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Bromine in PDB 5veh: Re-Refinement of the Pdb Structure 1YIZ of Aedes Aegypti Kynurenine Aminotransferase

Protein crystallography data

The structure of Re-Refinement of the Pdb Structure 1YIZ of Aedes Aegypti Kynurenine Aminotransferase, PDB code: 5veh was solved by A.Wlodawer, Z.Dauter, W.Minor, R.Stanfield, P.Porebski, M.Jaskolski, E.Pozharski, C.X.Weichenberger, B.Rupp, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.30 / 1.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.288, 94.984, 167.599, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 21.5

Bromine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Bromine atom in the Re-Refinement of the Pdb Structure 1YIZ of Aedes Aegypti Kynurenine Aminotransferase (pdb code 5veh). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 12 binding sites of Bromine where determined in the Re-Refinement of the Pdb Structure 1YIZ of Aedes Aegypti Kynurenine Aminotransferase, PDB code: 5veh:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Bromine binding site 1 out of 12 in 5veh

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Bromine binding site 1 out of 12 in the Re-Refinement of the Pdb Structure 1YIZ of Aedes Aegypti Kynurenine Aminotransferase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Re-Refinement of the Pdb Structure 1YIZ of Aedes Aegypti Kynurenine Aminotransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br501

b:24.2
occ:0.70
 N A:GLU230 3.4 18.1 1.0
CE A:MET322 3.5 22.8 1.0
CB A:SER318 3.8 16.1 1.0
CA A:PHE229 3.9 15.9 1.0
CG A:GLU230 3.9 22.7 1.0
C A:SER318 3.9 16.0 1.0
O A:SER318 4.0 15.1 1.0
O A:HOH806 4.0 34.2 1.0
CB A:GLU230 4.0 20.1 1.0
N A:GLY319 4.0 15.9 1.0
SD A:MET322 4.1 25.1 1.0
C A:PHE229 4.1 16.8 1.0
CD1 A:PHE229 4.2 15.2 1.0
CA A:GLY319 4.3 16.5 1.0
CB A:PHE229 4.3 15.7 1.0
CB A:MET322 4.3 19.0 1.0
CA A:GLU230 4.4 19.0 1.0
CA A:SER318 4.5 15.7 1.0
O A:VAL228 4.6 15.7 1.0
O A:HOH732 4.8 21.5 1.0
CG A:PHE229 4.8 15.3 1.0
CG A:MET322 4.8 21.0 1.0
OG A:SER318 4.9 18.7 1.0

Bromine binding site 2 out of 12 in 5veh

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Bromine binding site 2 out of 12 in the Re-Refinement of the Pdb Structure 1YIZ of Aedes Aegypti Kynurenine Aminotransferase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Re-Refinement of the Pdb Structure 1YIZ of Aedes Aegypti Kynurenine Aminotransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br502

b:26.7
occ:0.70
 O A:HOH929 3.1 36.8 1.0
O A:HOH877 3.2 32.8 1.0
N A:TYR54 3.6 17.2 1.0
O A:HOH869 3.6 30.6 1.0
CD2 A:TYR54 3.9 18.8 1.0
CB A:TYR54 4.0 18.0 1.0
N A:LYS53 4.1 16.9 1.0
CB A:LYS53 4.1 18.4 1.0
O A:HOH898 4.1 51.7 1.0
CA A:TYR54 4.3 17.4 1.0
C A:LYS53 4.4 17.1 1.0
CA A:LYS53 4.4 17.4 1.0
CG A:TYR54 4.4 18.4 1.0
C A:PRO52 4.9 16.8 1.0
CE2 A:TYR54 5.0 18.7 1.0

