Atomistry » Bromine » PDB 3ok5-3r1e » 3qbk
Atomistry »
  Bromine »
    PDB 3ok5-3r1e »
      3qbk »

Bromine in PDB 3qbk: Bromide-Bound Form of Pharaonis Halorhodopsin

Protein crystallography data

The structure of Bromide-Bound Form of Pharaonis Halorhodopsin, PDB code: 3qbk was solved by T.Kouyama, S.Kanada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 152.150, 99.720, 99.970, 90.00, 127.80, 90.00
R / Rfree (%) 24.8 / 26.7

Bromine Binding Sites:

The binding sites of Bromine atom in the Bromide-Bound Form of Pharaonis Halorhodopsin (pdb code 3qbk). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 6 binding sites of Bromine where determined in the Bromide-Bound Form of Pharaonis Halorhodopsin, PDB code: 3qbk:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6;

Bromine binding site 1 out of 6 in 3qbk

Go back to Bromine Binding Sites List in 3qbk
Bromine binding site 1 out of 6 in the Bromide-Bound Form of Pharaonis Halorhodopsin


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Bromide-Bound Form of Pharaonis Halorhodopsin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br401

b:28.7
occ:1.00
 OG A:SER130 3.2 24.9 1.0
OG1 A:THR126 3.2 30.4 1.0
O A:HOH502 3.2 33.2 1.0
NZ A:LYS256 3.6 23.8 1.0
CB A:THR126 3.6 28.8 1.0
CE A:LYS256 3.7 25.2 1.0
CB A:SER130 3.8 25.4 1.0
CG1 A:VAL77 3.8 26.7 1.0
CB A:SER81 3.9 27.1 1.0
C A:THR126 3.9 26.4 1.0
CD1 A:TRP127 3.9 26.0 1.0
O A:THR126 4.0 28.0 1.0
OG A:SER81 4.1 24.4 1.0
CA A:SER78 4.1 26.1 1.0
N A:TRP127 4.1 23.1 1.0
N A:SER78 4.3 26.0 1.0
CA A:THR126 4.4 28.2 1.0
C A:VAL77 4.5 28.5 1.0
CA A:TRP127 4.5 23.5 1.0
O A:HOH504 4.5 22.9 1.0
O A:VAL77 4.5 28.2 1.0
CB A:SER78 4.6 25.8 1.0
C15 A:RET292 4.6 23.5 1.0
CB A:VAL77 4.6 28.2 1.0
NE1 A:TRP127 4.7 23.9 1.0
CG2 A:THR126 4.8 29.1 1.0
O A:HOH503 4.8 20.9 1.0
CD A:LYS256 4.8 22.8 1.0
OG A:SER78 4.9 30.9 1.0
O A:ARG123 4.9 28.6 1.0

Bromine binding site 2 out of 6 in 3qbk

Go back to Bromine Binding Sites List in 3qbk
Bromine binding site 2 out of 6 in the Bromide-Bound Form of Pharaonis Halorhodopsin


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Bromide-Bound Form of Pharaonis Halorhodopsin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br402

b:43.1
occ:1.00
 O A:HOH530 3.2 44.9 1.0
O B:HOH527 3.3 49.2 1.0
ND2 A:ASN145 3.3 35.0 1.0
NZ B:LYS65 3.5 45.1 1.0
CB B:PRO62 3.8 38.7 1.0
CA B:PRO62 3.8 38.4 1.0
CE B:LYS65 3.8 41.4 1.0
CB A:THR147 3.8 30.0 1.0
CG2 A:THR147 3.8 29.9 1.0
CD B:LYS65 3.9 40.4 1.0
C24 B:22B300 4.0 60.6 1.0
CE A:LYS148 4.0 36.5 1.0
CG A:LYS148 4.1 30.1 1.0
CG A:ASN145 4.2 35.3 1.0
OD1 A:ASN145 4.3 33.2 1.0
OG1 A:THR147 4.4 31.0 1.0
N B:PRO62 4.5 38.9 1.0
CB B:LYS65 4.5 34.7 1.0
CD B:PRO62 4.7 39.1 1.0
O A:HOH526 4.7 55.5 1.0
CD A:LYS148 4.7 33.5 1.0
O A:HOH529 4.7 52.0 1.0
CG B:PRO62 4.8 40.0 1.0
CG B:LYS65 4.8 37.1 1.0
O B:PRO62 4.8 36.9 1.0
C B:PRO62 4.9 37.4 1.0
N A:LYS148 5.0 28.6 1.0

Bromine binding site 3 out of 6 in 3qbk

Go back to Bromine Binding Sites List in 3qbk
Bromine binding site 3 out of 6 in the Bromide-Bound Form of Pharaonis Halorhodopsin


