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Bromine in PDB 1jhd: Crystal Structure of Bacterial Atp Sulfurylase From the Riftia Pachyptila Symbiont

Enzymatic activity of Crystal Structure of Bacterial Atp Sulfurylase From the Riftia Pachyptila Symbiont

All present enzymatic activity of Crystal Structure of Bacterial Atp Sulfurylase From the Riftia Pachyptila Symbiont:
2.7.7.4;

Protein crystallography data

The structure of Crystal Structure of Bacterial Atp Sulfurylase From the Riftia Pachyptila Symbiont, PDB code: 1jhd was solved by J.D.Beynon, I.J.Macrae, S.L.Huston, D.C.Nelson, I.H.Segel, A.J.Fisher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.78 / 1.70
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 59.561, 75.546, 95.853, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 20.5

Bromine Binding Sites:

The binding sites of Bromine atom in the Crystal Structure of Bacterial Atp Sulfurylase From the Riftia Pachyptila Symbiont (pdb code 1jhd). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 8 binding sites of Bromine where determined in the Crystal Structure of Bacterial Atp Sulfurylase From the Riftia Pachyptila Symbiont, PDB code: 1jhd:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Bromine binding site 1 out of 8 in 1jhd

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Bromine binding site 1 out of 8 in the Crystal Structure of Bacterial Atp Sulfurylase From the Riftia Pachyptila Symbiont


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Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of Bacterial Atp Sulfurylase From the Riftia Pachyptila Symbiont within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br2004

b:26.4
occ:0.37
 O A:HOH3363 2.8 31.2 1.0
O A:HOH3382 3.0 35.3 1.0
CB A:SER193 3.6 20.3 1.0
CE A:LYS194 3.9 22.5 1.0
O A:HOH3333 4.1 25.0 1.0
CG A:LYS194 4.1 13.3 1.0
OG A:SER193 4.2 28.4 1.0
CD A:LYS194 4.5 17.3 1.0
O A:HOH3440 4.5 42.1 1.0
N A:LYS194 4.6 10.9 1.0
O A:HOH3224 4.8 38.8 1.0
CA A:SER193 4.9 14.5 1.0

Bromine binding site 2 out of 8 in 1jhd

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Bromine binding site 2 out of 8 in the Crystal Structure of Bacterial Atp Sulfurylase From the Riftia Pachyptila Symbiont


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 Bacterial Atp Sulfurylase From the Riftia Pachyptila Symbiont within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br2005

b:30.1
occ:0.46
 O A:HOH3331 2.9 24.3 1.0
N A:LEU10 3.0 10.3 1.0
O A:HOH3085 3.0 19.6 1.0
CA A:GLU9 3.6 12.7 1.0
C A:GLU9 3.8 10.0 1.0
CG A:LEU10 3.9 8.3 1.0
CB A:LEU10 3.9 8.4 1.0
CB A:GLU9 3.9 19.9 1.0
CA A:LEU10 4.0 8.9 1.0
CG A:GLU9 4.1 33.7 1.0
O A:HOH3286 4.1 28.7 1.0
CD1 A:LEU10 4.4 9.3 1.0
CD A:ARG184 4.4 8.6 1.0
CG A:PRO4 4.6 12.1 1.0
O A:ASP8 4.7 15.6 1.0
NH1 A:ARG184 4.7 13.9 1.0
O A:HOH3104 4.7 19.8 1.0
O A:LEU10 4.8 10.5 1.0
N A:GLU9 4.9 13.9 1.0
C A:LEU10 4.9 8.4 1.0
NE A:ARG184 5.0 8.3 1.0
O A:GLU9 5.0 12.8 1.0

Bromine binding site 3 out of 8 in 1jhd

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Bromine binding site 3 out of 8 in the Crystal Structure of Bacterial Atp Sulfurylase From the Riftia Pachyptila Symbiont


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 Bacterial Atp Sulfurylase From the Riftia Pachyptila Symbiont within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br2006

b:37.5
occ:0.36
 N A:ALA240 3.2 23.1 1.0
O A:HOH3411 3.4 32.2 1.0
CA A:PRO239 3.8 25.3 1.0
CD1 A:LEU233 3.8 31.2 1.0
CB A:ALA240 3.9 22.4 1.0
C A:PRO239 4.0 24.1 1.0
CB A:LEU233 4.0 27.8 1.0
CA A:ALA240 4.2 20.2 1.0
CB A:PRO239 4.3 25.6 1.0
CG A:LEU233 4.3 32.5 1.0
CD2 A:LEU233 4.5 36.5 1.0
CD A:PRO241 4.6 22.4 1.0
CE1 A:PHE173 4.7 18.2 1.0
CA A:LEU233 4.8 26.4 1.0
N A:LEU233 5.0 25.7 1.0
N A:PRO239 5.0 26.8 1.0
CZ A:PHE173 5.0 16.8 1.0
O A:ILE238 5.0 28.0 1.0