Bromine binding site 3 out of 12 in 5veh

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Bromine binding site 3 out of 12 in the Re-Refinement of the Pdb Structure 1YIZ of Aedes Aegypti Kynurenine Aminotransferase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Re-Refinement of the Pdb Structure 1YIZ of Aedes Aegypti Kynurenine Aminotransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br503

b:18.9
occ:0.70
 O A:HOH901 2.9 32.1 1.0
CA A:GLY242 3.5 16.1 1.0
C A:GLY242 3.5 15.9 1.0
N A:GLU245 3.6 16.5 1.0
N A:TRP244 3.7 15.7 1.0
CG A:GLU245 3.8 20.2 1.0
O A:GLY242 3.8 16.8 1.0
CB A:TRP244 3.9 16.6 1.0
N A:MET243 4.0 16.0 1.0
O A:HOH860 4.0 27.8 1.0
CB A:GLU245 4.0 18.5 1.0
N A:GLY242 4.1 16.1 1.0
CA A:TRP244 4.2 16.3 1.0
C A:TRP244 4.3 16.3 1.0
O A:HOH705 4.4 18.6 1.0
CA A:GLU245 4.4 17.2 1.0
C A:MET243 4.5 15.8 1.0
CA A:MET243 4.8 15.6 1.0
NH2 A:ARG96 4.9 30.8 1.0
O A:HOH609 4.9 31.1 1.0

Bromine binding site 4 out of 12 in 5veh

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Bromine binding site 4 out of 12 in the Re-Refinement of the Pdb Structure 1YIZ of Aedes Aegypti Kynurenine Aminotransferase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Re-Refinement of the Pdb Structure 1YIZ of Aedes Aegypti Kynurenine Aminotransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br504

b:19.4
occ:0.50
 O A:HOH862 2.7 18.4 1.0
NH2 A:ARG201 3.2 24.3 1.0
CD A:GLU205 3.6 20.8 1.0
O A:HOH736 3.6 25.1 1.0
CG A:GLU205 3.7 19.6 1.0
OE2 A:GLU205 3.8 22.4 1.0
CD A:PRO241 3.8 16.8 1.0
CG A:PRO241 3.9 16.8 1.0
OE1 A:GLU205 4.0 22.8 1.0
CZ A:ARG201 4.4 24.3 1.0
NE A:ARG201 4.6 24.1 1.0
O A:HOH710 4.7 32.7 1.0
CB A:GLU205 4.7 18.4 1.0
CD2 A:LEU240 4.8 16.8 1.0
CB A:PRO241 4.8 16.8 1.0
CG A:LEU240 4.9 16.7 1.0
NZ A:LYS212 4.9 16.9 1.0

Bromine binding site 5 out of 12 in 5veh

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Bromine binding site 5 out of 12 in the Re-Refinement of the Pdb Structure 1YIZ of Aedes Aegypti Kynurenine Aminotransferase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Re-Refinement of the Pdb Structure 1YIZ of Aedes Aegypti Kynurenine Aminotransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br505

b:20.1
occ:0.50
 O A:HOH916 2.5 29.0 1.0
NE2 A:GLN384 3.4 14.4 1.0
ND2 A:ASN41 3.7 17.4 1.0
OD1 A:ASN41 3.9 18.8 1.0
C A:GLY43 4.0 18.9 1.0
O A:TYR30 4.0 14.6 1.0
CG A:GLN44 4.1 21.9 1.0
N A:GLN44 4.1 19.4 1.0
C A:TYR30 4.2 15.2 1.0
CG A:ASN41 4.2 17.7 1.0
CA A:GLY43 4.3 17.7 1.0
O A:GLY43 4.3 20.3 1.0
CB A:TYR30 4.4 14.6 1.0
N A:ILE31 4.4 15.8 1.0
CG1 A:ILE31 4.4 17.2 1.0
CD A:GLN384 4.5 14.6 1.0
CA A:ILE31 4.6 16.4 1.0
CA A:GLN44 4.6 20.3 1.0
CB A:ALA34 4.6 14.9 1.0
O A:HOH952 4.7 32.8 1.0
CD1 A:ILE386 4.7 15.3 1.0
CG A:GLN384 4.9 14.6 1.0
CA A:TYR30 4.9 15.2 1.0
N A:GLY43 5.0 16.7 1.0
CB A:GLN44 5.0 20.9 1.0

