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Bromine in PDB 3dd7: Structure of DOCH66Y in Complex with the C-Terminal Domain of Phd

Protein crystallography data

The structure of Structure of DOCH66Y in Complex with the C-Terminal Domain of Phd, PDB code: 3dd7 was solved by A.Garcia-Pino, R.Loris, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 11.00 / 1.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 110.944, 38.201, 63.734, 90.00, 99.26, 90.00
R / Rfree (%) 18.2 / 19.8

Bromine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Bromine atom in the Structure of DOCH66Y in Complex with the C-Terminal Domain of Phd (pdb code 3dd7). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 16 binding sites of Bromine where determined in the Structure of DOCH66Y in Complex with the C-Terminal Domain of Phd, PDB code: 3dd7:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Bromine binding site 1 out of 16 in 3dd7

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Bromine binding site 1 out of 16 in the Structure of DOCH66Y in Complex with the C-Terminal Domain of Phd


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Structure of DOCH66Y in Complex with the C-Terminal Domain of Phd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br136

b:18.1
occ:0.60
 N A:ARG74 3.4 18.8 1.0
O A:HOH192 3.4 25.6 1.0
NE A:ARG74 3.5 20.5 1.0
CA A:ALA71 3.5 18.6 1.0
CB A:LYS73 3.7 19.8 1.0
CG A:ARG74 3.8 17.9 1.0
N A:LYS73 3.8 19.3 1.0
C A:ALA71 4.0 18.6 1.0
CB A:ARG74 4.1 18.1 1.0
O B:MSE70 4.1 25.6 1.0
CA A:LYS73 4.1 19.9 1.0
CE A:LYS73 4.1 26.4 1.0
N A:ALA71 4.2 18.1 1.0
C A:LYS73 4.2 19.2 1.0
CD A:ARG74 4.3 18.5 1.0
N A:ASN72 4.3 18.6 1.0
BR A:BR144 4.3 23.3 0.3
NH2 A:ARG74 4.3 20.1 1.0
CA A:ARG74 4.3 17.7 1.0
CZ A:ARG74 4.3 22.6 1.0
NZ A:LYS73 4.5 28.5 1.0
CB A:ALA71 4.5 18.6 1.0
CG A:LYS73 4.6 21.1 1.0
O A:ALA71 4.6 18.6 1.0
CB B:MSE70 4.7 23.4 0.6
CB B:MSE70 4.7 24.6 0.4
C A:ASN72 4.8 19.1 1.0
C B:MSE70 4.8 24.9 1.0
OD1 A:ASP70 4.9 24.5 1.0
CD A:LYS73 4.9 22.3 1.0
CE B:MSE70 4.9 26.7 0.4

Bromine binding site 2 out of 16 in 3dd7

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Bromine binding site 2 out of 16 in the Structure of DOCH66Y in Complex with the C-Terminal Domain of Phd


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Structure of DOCH66Y in Complex with the C-Terminal Domain of Phd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br137

b:24.8
occ:0.40
 N A:VAL111 3.3 20.5 1.0
CG2 A:VAL111 3.7 21.4 1.0
NH1 A:ARG64 3.8 30.1 1.0
CA A:SER110 3.8 21.3 1.0
CB A:SER110 4.0 21.4 1.0
O A:HOH153 4.0 23.0 1.0
C A:SER110 4.1 20.6 1.0
CB A:VAL111 4.1 19.8 1.0
CA A:VAL111 4.3 19.8 1.0
CZ A:ARG64 4.5 31.2 1.0
NH2 A:ARG64 4.5 30.7 1.0
CG1 A:VAL60 4.6 17.8 1.0

Bromine binding site 3 out of 16 in 3dd7

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Bromine binding site 3 out of 16 in the Structure of DOCH66Y in Complex with the C-Terminal Domain of Phd


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Structure of DOCH66Y in Complex with the C-Terminal Domain of Phd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br138

b:23.6
occ:0.40
 O B:HOH76 3.2 27.4 1.0
CG A:ASP93 3.8 23.6 1.0
CB A:ASP93 3.8 22.7 1.0
N A:PRO95 3.8 20.7 1.0
C A:ASP93 3.9 22.6 1.0
C A:SER94 3.9 21.0 1.0
CD A:PRO95 3.9 20.4 1.0
N A:SER94 3.9 22.1 1.0
O A:ASP93 4.0 23.1 1.0
CA A:SER94 4.0 21.7 1.0
OD1 A:ASP93 4.1 24.6 1.0
OD2 A:ASP93 4.1 22.1 1.0
O A:SER94 4.4 20.2 1.0
CA A:PRO95 4.5 20.0 1.0
CA A:ASP93 4.5 22.7 1.0
OG B:SER65 4.5 13.6 0.5
CB B:SER65 4.5 15.2 0.5
CB B:SER65 4.7 15.9 0.5
CB A:PRO95 4.8 20.4 1.0
CG A:PRO95 4.8 19.7 1.0
O A:HOH147 4.9 14.0 1.0