Bromine binding site 4 out of 8 in 1jhd

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Bromine binding site 4 out of 8 in the Crystal Structure of Bacterial Atp Sulfurylase From the Riftia Pachyptila Symbiont


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 Bacterial Atp Sulfurylase From the Riftia Pachyptila Symbiont within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br2007

b:20.6
occ:0.32
 O A:HOH3074 2.9 23.3 1.0
O A:HOH3043 3.0 15.1 1.0
N A:GLN39 3.0 10.7 1.0
O A:HOH3396 3.2 43.0 1.0
O A:HOH3179 3.2 26.9 1.0
N A:SER38 3.4 12.3 1.0
CB A:GLN39 3.6 12.8 1.0
CB A:SER37 3.7 15.8 1.0
CB A:SER38 3.8 12.8 1.0
O A:HOH3242 3.8 27.0 1.0
CG2 A:THR148 3.8 18.5 1.0
CA A:SER38 3.9 13.3 1.0
CA A:GLN39 3.9 11.1 1.0
C A:SER38 3.9 12.2 1.0
OG A:SER37 4.0 15.4 1.0
C A:SER37 4.2 14.7 1.0
OE1 A:GLN152 4.4 16.2 1.0
CA A:SER37 4.4 14.9 1.0
O A:HOH3385 4.5 41.0 1.0
CG A:GLN152 4.6 19.6 1.0
CD A:GLN152 4.7 14.4 1.0
OG A:SER38 4.9 14.2 1.0
OD2 A:ASP268 4.9 16.4 1.0
O A:THR148 4.9 15.2 1.0

Bromine binding site 5 out of 8 in 1jhd

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Bromine binding site 5 out of 8 in the Crystal Structure of Bacterial Atp Sulfurylase From the Riftia Pachyptila Symbiont


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 Bacterial Atp Sulfurylase From the Riftia Pachyptila Symbiont within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br2008

b:38.8
occ:0.41
 NE2 A:GLN199 3.1 22.4 1.0
O A:HOH3391 3.4 39.1 1.0
NE A:ARG201 3.6 42.7 1.0
O A:HOH3128 3.6 30.5 1.0
O A:HOH3105 3.7 25.7 1.0
CG A:GLN199 3.8 16.5 1.0
N A:ARG201 3.9 16.6 1.0
CA A:THR200 3.9 13.9 1.0
CD A:GLN199 4.0 21.3 1.0
CG A:ARG201 4.0 23.0 1.0
C A:THR200 4.0 19.5 1.0
N A:THR200 4.3 15.8 1.0
CD A:ARG201 4.3 33.2 1.0
O A:GLN199 4.3 12.6 1.0
NH2 A:ARG201 4.4 45.5 1.0
CZ A:ARG201 4.4 45.7 1.0
C A:GLN199 4.4 14.5 1.0
CB A:ARG201 4.5 19.9 1.0
O A:THR200 4.7 16.6 1.0
CB A:GLN199 4.7 13.1 1.0
CA A:ARG201 4.8 16.7 1.0
O A:HOH3183 4.9 30.3 1.0

Bromine binding site 6 out of 8 in 1jhd

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Bromine binding site 6 out of 8 in the Crystal Structure of Bacterial Atp Sulfurylase From the Riftia Pachyptila Symbiont


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 Bacterial Atp Sulfurylase From the Riftia Pachyptila Symbiont within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br2001

b:20.8
occ:0.72
 OG A:SER379 3.0 24.5 1.0
O A:HOH3010 3.2 14.5 1.0
ND1 A:HIS205 3.3 16.9 1.0
CG1 A:VAL383 3.7 15.7 1.0
CB A:SER379 3.8 16.4 1.0
N A:ALA384 3.8 16.9 1.0
CD1 A:LEU368 3.9 17.7 1.0
CA A:ALA384 4.0 16.3 1.0
CD1 A:LEU387 4.1 20.3 1.0
CA A:SER379 4.1 10.9 1.0
CE1 A:HIS205 4.1 17.5 1.0
CB A:VAL383 4.1 13.8 1.0
CB A:ALA384 4.2 17.4 1.0
CG A:HIS205 4.3 15.2 1.0
C A:VAL383 4.3 18.9 1.0
N A:ARG380 4.3 14.5 1.0
O A:ARG380 4.3 14.0 1.0
CG1 A:VAL364 4.5 17.6 1.0
CB A:HIS205 4.5 14.9 1.0
CA A:HIS205 4.5 12.7 1.0
C A:SER379 4.6 14.6 1.0
CD2 A:LEU368 4.7 21.3 1.0
O A:VAL383 4.7 18.6 1.0
CA A:VAL383 4.9 14.7 1.0
CG A:LEU368 4.9 20.9 1.0
O A:PHE378 4.9 15.6 1.0

