine where determined in the Crystal Structure of Hyperthermophilic Nitrilase, PDB code: 3klc:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Bromine binding site 1 out of 14 in 3klc

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Bromine binding site 1 out of 14 in the Crystal Structure of Hyperthermophilic Nitrilase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of Hyperthermophilic Nitrilase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br263

b:43.9
occ:0.50
 NH2 A:ARG132 3.4 41.0 1.0
N A:LYS110 3.5 21.4 1.0
O A:HOH316 3.5 33.5 1.0
CZ A:PHE107 3.6 27.0 1.0
CA A:GLY109 3.7 23.3 1.0
CE2 A:PHE107 3.7 27.1 1.0
CG A:LYS110 3.8 26.4 1.0
C A:GLY109 4.0 21.8 1.0
CE A:LYS110 4.2 28.5 1.0
CD A:LYS110 4.4 27.6 1.0
CZ A:ARG132 4.4 42.2 1.0
CB A:LYS110 4.5 22.6 1.0
CA A:LYS110 4.5 22.3 1.0
NH1 A:ARG132 4.6 41.1 1.0
O A:HOH314 4.6 36.1 1.0
O A:LYS110 4.7 22.5 1.0
N A:GLY109 4.8 24.3 1.0
CE1 A:PHE107 4.8 24.2 1.0
O A:ILE108 5.0 25.6 1.0

Bromine binding site 2 out of 14 in 3klc

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Bromine binding site 2 out of 14 in the Crystal Structure of Hyperthermophilic Nitrilase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of Hyperthermophilic Nitrilase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br264

b:47.3
occ:0.30
 BR A:BR264 0.0 47.3 0.3
BR A:BR264 1.4 48.0 0.3
N A:LYS18 3.4 33.5 1.0
C A:GLU15 3.6 28.9 1.0
CB A:ASP17 3.6 34.8 1.0
N A:ASP17 3.6 32.9 1.0
CG A:LYS18 3.7 36.9 1.0
CA A:GLU15 3.7 30.0 1.0
O A:GLU15 3.7 27.4 1.0
CB A:GLU15 3.8 30.6 1.0
CA A:ASP17 3.9 34.1 1.0
CB A:LYS18 4.0 33.5 1.0
N A:PRO16 4.0 29.0 1.0
C A:ASP17 4.1 33.8 1.0
OD1 A:ASP17 4.2 45.6 1.0
OE2 A:GLU15 4.2 44.9 1.0
CG A:ASP17 4.3 37.4 1.0
CA A:LYS18 4.3 32.3 1.0
CG A:GLU15 4.4 33.2 1.0
C A:PRO16 4.5 31.2 1.0
CD A:GLU15 4.6 39.8 1.0
CD A:LYS18 4.7 41.5 1.0
CD A:PRO16 4.8 28.8 1.0
CA A:PRO16 4.8 30.0 1.0
NZ A:LYS18 4.9 44.2 1.0

Bromine binding site 3 out of 14 in 3klc

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Bromine binding site 3 out of 14 in the Crystal Structure of Hyperthermophilic Nitrilase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Crystal Structure of Hyperthermophilic Nitrilase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br264

b:48.0
occ:0.30
 BR A:BR264 0.0 48.0 0.3
BR A:BR264 1.4 47.3 0.3
N A:ASP17 3.4 32.9 1.0
C A:GLU15 3.5 28.9 1.0
OD1 A:ASP17 3.5 45.6 1.0
N A:PRO16 3.5 29.0 1.0
CA A:GLU15 3.6 30.0 1.0
CB A:ASP17 3.7 34.8 1.0
CG A:ASP17 3.8 37.4 1.0
CD A:PRO16 3.9 28.8 1.0
CA A:ASP17 4.1 34.1 1.0
O A:GLU15 4.1 27.4 1.0
CB A:GLU15 4.2 30.6 1.0
N A:LYS18 4.2 33.5 1.0
C A:PRO16 4.3 31.2 1.0
CA A:PRO16 4.4 30.0 1.0
O A:LEU14 4.6 30.7 1.0
C A:ASP17 4.7 33.8 1.0
CG A:GLU15 4.7 33.2 1.0
OD2 A:ASP17 4.8 39.3 1.0
N A:GLU15 4.8 30.2 1.0
OE2 A:GLU15 4.9 44.9 1.0