Bromine binding site 4 out of 16 in 3dd7

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Bromine binding site 4 out of 16 in the Structure of DOCH66Y in Complex with the C-Terminal Domain of Phd


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Structure of DOCH66Y in Complex with the C-Terminal Domain of Phd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br139

b:30.1
occ:0.45
 OG1 B:THR62 3.1 19.7 1.0
NH1 A:ARG85 3.3 24.2 1.0
CD A:ARG85 3.6 22.1 1.0
O A:HOH161 3.6 24.5 1.0
O B:SER58 3.7 16.7 1.0
CB B:THR62 3.8 16.7 1.0
CA B:LEU59 4.1 15.3 1.0
C B:SER58 4.2 16.9 1.0
CG2 B:THR62 4.3 18.4 1.0
CZ A:ARG85 4.3 25.4 1.0
CG2 A:VAL91 4.3 22.9 1.0
N B:LEU59 4.3 16.3 1.0
NE A:ARG85 4.4 25.2 1.0
O B:HOH88 4.4 33.8 1.0
OG B:SER58 4.5 23.6 1.0
CD1 B:LEU59 4.7 18.5 1.0
CG A:ARG85 4.7 22.5 1.0
CB B:SER58 4.9 19.2 1.0
CB B:LEU59 4.9 16.1 1.0
O A:HOH177 4.9 32.8 1.0
O A:VAL91 5.0 23.6 1.0

Bromine binding site 5 out of 16 in 3dd7

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Bromine binding site 5 out of 16 in the Structure of DOCH66Y in Complex with the C-Terminal Domain of Phd


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Structure of DOCH66Y in Complex with the C-Terminal Domain of Phd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br140

b:25.1
occ:0.30
 SD A:MET26 2.9 23.8 0.6
O A:ASP28 3.0 31.9 1.0
N A:ALA32 3.4 24.1 1.0
N A:GLY30 3.4 28.7 1.0
O A:HOH201 3.4 23.9 1.0
CG A:MET26 3.5 25.4 0.4
N A:ARG31 3.6 25.6 1.0
CE A:MET26 3.7 25.8 0.6
CB A:ALA32 3.7 24.1 1.0
CG A:MET26 3.8 22.8 0.6
CB A:MET26 3.8 24.4 0.4
CB A:MET26 3.8 23.6 0.6
CA A:PRO29 3.9 30.4 1.0
C A:ASP28 4.0 31.2 1.0
C A:PRO29 4.0 29.4 1.0
CG2 A:ILE67 4.2 20.1 1.0
CA A:ALA32 4.2 23.8 1.0
C A:GLY30 4.2 26.2 1.0
CA A:ARG31 4.3 25.2 1.0
CA A:GLY30 4.3 27.1 1.0
C A:ARG31 4.3 24.6 1.0
N A:PRO29 4.4 31.0 1.0
CB A:ARG31 4.5 25.5 1.0
O A:ILE67 4.7 21.0 1.0
CD1 A:ILE10 4.7 20.1 1.0
CE A:MET26 4.8 29.1 0.4

Bromine binding site 6 out of 16 in 3dd7

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Bromine binding site 6 out of 16 in the Structure of DOCH66Y in Complex with the C-Terminal Domain of Phd


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Structure of DOCH66Y in Complex with the C-Terminal Domain of Phd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br141

b:43.7
occ:0.20
 O A:HOH203 2.5 29.6 1.0
NH1 A:ARG19 3.3 20.7 1.0
CB B:ALA57 3.8 18.5 1.0
O B:HOH210 4.1 35.2 1.0
CD A:ARG19 4.2 19.4 1.0
CZ A:ARG19 4.2 21.4 1.0
BR B:BR9 4.4 26.9 0.3
CA B:ALA57 4.5 18.3 1.0
NE A:ARG19 4.5 21.9 1.0

Bromine binding site 7 out of 16 in 3dd7

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Bromine binding site 7 out of 16 in the Structure of DOCH66Y in Complex with the C-Terminal Domain of Phd


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of Structure of DOCH66Y in Complex with the C-Terminal Domain of Phd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br142

b:20.8
occ:0.20
 O A:HOH206 3.3 53.6 1.0
CD A:ARG42 3.7 23.5 1.0
CG2 A:THR57 3.8 17.5 1.0
O A:HOH213 3.9 40.6 1.0
CG2 A:VAL39 4.0 22.5 1.0
CA A:VAL39 4.0 20.5 1.0
N A:VAL39 4.3 20.9 1.0
O A:ARG38 4.3 22.6 1.0
C A:ARG38 4.4 22.2 1.0
CB A:VAL39 4.6 19.8 1.0
CB A:ARG42 4.6 21.7 1.0
CB A:ALA61 4.7 19.1 1.0
CB A:ARG38 4.7 23.6 1.0
CG A:ARG42 4.8 22.8 1.0