Bromine binding site 6 out of 12 in 5veh

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Bromine binding site 6 out of 12 in the Re-Refinement of the Pdb Structure 1YIZ of Aedes Aegypti Kynurenine Aminotransferase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Re-Refinement of the Pdb Structure 1YIZ of Aedes Aegypti Kynurenine Aminotransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br506

b:30.2
occ:0.50
 O A:HOH964 2.9 38.8 1.0
O A:HOH1013 3.2 34.7 1.0
O A:HOH851 3.3 29.3 1.0
N A:ALA202 3.4 17.6 1.0
N A:ARG201 3.7 17.5 1.0
CG A:ASP200 3.7 18.5 1.0
CB A:ALA202 3.8 17.8 1.0
CB A:ARG201 3.9 19.2 1.0
O A:HOH823 3.9 31.9 1.0
OD1 A:ASP200 3.9 19.0 1.0
OD2 A:ASP200 4.0 20.2 1.0
CB A:ASP200 4.0 17.9 1.0
CA A:ARG201 4.1 18.1 1.0
C A:ARG201 4.2 17.7 1.0
CA A:ALA202 4.2 17.7 1.0
C A:ASP200 4.5 17.1 1.0
CG A:ARG201 4.8 20.9 1.0
CA A:ASP200 4.8 17.4 1.0

Bromine binding site 7 out of 12 in 5veh

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Bromine binding site 7 out of 12 in the Re-Refinement of the Pdb Structure 1YIZ of Aedes Aegypti Kynurenine Aminotransferase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of Re-Refinement of the Pdb Structure 1YIZ of Aedes Aegypti Kynurenine Aminotransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br507

b:23.3
occ:0.50
 BR B:BR504 2.9 23.7 0.5
O B:HOH945 3.1 31.9 1.0
O B:HOH898 3.1 34.3 1.0
O B:HOH853 3.4 21.1 1.0
CG B:ARG75 3.8 15.6 1.0
CD1 A:ILE31 4.0 17.4 1.0
CG2 A:VAL28 4.1 19.1 1.0
CG1 A:VAL28 4.1 19.0 1.0
CG2 A:ILE31 4.2 16.9 1.0
CA A:VAL28 4.2 18.6 1.0
CB A:VAL28 4.4 18.8 1.0
CB A:ILE31 4.4 16.9 1.0
CD B:ARG75 4.4 16.1 1.0
CB B:ARG75 4.5 14.7 1.0
CA B:ARG75 4.5 14.3 1.0
NE B:ARG75 4.7 16.4 1.0
N B:GLY76 4.7 14.2 1.0
O A:VAL28 4.8 18.0 1.0
CG1 A:ILE31 4.9 17.2 1.0

Bromine binding site 8 out of 12 in 5veh

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Bromine binding site 8 out of 12 in the Re-Refinement of the Pdb Structure 1YIZ of Aedes Aegypti Kynurenine Aminotransferase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of Re-Refinement of the Pdb Structure 1YIZ of Aedes Aegypti Kynurenine Aminotransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br501

b:24.6
occ:0.70
 O B:HOH952 3.4 34.2 1.0
N B:GLU230 3.4 21.2 1.0
CE B:MET322 3.5 26.5 1.0
CB B:SER318 3.8 16.4 1.0
CA B:PHE229 3.8 18.3 1.0
C B:SER318 3.9 16.9 1.0
O B:SER318 4.0 16.8 1.0
N B:GLY319 4.0 17.5 1.0
CG B:GLU230 4.1 27.7 1.0
CB B:GLU230 4.1 24.8 1.0
CD1 B:PHE229 4.2 17.5 1.0
C B:PHE229 4.2 19.6 1.0
CB B:PHE229 4.3 17.8 1.0
CA B:GLY319 4.3 18.6 1.0
CB B:MET322 4.4 21.7 1.0
SD B:MET322 4.4 28.9 1.0
CA B:GLU230 4.4 22.9 1.0
CA B:SER318 4.5 16.5 1.0
O B:VAL228 4.5 17.6 1.0
CG B:PHE229 4.7 17.4 1.0
O B:HOH681 4.9 25.3 1.0
OG B:SER318 4.9 15.9 0.5
CG B:MET322 4.9 24.0 1.0
N B:PHE229 5.0 17.7 1.0