Bromine binding site 4 out of 14 in 3klc

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Bromine binding site 4 out of 14 in the Crystal Structure of Hyperthermophilic Nitrilase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Crystal Structure of Hyperthermophilic Nitrilase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br265

b:44.8
occ:0.50
 N A:ARG105 3.3 30.4 1.0
CB A:ARG105 3.4 33.8 1.0
CA A:GLY103 3.6 27.8 1.0
C A:GLY103 3.7 27.9 1.0
CA A:ARG105 3.7 32.3 1.0
CD1 A:ILE108 3.8 30.6 1.0
CE1 A:TYR82 3.9 28.1 1.0
N A:PRO104 3.9 29.3 1.0
CG1 A:ILE108 3.9 26.2 1.0
CD A:PRO104 3.9 28.3 1.0
N A:GLY106 4.1 30.4 1.0
CG A:ARG105 4.1 37.2 1.0
N A:GLY103 4.1 27.3 1.0
O A:GLY103 4.2 28.4 1.0
C A:ARG105 4.2 32.0 1.0
NH2 A:ARG105 4.2 48.4 1.0
O A:GLY106 4.3 29.6 1.0
O A:HOH345 4.4 37.1 1.0
OH A:TYR82 4.4 33.9 1.0
C A:PRO104 4.4 30.4 1.0
CZ A:TYR82 4.5 29.5 1.0
CD1 A:TYR82 4.6 24.6 1.0
CA A:PRO104 4.7 29.8 1.0
C A:GLY106 4.9 29.4 1.0

Bromine binding site 5 out of 14 in 3klc

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Bromine binding site 5 out of 14 in the Crystal Structure of Hyperthermophilic Nitrilase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Crystal Structure of Hyperthermophilic Nitrilase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br266

b:52.9
occ:0.30
 CD A:LYS3 3.6 34.8 1.0
CA A:GLY34 3.7 31.3 1.0
O A:GLY34 3.9 29.1 1.0
NZ A:LYS3 3.9 38.4 1.0
CE A:LYS3 4.0 39.0 1.0
C A:GLY34 4.2 29.1 1.0
CG A:LYS3 4.4 32.0 1.0
O A:GLN33 4.6 35.3 1.0
N A:GLY34 4.8 32.5 1.0

Bromine binding site 6 out of 14 in 3klc

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Bromine binding site 6 out of 14 in the Crystal Structure of Hyperthermophilic Nitrilase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Crystal Structure of Hyperthermophilic Nitrilase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br267

b:47.0
occ:0.50
 N A:VAL133 3.1 24.3 1.0
O A:VAL133 3.5 24.9 1.0
CA A:ARG132 3.7 26.2 1.0
O A:HOH350 3.8 49.8 1.0
CD A:LYS161 3.8 29.6 1.0
C A:ARG132 3.9 24.2 1.0
NZ A:LYS161 4.0 37.0 1.0
CA A:VAL133 4.0 24.4 1.0
CB A:VAL133 4.1 24.8 1.0
CB A:ARG132 4.2 26.4 1.0
C A:VAL133 4.2 25.1 1.0
O A:PHE131 4.4 28.5 1.0
CE A:LYS161 4.6 34.5 1.0
CG A:ARG132 4.6 27.3 1.0
CG2 A:VAL133 4.8 24.4 1.0
CG A:LYS161 4.8 28.6 1.0
N A:ARG132 4.9 26.6 1.0
CB A:LYS161 4.9 26.9 1.0

Bromine binding site 7 out of 14 in 3klc

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Bromine binding site 7 out of 14 in the Crystal Structure of Hyperthermophilic Nitrilase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of Crystal Structure of Hyperthermophilic Nitrilase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br268

b:56.4
occ:0.50
 CG B:GLU153 3.5 22.2 1.0
CZ B:PHE261 3.5 44.2 1.0
CG A:GLU153 3.6 20.5 1.0
CE1 B:PHE261 3.7 43.1 1.0
N A:GLU153 3.8 20.5 1.0
CD B:GLU153 3.8 25.1 1.0
CG B:PRO152 3.9 24.1 1.0
CA A:GLU153 3.9 19.4 1.0
OE2 B:GLU153 4.0 27.6 1.0
C A:PRO152 4.0 20.3 1.0
CB A:PRO152 4.0 20.3 1.0
CB B:PRO152 4.1 22.6 1.0
N B:GLU153 4.2 22.4 1.0
CB A:ARG156 4.2 23.7 1.0
CD A:GLU153 4.2 17.8 1.0
O A:PRO152 4.3 21.9 1.0
CG A:ARG156 4.4 27.9 1.0
CB A:GLU153 4.4 19.1 1.0
OE1 B:GLU153 4.4 24.2 1.0
C B:PRO152 4.4 21.0 1.0
CA B:GLU153 4.4 22.0 1.0
CG A:PRO152 4.5 21.3 1.0
CB B:GLU153 4.6 23.1 1.0
OE2 A:GLU153 4.6 21.1 1.0
CA A:PRO152 4.7 20.9 1.0
OE1 A:GLU153 4.8 18.6 1.0
CE2 B:PHE261 4.8 45.0 1.0
CA B:PRO152 4.8 22.2 1.0
NE A:ARG156 4.9 28.3 1.0
O B:PRO152 4.9 21.9 1.0

