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Bromine in PDB 4dr9: Crystal Structure of A Peptide Deformylase From Synechococcus Elongatus in Complex with Actinonin

Enzymatic activity of Crystal Structure of A Peptide Deformylase From Synechococcus Elongatus in Complex with Actinonin

All present enzymatic activity of Crystal Structure of A Peptide Deformylase From Synechococcus Elongatus in Complex with Actinonin:
3.5.1.88;

Protein crystallography data

The structure of Crystal Structure of A Peptide Deformylase From Synechococcus Elongatus in Complex with Actinonin, PDB code: 4dr9 was solved by D.Lorimer, J.Abendroth, T.Craig, A.Burgin, A.Segall, F.Rohwler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.90
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 43.250, 65.780, 68.290, 80.87, 76.82, 82.75
R / Rfree (%) 18.2 / 23.5

Other elements in 4dr9:

The structure of Crystal Structure of A Peptide Deformylase From Synechococcus Elongatus in Complex with Actinonin also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Bromine Binding Sites:

The binding sites of Bromine atom in the Crystal Structure of A Peptide Deformylase From Synechococcus Elongatus in Complex with Actinonin (pdb code 4dr9). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 5 binding sites of Bromine where determined in the Crystal Structure of A Peptide Deformylase From Synechococcus Elongatus in Complex with Actinonin, PDB code: 4dr9:
Jump to Bromine binding site number: 1; 2; 3; 4; 5;

Bromine binding site 1 out of 5 in 4dr9

Go back to Bromine Binding Sites List in 4dr9
Bromine binding site 1 out of 5 in the Crystal Structure of A Peptide Deformylase From Synechococcus Elongatus in Complex with Actinonin


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 A Peptide Deformylase From Synechococcus Elongatus in Complex with Actinonin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br202

b:30.8
occ:0.50
 NH2 A:ARG186 3.0 21.8 1.0
BR D:BR202 3.1 22.2 0.5
O A:HOH442 3.1 28.0 1.0
O A:HOH327 3.7 12.2 1.0
CZ A:ARG186 3.8 20.8 1.0
CA A:ALA184 3.8 13.1 1.0
CB D:ALA181 3.9 20.5 1.0
NH1 A:ARG186 4.0 20.6 1.0
N D:ALA184 4.0 17.3 1.0
CB D:GLN183 4.0 21.1 1.0
CB D:ALA184 4.1 16.0 1.0
CB A:ALA184 4.2 12.6 1.0
O A:GLN183 4.2 14.7 1.0
O A:GLY25 4.2 14.2 1.0
CA D:ALA184 4.2 16.6 1.0
C D:GLN183 4.3 18.2 1.0
O A:HOH415 4.5 27.0 1.0
N A:ALA184 4.6 13.5 1.0
CA A:GLY25 4.6 13.0 1.0
O D:GLN183 4.7 18.2 1.0
C A:GLN183 4.7 14.2 1.0
C A:ALA184 4.8 12.4 1.0
O A:ALA184 4.8 11.8 1.0
CA D:GLN183 4.8 19.5 1.0
C A:GLY25 4.9 13.5 1.0
O D:HOH413 4.9 24.1 1.0
CA D:GLY25 5.0 14.0 1.0

Bromine binding site 2 out of 5 in 4dr9

Go back to Bromine Binding Sites List in 4dr9
Bromine binding site 2 out of 5 in the Crystal Structure of A Peptide Deformylase From Synechococcus Elongatus in Complex with Actinonin


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 A Peptide Deformylase From Synechococcus Elongatus in Complex with Actinonin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br202

b:32.2
occ:0.50
 BR C:BR203 2.4 32.1 0.5
O B:HOH356 2.9 22.5 1.0
NH2 B:ARG186 3.4 24.1 1.0
CA B:ALA184 3.6 18.6 1.0
N C:ALA184 3.8 20.6 1.0
CB C:ALA184 3.9 19.7 1.0
CA C:ALA184 3.9 20.2 1.0
O B:GLN183 3.9 20.8 1.0
N B:ALA184 4.0 19.6 1.0
CB B:ALA184 4.1 17.6 1.0
C C:GLN183 4.1 21.6 1.0
C B:GLN183 4.1 20.7 1.0
CB C:ALA181 4.3 23.2 1.0
NH1 B:ARG186 4.3 23.8 1.0
CZ B:ARG186 4.3 23.4 1.0
CB C:GLN183 4.3 24.2 1.0
O C:GLN183 4.4 21.1 1.0
O B:HOH327 4.5 14.7 1.0
C B:ALA184 4.7 17.5 1.0
CA C:GLN183 4.8 22.7 1.0
O B:GLY25 4.8 15.5 1.0
O C:HOH334 4.9 22.6 1.0
O B:ALA184 4.9 16.7 1.0
CA C:GLY25 5.0 17.3 1.0

Bromine binding site 3 out of 5 in 4dr9

Go back to Bromine Binding Sites List in 4dr9
Bromine binding site 3 out of 5 in the Crystal Structure of A Peptide Deformylase From Synechococcus Elongatus in Complex with Actinonin


