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Bromine in PDB 2d6b: Novel Bromate Species Trapped Within A Protein Crystal

Enzymatic activity of Novel Bromate Species Trapped Within A Protein Crystal

All present enzymatic activity of Novel Bromate Species Trapped Within A Protein Crystal:
3.2.1.17;

Protein crystallography data

The structure of Novel Bromate Species Trapped Within A Protein Crystal, PDB code: 2d6b was solved by J.Ondracek, J.R.Mesters, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 1.25
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.210, 77.210, 38.191, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 21.3

Other elements in 2d6b:

The structure of Novel Bromate Species Trapped Within A Protein Crystal also contains other interesting chemical elements:

Chlorine (Cl) 20 atoms
Sodium (Na) 10 atoms

Bromine Binding Sites:

The binding sites of Bromine atom in the Novel Bromate Species Trapped Within A Protein Crystal (pdb code 2d6b). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 9 binding sites of Bromine where determined in the Novel Bromate Species Trapped Within A Protein Crystal, PDB code: 2d6b:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Bromine binding site 1 out of 9 in 2d6b

Go back to Bromine Binding Sites List in 2d6b
Bromine binding site 1 out of 9 in the Novel Bromate Species Trapped Within A Protein Crystal


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Novel Bromate Species Trapped Within A Protein Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br131

b:14.7
occ:0.57
 BR A:202131 0.0 14.7 0.6
O1 A:202131 1.5 25.2 1.0
O3 A:202131 1.6 19.1 0.6
O2 A:202131 1.6 14.0 0.6
O A:GLY67 3.2 16.5 1.0
O A:HOH1031 3.3 28.6 1.0
O2 A:202132 3.4 16.1 0.7
BR A:202132 3.7 13.3 0.7
C A:GLY67 3.9 14.6 1.0
O A:HOH1155 3.9 21.4 0.5
O A:HOH1026 3.9 19.4 1.0
O A:HOH1162 4.0 22.2 0.5
CG A:PRO70 4.2 18.1 1.0
CA A:PRO70 4.2 15.3 1.0
CA A:ARG68 4.3 13.8 1.0
N A:ARG68 4.3 13.5 1.0
O1 A:202132 4.3 14.5 1.0
N A:PRO70 4.4 19.1 1.0
CB A:PRO70 4.5 20.7 1.0
N A:THR69 4.5 13.4 1.0
CD A:PRO70 4.5 17.8 1.0
C A:ARG68 4.6 15.8 1.0
CA A:GLY67 4.8 14.2 1.0
C A:THR69 4.8 14.8 1.0

Bromine binding site 2 out of 9 in 2d6b

Go back to Bromine Binding Sites List in 2d6b
Bromine binding site 2 out of 9 in the Novel Bromate Species Trapped Within A Protein Crystal


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Novel Bromate Species Trapped Within A Protein Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br132

b:13.3
occ:0.66
 BR A:202132 0.0 13.3 0.7
O2 A:202132 1.6 16.1 0.7
O3 A:202132 1.6 14.5 0.7
O1 A:202132 1.7 14.5 1.0
O A:THR69 3.0 13.8 1.0
O2 A:202131 3.0 14.0 0.6
O A:HOH1026 3.1 19.4 1.0
C A:THR69 3.5 14.8 1.0
BR A:202131 3.7 14.7 0.6
N A:THR69 3.8 13.4 1.0
OG A:SER72 3.9 16.0 1.0
O3 A:202131 3.9 19.1 0.6
O A:HOH1046 3.9 26.8 1.0
O A:HOH1033 4.0 19.3 1.0
O A:HOH1012 4.1 13.2 1.0
N A:PRO70 4.1 19.1 1.0
CA A:PRO70 4.1 15.3 1.0
C A:GLY67 4.2 14.6 1.0
CA A:THR69 4.3 14.3 1.0
OD1 A:ASN65 4.3 16.2 1.0
CA A:GLY67 4.3 14.2 1.0
N A:ARG68 4.4 13.5 1.0
O A:HOH1010 4.4 17.8 1.0
O A:HOH1230 4.4 29.4 0.5
O A:HOH1245 4.5 25.7 0.5
N A:GLY71 4.6 15.3 1.0
N A:GLY67 4.6 13.0 1.0
O A:GLY67 4.6 16.5 1.0
N A:SER72 4.7 15.5 1.0
C A:PRO70 4.7 17.6 1.0
CB A:THR69 4.8 12.3 1.0
C A:ARG68 4.9 15.8 1.0
CB A:SER72 4.9 15.8 1.0

Bromine binding site 3 out of 9 in 2d6b

Go back to Bromine Binding Sites List in 2d6b
Bromine binding site 3 out of 9 in the Novel Bromate Species Trapped Within A Protein Crystal