Bromine binding site 8 out of 14 in 3klc

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Bromine binding site 8 out of 14 in the Crystal Structure of Hyperthermophilic Nitrilase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of Crystal Structure of Hyperthermophilic Nitrilase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br270

b:59.8
occ:0.40
 C A:ACY269 0.5 24.3 0.6
O A:ACY269 1.0 25.3 0.6
OXT A:ACY269 1.3 23.9 0.6
CH3 A:ACY269 1.9 24.9 0.6
O A:HOH306 2.9 30.1 1.0
O A:HOH322 3.1 14.7 0.4
CD2 A:LEU172 3.4 21.6 1.0
NE1 A:TRP149 3.5 20.8 1.0
N A:VAL173 3.7 28.7 1.0
N A:MET174 3.8 33.4 1.0
CA A:LEU172 3.8 25.4 1.0
CE A:MET174 3.8 41.3 1.0
CB A:MET174 3.9 34.6 1.0
CB A:LEU172 4.0 25.0 1.0
O A:MET174 4.2 32.1 1.0
CG A:MET174 4.2 37.6 1.0
C A:LEU172 4.3 27.0 1.0
CG A:LEU172 4.3 24.4 1.0
CA A:MET174 4.3 33.0 1.0
CE2 A:TRP149 4.4 19.3 1.0
CD1 A:TRP149 4.5 18.3 1.0
CZ2 A:TRP149 4.6 22.9 1.0
C A:MET174 4.6 32.5 1.0
CG2 A:VAL173 4.7 33.1 1.0
SG A:CSX146 4.8 30.8 1.0
CA A:VAL173 4.8 30.7 1.0
C A:VAL173 4.8 32.4 1.0
O A:HOH327 4.9 46.1 1.0
SD A:MET174 4.9 46.9 1.0
CB A:ALA177 4.9 24.7 1.0
OD A:CSX146 5.0 35.2 1.0

Bromine binding site 9 out of 14 in 3klc

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Bromine binding site 9 out of 14 in the Crystal Structure of Hyperthermophilic Nitrilase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 9 of Crystal Structure of Hyperthermophilic Nitrilase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br263

b:42.6
occ:0.80
 N B:ARG105 3.2 25.2 1.0
C B:GLY103 3.5 22.8 1.0
CA B:GLY103 3.5 22.9 1.0
O B:HOH310 3.5 40.7 1.0
CB B:ARG105 3.6 27.9 1.0
N B:PRO104 3.6 23.0 1.0
CA B:ARG105 3.8 26.2 1.0
CD B:PRO104 3.8 23.6 1.0
CE1 B:TYR82 3.8 25.6 1.0
O B:GLY103 3.9 20.5 1.0
N B:GLY106 3.9 26.5 1.0
N B:GLY103 4.1 23.2 1.0
CG B:ARG105 4.2 29.0 1.0
CD1 B:ILE108 4.2 27.1 1.0
C B:ARG105 4.2 27.8 1.0
C B:PRO104 4.3 25.5 1.0
O B:GLY106 4.3 25.7 1.0
CG1 B:ILE108 4.4 25.7 1.0
O B:HOH309 4.4 30.3 1.0
OH B:TYR82 4.5 29.6 1.0
CZ B:TYR82 4.5 26.0 1.0
CA B:PRO104 4.5 24.6 1.0
O B:HOH277 4.5 23.6 1.0
CD1 B:TYR82 4.6 22.9 1.0
C B:GLY106 5.0 25.9 1.0

Bromine binding site 10 out of 14 in 3klc

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Bromine binding site 10 out of 14 in the Crystal Structure of Hyperthermophilic Nitrilase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 10 of Crystal Structure of Hyperthermophilic Nitrilase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br264

b:47.2
occ:0.80
 NH1 B:ARG132 3.3 38.3 1.0
CG B:LYS110 3.7 26.8 1.0
N B:LYS110 3.8 26.4 1.0
CA B:GLY109 3.9 25.8 1.0
CE2 B:PHE107 3.9 23.6 1.0
CZ B:PHE107 3.9 24.6 1.0
O B:HOH384 4.0 38.1 1.0
CE B:LYS110 4.1 34.1 1.0
CD B:LYS110 4.2 31.1 1.0
C B:GLY109 4.2 24.8 1.0
CZ B:ARG132 4.3 39.7 1.0
NH2 B:ARG132 4.3 39.4 1.0
CB B:LYS110 4.4 26.3 1.0
CA B:LYS110 4.7 25.2 1.0
O B:LYS110 4.8 25.3 1.0
N B:GLY109 5.0 25.5 1.0

Reference:

J.E.Raczynska, C.E.Vorgias, G.Antranikian, W.Rypniewski. Crystallographic Analysis of A Thermoactive Nitrilase. J.Struct.Biol. V. 173 294 2010.
ISSN: ISSN 1047-8477
PubMed: 21095228
DOI: 10.1016/J.JSB.2010.11.017
Page generated: Wed Jul 10 19:50:59 2024

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