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 A Peptide Deformylase From Synechococcus Elongatus in Complex with Actinonin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br202

b:29.3
occ:0.50
 NZ C:LYS71 3.3 25.2 1.0
N C:SER37 3.6 26.4 1.0
N C:ARG38 3.8 28.6 1.0
O C:HOH408 4.0 34.2 1.0
CG1 C:VAL36 4.1 21.4 1.0
CA C:VAL36 4.1 22.5 1.0
CE C:LYS71 4.2 24.1 1.0
CB C:ARG38 4.3 31.2 1.0
OG C:SER37 4.3 30.9 1.0
C C:VAL36 4.3 24.4 1.0
O C:ARG38 4.4 28.5 1.0
CA C:SER37 4.5 28.1 1.0
CA C:ARG38 4.5 29.5 1.0
CD C:LYS71 4.6 22.2 1.0
C C:SER37 4.6 28.8 1.0
CB C:VAL36 4.6 21.1 1.0
O C:ARG35 4.9 23.5 1.0
C C:ARG38 4.9 28.3 1.0
CB C:SER37 5.0 30.1 1.0
CG2 C:VAL36 5.0 19.9 1.0

Bromine binding site 4 out of 5 in 4dr9

Go back to Bromine Binding Sites List in 4dr9
Bromine binding site 4 out of 5 in the Crystal Structure of A Peptide Deformylase From Synechococcus Elongatus in Complex with Actinonin


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 A Peptide Deformylase From Synechococcus Elongatus in Complex with Actinonin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br203

b:32.1
occ:0.50
 BR B:BR202 2.4 32.2 0.5
O C:HOH334 3.2 22.6 1.0
NH2 C:ARG186 3.3 25.5 1.0
CA C:ALA184 3.6 20.2 1.0
N B:ALA184 3.8 19.6 1.0
CA B:ALA184 3.9 18.6 1.0
CB B:ALA184 3.9 17.6 1.0
O C:GLN183 3.9 21.1 1.0
CB C:ALA184 4.0 19.7 1.0
C B:GLN183 4.1 20.7 1.0
CB B:ALA181 4.1 22.3 1.0
N C:ALA184 4.1 20.6 1.0
CB B:GLN183 4.1 23.6 1.0
O C:HOH327 4.2 16.0 1.0
NH1 C:ARG186 4.2 24.6 1.0
CZ C:ARG186 4.2 24.9 1.0
C C:GLN183 4.3 21.6 1.0
O B:GLN183 4.5 20.8 1.0
O B:HOH356 4.5 22.5 1.0
CA B:GLN183 4.7 22.1 1.0
O C:GLY25 4.7 19.1 1.0
C C:ALA184 4.7 19.6 1.0
O C:HOH386 4.7 23.0 1.0
CA C:GLY25 4.8 17.3 1.0
O C:ALA184 4.9 19.2 1.0

Bromine binding site 5 out of 5 in 4dr9

Go back to Bromine Binding Sites List in 4dr9
Bromine binding site 5 out of 5 in the Crystal Structure of A Peptide Deformylase From Synechococcus Elongatus in Complex with Actinonin


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 A Peptide Deformylase From Synechococcus Elongatus in Complex with Actinonin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br202

b:22.2
occ:0.50
 O D:HOH413 2.8 24.1 1.0
BR A:BR202 3.1 30.8 0.5
NH2 D:ARG186 3.3 19.5 1.0
CA D:ALA184 3.6 16.6 1.0
N A:ALA184 3.7 13.5 1.0
CB A:ALA184 3.7 12.6 1.0
CA A:ALA184 3.8 13.1 1.0
O D:GLN183 3.8 18.2 1.0
C A:GLN183 3.9 14.2 1.0
CB D:ALA184 4.1 16.0 1.0
NH1 D:ARG186 4.1 18.9 1.0
N D:ALA184 4.1 17.3 1.0
O A:GLN183 4.1 14.7 1.0
CZ D:ARG186 4.1 18.9 1.0
C D:GLN183 4.2 18.2 1.0
O D:HOH412 4.3 11.6 1.0
CB A:GLN183 4.3 16.2 1.0
CB A:ALA181 4.3 15.6 1.0
CA A:GLN183 4.7 14.9 1.0
C D:ALA184 4.7 15.6 1.0
O D:GLY25 4.8 15.5 1.0
CA A:GLY25 4.8 13.0 1.0
CA D:GLY25 5.0 14.0 1.0
O D:ALA184 5.0 15.4 1.0

Reference:

J.A.Frank, D.Lorimer, M.Youle, P.Witte, T.Craig, J.Abendroth, F.Rohwer, R.A.Edwards, A.M.Segall, A.B.Burgin. Structure and Function of A Cyanophage-Encoded Peptide Deformylase. Isme J V. 7 1150 2013.
ISSN: ISSN 1751-7362
PubMed: 23407310
DOI: 10.1038/ISMEJ.2013.4
Page generated: Sat Dec 12 02:19:03 2020

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