Bromine binding site 7 out of 8 in 1jhd

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Bromine binding site 7 out of 8 in the Crystal Structure of Bacterial Atp Sulfurylase From the Riftia Pachyptila Symbiont


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 Bacterial Atp Sulfurylase From the Riftia Pachyptila Symbiont within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br2002

b:21.9
occ:0.43
 N A:ASP175 3.1 12.2 1.0
C A:PHE173 3.3 11.5 1.0
CA A:PHE173 3.3 9.4 1.0
OG1 A:THR176 3.5 24.8 1.0
N A:PRO174 3.5 11.3 1.0
CB A:ASP175 3.6 11.5 1.0
N A:THR176 3.6 10.6 1.0
O A:HOH3274 3.7 37.4 1.0
CD A:PRO174 3.7 11.6 1.0
O A:PHE173 3.7 12.5 1.0
CA A:ASP175 3.7 11.3 1.0
O A:HOH3228 3.9 33.9 1.0
CB A:PHE173 4.0 10.5 1.0
C A:ASP175 4.1 13.3 1.0
CB A:THR176 4.1 15.1 1.0
C A:PRO174 4.2 11.5 1.0
CG A:ASP175 4.2 10.4 1.0
OD2 A:ASP244 4.2 24.0 1.0
O A:HOH3042 4.2 16.1 1.0
CG A:PRO174 4.3 12.8 1.0
CA A:PRO174 4.3 11.2 1.0
OD2 A:ASP175 4.5 11.8 1.0
CA A:THR176 4.6 10.0 1.0
N A:PHE173 4.6 12.4 1.0
O A:HOH3335 4.6 25.4 1.0
O A:ASP172 4.6 13.9 1.0
CD1 A:PHE173 4.9 17.5 1.0
CG A:PHE173 4.9 10.6 1.0

Bromine binding site 8 out of 8 in 1jhd

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Bromine binding site 8 out of 8 in the Crystal Structure of Bacterial Atp Sulfurylase From the Riftia Pachyptila Symbiont


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 Bacterial Atp Sulfurylase From the Riftia Pachyptila Symbiont within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br2003

b:26.0
occ:0.39
 O A:HOH3251 2.8 28.7 1.0
O A:HOH3422 2.9 46.5 1.0
N A:ARG296 3.0 13.4 1.0
C A:ASP331 3.5 14.7 1.0
CA A:GLY295 3.6 12.3 1.0
CA A:ASP331 3.6 10.8 1.0
O A:HOH3046 3.7 18.3 1.0
O A:ASP331 3.7 13.4 1.0
CG A:ARG296 3.8 22.9 1.0
C A:GLY295 3.8 14.9 1.0
O A:HOH3354 3.8 33.9 1.0
N A:ASP331 3.9 11.9 1.0
CB A:ARG296 3.9 19.1 1.0
N A:HIS332 3.9 12.5 1.0
CD A:ARG296 4.0 33.7 1.0
CA A:ARG296 4.1 11.4 1.0
C A:ALA330 4.3 13.2 1.0
O A:ALA330 4.4 14.7 1.0
O2 A:SO41003 4.4 17.8 0.7
CD2 A:HIS332 4.5 23.3 1.0
CA A:HIS332 4.5 13.1 1.0
O A:HOH3339 4.6 28.8 1.0
CB A:ALA330 4.7 15.0 1.0
O A:ARG296 4.7 11.6 1.0
C A:ARG296 4.9 11.9 1.0
N A:GLY295 4.9 13.1 1.0

Reference:

J.D.Beynon, I.J.Macrae, S.L.Huston, D.C.Nelson, I.H.Segel, A.J.Fisher. Crystal Structure of Atp Sulfurylase From the Bacterial Symbiont of the Hydrothermal Vent Tubeworm Riftia Pachyptila. Biochemistry V. 40 14509 2001.
ISSN: ISSN 0006-2960
PubMed: 11724564
DOI: 10.1021/BI015643L
Page generated: Wed Jul 10 16:45:24 2024

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