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Novel Bromate Species Trapped Within A Protein Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br133

b:24.6
occ:0.35
 BR A:202133 0.0 24.6 0.3
O2 A:202133 1.4 29.1 1.0
O1 A:202133 1.8 30.4 1.0
O3 A:202133 2.0 23.0 0.3
O A:HOH1039 3.3 20.9 1.0
NE2 A:GLN41 3.8 14.0 1.0
N A:LYS1 4.2 15.3 1.0
O A:HOH1005 4.4 13.9 1.0
O A:HOH1182 4.4 22.4 0.5
CA A:LYS1 4.6 15.7 1.0
CD A:GLN41 4.8 11.2 1.0
O A:HOH1206 4.8 31.9 0.5

Bromine binding site 4 out of 9 in 2d6b

Go back to Bromine Binding Sites List in 2d6b
Bromine binding site 4 out of 9 in the Novel Bromate Species Trapped Within A Protein Crystal


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Novel Bromate Species Trapped Within A Protein Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br134

b:19.3
occ:0.21
 BR A:202134 0.0 19.3 0.2
O1 A:202134 1.6 22.6 1.0
O2 A:202134 1.6 19.7 1.0
O A:HOH1168 2.8 23.4 0.5
O A:HOH1104 3.5 33.1 1.0
N A:CYS6 3.6 15.4 1.0
CB A:CYS6 3.8 14.8 1.0
O A:HOH1241 4.0 25.1 0.5
O A:HOH1047 4.0 28.8 1.0
N A:ARG5 4.0 15.8 1.0
O A:HOH1224 4.1 26.2 0.5
CA A:GLY4 4.2 17.9 1.0
N A:GLU7 4.2 15.5 1.0
CA A:CYS6 4.2 14.7 1.0
C A:GLY4 4.2 13.7 1.0
SG A:CYS6 4.5 19.7 1.0
O A:HOH1293 4.5 41.3 0.5
C A:ARG5 4.6 13.4 1.0
CA A:ARG5 4.7 14.6 1.0
C A:CYS6 4.7 14.9 1.0
O A:GLY4 4.9 14.4 1.0
CB A:ARG5 4.9 16.5 1.0

Bromine binding site 5 out of 9 in 2d6b

Go back to Bromine Binding Sites List in 2d6b
Bromine binding site 5 out of 9 in the Novel Bromate Species Trapped Within A Protein Crystal


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Novel Bromate Species Trapped Within A Protein Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br135

b:36.1
occ:0.32
 BR A:202135 0.0 36.1 0.3
O1 A:202135 1.7 20.4 1.0
N A:ILE88 3.4 14.3 1.0
O A:HOH1249 3.6 25.3 0.5
O A:HOH1070 3.6 32.4 1.0
NH2 A:ARG14 3.7 24.4 1.0
OD1 A:ASP87 3.8 19.1 1.0
CA A:ASP87 3.8 15.8 1.0
CG1 A:ILE88 3.9 15.9 1.0
NE2 A:HIS15 4.1 18.3 1.0
C A:ASP87 4.1 16.6 1.0
O A:HOH1174 4.2 26.4 0.5
O A:SER86 4.2 20.7 1.0
CG A:ASP87 4.4 24.2 1.0
O A:HOH1135 4.4 24.7 0.5
CB A:ASP87 4.5 20.4 1.0
CA A:ILE88 4.5 14.9 1.0
CB A:ALA11 4.5 14.5 1.0
O A:HOH1097 4.5 37.2 1.0
CB A:ILE88 4.6 15.8 1.0
CZ A:PHE3 4.6 15.9 1.0
CZ A:ARG14 4.6 20.4 1.0
CG2 A:ILE88 4.7 17.8 1.0
CD2 A:HIS15 4.8 17.9 1.0
CD1 A:ILE88 4.8 16.6 1.0
NH1 A:ARG14 4.9 24.8 1.0
N A:ASP87 4.9 16.6 1.0
N A:THR89 4.9 14.3 1.0

Bromine binding site 6 out of 9 in 2d6b

Go back to Bromine Binding Sites List in 2d6b
Bromine binding site 6 out of 9 in the Novel Bromate Species Trapped Within A Protein Crystal


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Novel Bromate Species Trapped Within A Protein Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br136

b:29.0
occ:0.21
 BR A:202136 0.0 29.0 0.2
O1 A:202136 1.6 20.7 0.2
O2 A:202136 1.9 16.1 0.2
O A:HOH1267 3.3 22.4 0.5
NH2 A:ARG68 4.1 19.3 1.0
NH2 A:ARG45 4.2 20.9 1.0
NH1 A:ARG68 4.5 22.4 1.0
CZ A:ARG68 4.8 17.8 1.0
O A:HOH1281 4.8 31.4 0.5
CD A:ARG45 5.0 17.6 1.0