Bromine binding site 8 out of 16 in 3dd7

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Bromine binding site 8 out of 16 in the Structure of DOCH66Y in Complex with the C-Terminal Domain of Phd


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of Structure of DOCH66Y in Complex with the C-Terminal Domain of Phd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br143

b:18.7
occ:0.25
 O A:HOH217 2.2 39.6 1.0
OD1 A:ASP14 2.8 20.8 1.0
N A:GLY25 3.1 21.3 1.0
CE1 A:HIS13 3.4 22.9 1.0
CA A:PRO24 3.4 21.0 1.0
O A:HOH166 3.6 29.4 1.0
CG A:ASP14 3.6 21.2 1.0
CB A:PRO24 3.6 21.0 1.0
ND1 A:HIS13 3.7 20.6 1.0
C A:PRO24 3.8 21.3 1.0
CA A:ASP14 4.1 18.8 1.0
CB A:ASP14 4.2 19.0 1.0
CG1 A:ILE17 4.2 22.3 1.0
CA A:GLY25 4.2 22.0 1.0
CG2 A:ILE17 4.3 21.5 1.0
CB A:ILE17 4.3 21.4 1.0
OD2 A:ASP14 4.4 22.5 1.0
NE2 A:HIS13 4.6 18.1 1.0
O A:HOH145 4.7 13.3 1.0
N A:PRO24 4.7 21.0 1.0
O A:LEU23 4.9 20.9 1.0
N A:ASP14 4.9 17.7 1.0

Bromine binding site 9 out of 16 in 3dd7

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Bromine binding site 9 out of 16 in the Structure of DOCH66Y in Complex with the C-Terminal Domain of Phd


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 9 of Structure of DOCH66Y in Complex with the C-Terminal Domain of Phd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br144

b:23.3
occ:0.33
 N A:ASN72 3.3 18.6 1.0
ND2 A:ASN72 3.5 19.5 1.0
O A:HOH211 3.5 40.4 1.0
N A:ALA71 3.6 18.1 1.0
CB A:ASN72 3.7 19.1 1.0
NZ A:LYS73 4.0 28.5 1.0
OD1 A:ASP70 4.0 24.5 1.0
CA A:ASN72 4.1 18.6 1.0
CG A:ASN72 4.1 17.9 1.0
C A:ASP70 4.1 18.1 1.0
CA A:ASP70 4.2 18.7 1.0
N A:LYS73 4.2 19.3 1.0
CA A:ALA71 4.2 18.6 1.0
C A:ALA71 4.2 18.6 1.0
BR A:BR136 4.3 18.1 0.6
C A:ASN72 4.7 19.1 1.0
CE A:LYS73 4.9 26.4 1.0
CG A:LYS73 5.0 21.1 1.0
O A:ASP70 5.0 16.9 1.0

Bromine binding site 10 out of 16 in 3dd7

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Bromine binding site 10 out of 16 in the Structure of DOCH66Y in Complex with the C-Terminal Domain of Phd


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 10 of Structure of DOCH66Y in Complex with the C-Terminal Domain of Phd within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br9

b:26.9
occ:0.35
 O A:HOH203 2.1 29.6 1.0
O A:HOH187 3.0 28.7 1.0
N B:ALA57 3.6 18.4 1.0
CD2 B:PHE60 3.7 13.4 1.0
CE2 B:PHE60 3.8 15.1 1.0
CA B:ALA57 3.8 18.3 1.0
CB A:ALA15 3.9 19.5 1.0
CB B:PHE56 4.0 20.3 1.0
C B:PHE56 4.1 19.0 1.0
CB B:ALA57 4.1 18.5 1.0
BR A:BR141 4.4 43.7 0.2
O B:PHE56 4.5 17.9 1.0
O A:ALA15 4.6 21.6 1.0
CA B:PHE56 4.7 20.3 1.0
CG B:PHE60 4.8 12.4 1.0
CA A:ALA15 4.8 19.9 1.0
C A:ALA15 4.9 20.0 1.0
CZ B:PHE60 5.0 14.9 1.0
CD A:ARG19 5.0 19.4 1.0
NH1 A:ARG19 5.0 20.7 1.0

Reference:

A.Garcia-Pino, M.Christensen-Dalsgaard, L.Wyns, M.Yarmolinsky, R.D.Magnuson, K.Gerdes, R.Loris. Doc of Prophage P1 Is Inhibited By Its Antitoxin Partner Phd Through Fold Complementation J.Biol.Chem. V. 283 30821 2008.
ISSN: ISSN 0021-9258
PubMed: 18757857
DOI: 10.1074/JBC.M805654200
Page generated: Wed Jul 10 19:16:20 2024

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