Bromine binding site 9 out of 12 in 5veh

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Bromine binding site 9 out of 12 in the Re-Refinement of the Pdb Structure 1YIZ of Aedes Aegypti Kynurenine Aminotransferase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 9 of Re-Refinement of the Pdb Structure 1YIZ of Aedes Aegypti Kynurenine Aminotransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br502

b:31.0
occ:0.70
 N B:GLU245 3.4 21.3 1.0
C B:GLY242 3.7 21.6 1.0
N B:TRP244 3.8 19.7 1.0
CB B:GLU245 3.8 23.4 1.0
CG B:GLU245 3.8 25.1 1.0
CA B:GLY242 3.8 21.5 1.0
CB B:TRP244 3.9 20.5 1.0
O B:GLY242 3.9 22.3 1.0
CA B:TRP244 4.1 20.2 1.0
N B:MET243 4.1 21.1 1.0
C B:TRP244 4.2 20.8 1.0
CA B:GLU245 4.2 22.0 1.0
O B:HOH780 4.4 23.8 1.0
N B:GLY242 4.4 21.4 1.0
CD B:GLU245 4.5 27.0 1.0
O B:HOH761 4.6 34.5 1.0
C B:MET243 4.6 19.9 1.0
CG B:TRP244 4.9 20.7 1.0
OE2 B:GLU245 4.9 28.4 1.0
NH2 B:ARG96 4.9 36.0 1.0
CA B:MET243 4.9 20.1 1.0
CD1 B:TRP244 4.9 20.7 1.0

Bromine binding site 10 out of 12 in 5veh

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Bromine binding site 10 out of 12 in the Re-Refinement of the Pdb Structure 1YIZ of Aedes Aegypti Kynurenine Aminotransferase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 10 of Re-Refinement of the Pdb Structure 1YIZ of Aedes Aegypti Kynurenine Aminotransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br503

b:30.3
occ:0.50
 O B:HOH699 2.9 31.1 1.0
CA B:PRO140 3.7 17.0 1.0
CB B:PRO140 3.7 17.0 1.0
CD B:LYS143 3.8 25.2 1.0
N B:PRO140 3.9 17.1 1.0
CG B:GLU139 4.0 19.8 1.0
CD B:PRO140 4.0 17.1 1.0
CD B:GLU139 4.1 20.9 1.0
C B:GLU139 4.3 17.0 1.0
OE1 B:GLU139 4.4 21.8 1.0
OE2 B:GLU139 4.4 22.6 1.0
CG B:PRO140 4.4 17.2 1.0
NZ B:LYS143 4.5 28.6 1.0
CB B:GLU139 4.6 18.2 1.0
O B:GLU139 4.6 16.7 1.0
CE B:LYS143 4.7 26.7 1.0
CG B:LYS143 4.7 23.2 1.0
O B:HOH741 4.9 30.3 1.0
CB B:LYS143 4.9 21.2 1.0
O B:HOH654 5.0 28.5 1.0

Reference:

A.Wlodawer, Z.Dauter, P.J.Porebski, W.Minor, R.Stanfield, M.Jaskolski, E.Pozharski, C.X.Weichenberger, B.Rupp. Detect, Correct, Retract: How to Manage Incorrect Structural Models. Febs J. V. 285 444 2018.
ISSN: ISSN 1742-4658
PubMed: 29113027
DOI: 10.1111/FEBS.14320
Page generated: Thu Jul 11 01:13:57 2024

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