Bromine binding site 7 out of 9 in 2d6b

Go back to Bromine Binding Sites List in 2d6b
Bromine binding site 7 out of 9 in the Novel Bromate Species Trapped Within A Protein Crystal


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of Novel Bromate Species Trapped Within A Protein Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br137

b:18.7
occ:0.22
 BR A:202137 0.0 18.7 0.2
O1 A:202137 1.3 13.2 0.2
O A:HOH1273 2.0 24.4 0.5
O A:HOH1290 2.2 26.2 0.5
O A:HOH1020 2.8 21.9 1.0
O A:LYS33 3.1 11.9 1.0
CB A:ASN37 3.6 17.9 1.0
CG A:ASN37 3.6 15.0 1.0
ND2 A:ASN37 3.7 19.2 1.0
O A:HOH1073 3.9 39.8 1.0
CA A:ASN37 4.0 13.2 1.0
C A:LYS33 4.1 10.0 1.0
N A:ASN37 4.2 11.6 1.0
CE A:LYS33 4.2 20.1 1.0
OD1 A:ASN37 4.2 26.4 1.0
CA A:PHE34 4.3 10.8 1.0
CD1 A:PHE34 4.4 11.5 1.0
CD A:LYS33 4.5 16.5 1.0
NZ A:LYS33 4.5 23.4 1.0
O A:HOH1250 4.5 23.0 0.5
O A:HOH1220 4.6 28.4 0.5
O A:PHE34 4.6 14.3 1.0
CG A:LYS33 4.7 16.6 1.0
N A:PHE34 4.7 10.6 1.0
C A:PHE34 4.8 12.3 1.0
CE1 A:PHE34 4.9 12.6 1.0

Bromine binding site 8 out of 9 in 2d6b

Go back to Bromine Binding Sites List in 2d6b
Bromine binding site 8 out of 9 in the Novel Bromate Species Trapped Within A Protein Crystal


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of Novel Bromate Species Trapped Within A Protein Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br138

b:24.3
occ:0.23
 BR A:202138 0.0 24.3 0.2
O1 A:202138 1.6 16.8 1.0
O A:HOH1127 1.9 22.5 0.5
O A:HOH1090 3.0 38.8 1.0
O A:HOH1144 3.4 23.0 0.5
O A:ALA107 3.6 18.4 1.0
O A:HOH1051 3.9 30.4 1.0
NE1 A:TRP63 4.2 15.2 1.0
C A:ALA107 4.4 16.5 1.0
N A:ASN59 4.5 11.1 1.0
CB A:ALA107 4.5 15.7 1.0
CB A:ASN59 4.5 17.0 1.0
NE1 A:TRP108 4.5 13.4 1.0
O A:GLN57 4.5 12.5 1.0
CD1 A:TRP63 4.5 15.0 1.0
CG2 A:ILE98 4.5 14.4 1.0
O A:HOH1048 4.5 27.4 1.0
CD1 A:ILE98 4.6 16.6 1.0
CD1 A:TRP108 4.7 13.4 1.0
CE2 A:TRP108 4.8 12.9 1.0
CA A:ILE58 4.8 11.4 1.0
CA A:ALA107 5.0 13.4 1.0

Bromine binding site 9 out of 9 in 2d6b

Go back to Bromine Binding Sites List in 2d6b
Bromine binding site 9 out of 9 in the Novel Bromate Species Trapped Within A Protein Crystal


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 9 of Novel Bromate Species Trapped Within A Protein Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br139

b:22.8
occ:0.21
 BR A:202139 0.0 22.8 0.2
O1 A:202139 1.7 17.7 1.0
O A:HOH1236 2.6 22.1 0.5
OG A:SER24 3.1 18.7 1.0
CB A:SER24 3.4 14.9 1.0
ND2 A:ASN27 3.8 15.1 1.0
N A:SER24 4.1 13.3 1.0
CA A:SER24 4.4 14.6 1.0
O A:HOH1187 4.5 21.6 0.5
O A:GLY22 4.6 16.2 1.0
O A:HOH1260 4.9 27.6 0.5

Reference:

J.Ondracek, J.R.Mesters. An Ensemble of Crystallographic Models Enables the Description of Novel Bromate-Oxoanion Species Trapped Within A Protein Crystal Acta Crystallogr.,Sect.D V. 62 996 2006.
ISSN: ISSN 0907-4449
PubMed: 16929100
DOI: 10.1107/S0907444906021627
Page generated: Wed Jul 10 17:55:11 2024

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