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Bromide-Bound Form of Pharaonis Halorhodopsin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br293

b:58.4
occ:1.00
 OD1 D:ASN145 3.5 43.4 1.0
NZ D:LYS148 3.7 47.0 1.0
CA A:PRO62 3.7 41.9 1.0
CG2 D:THR147 3.7 36.5 1.0
CB A:PRO62 3.8 42.1 1.0
CD A:LYS65 3.9 42.4 1.0
CB D:THR147 3.9 38.7 1.0
NZ A:LYS65 4.0 45.4 1.0
C24 A:22B300 4.0 85.6 1.0
CE D:LYS148 4.0 48.2 1.0
CG D:LYS148 4.1 45.4 1.0
CE A:LYS65 4.2 42.1 1.0
CG D:ASN145 4.3 38.5 1.0
ND2 D:ASN145 4.3 38.4 1.0
N A:PRO62 4.5 43.4 1.0
OG1 D:THR147 4.6 38.9 1.0
CB A:LYS65 4.6 37.0 1.0
O A:PRO62 4.7 38.4 1.0
CD D:LYS148 4.7 49.3 1.0
C A:PRO62 4.8 40.2 1.0
CG A:LYS65 4.8 41.8 1.0
CD A:PRO62 4.9 41.8 1.0
N D:LYS148 4.9 39.8 1.0
CG A:PRO62 4.9 42.4 1.0
O A:ASP60 5.0 47.4 1.0

Bromine binding site 4 out of 6 in 3qbk

Go back to Bromine Binding Sites List in 3qbk
Bromine binding site 4 out of 6 in the Bromide-Bound Form of Pharaonis Halorhodopsin


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Bromide-Bound Form of Pharaonis Halorhodopsin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br401

b:32.6
occ:1.00
 OG1 B:THR126 3.1 25.2 1.0
O B:HOH502 3.2 24.2 1.0
OG B:SER130 3.2 26.0 1.0
NZ B:LYS256 3.5 29.5 1.0
CE B:LYS256 3.6 28.2 1.0
CB B:SER130 3.7 24.4 1.0
CB B:THR126 3.7 25.8 1.0
CB B:SER81 3.9 26.7 1.0
CD1 B:TRP127 3.9 26.3 1.0
O B:THR126 3.9 26.8 1.0
OG B:SER81 3.9 23.3 1.0
C B:THR126 4.0 26.9 1.0
CG1 B:VAL77 4.1 23.9 1.0
CA B:SER78 4.1 28.0 1.0
N B:TRP127 4.2 27.1 1.0
O B:HOH504 4.3 29.6 1.0
N B:SER78 4.4 27.7 1.0
CA B:TRP127 4.5 27.7 1.0
O B:VAL77 4.5 28.5 1.0
CA B:THR126 4.5 27.1 1.0
C15 B:RET292 4.5 25.4 1.0
C B:VAL77 4.6 28.7 1.0
NE1 B:TRP127 4.6 24.9 1.0
CB B:SER78 4.7 27.4 1.0
O B:HOH503 4.7 27.0 1.0
OG B:SER78 4.8 25.2 1.0
CD B:LYS256 4.9 29.7 1.0
CG B:TRP127 5.0 29.0 1.0
CG2 B:THR126 5.0 26.3 1.0

Bromine binding site 5 out of 6 in 3qbk

Go back to Bromine Binding Sites List in 3qbk
Bromine binding site 5 out of 6 in the Bromide-Bound Form of Pharaonis Halorhodopsin


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Bromide-Bound Form of Pharaonis Halorhodopsin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br402

b:58.4
occ:1.00
 NZ D:LYS65 3.4 58.5 1.0
ND2 B:ASN145 3.5 43.8 1.0
CE D:LYS65 3.5 54.7 1.0
CG2 B:THR147 3.7 43.6 1.0
CB D:PRO62 3.8 49.8 1.0
CA D:PRO62 3.8 50.9 1.0
CB B:THR147 3.8 44.2 1.0
CE B:LYS148 3.9 47.4 1.0
OD1 B:ASN145 4.1 44.4 1.0
CG B:LYS148 4.1 44.0 1.0
CG B:ASN145 4.2 42.0 1.0
CD D:LYS65 4.2 52.2 1.0
N D:PRO62 4.5 51.1 1.0
OG1 B:THR147 4.5 46.1 1.0
CD B:LYS148 4.6 46.3 1.0
CB D:LYS65 4.7 49.2 1.0
CD D:PRO62 4.8 50.9 1.0
O D:PRO62 4.9 50.6 1.0
C D:PRO62 4.9 50.2 1.0
CG D:PRO62 4.9 51.3 1.0
N B:LYS148 4.9 41.1 1.0

Bromine binding site 6 out of 6 in 3qbk

Go back to Bromine Binding Sites List in 3qbk
Bromine binding site 6 out of 6 in the Bromide-Bound Form of Pharaonis Halorhodopsin


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Bromide-Bound Form of Pharaonis Halorhodopsin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br401

b:50.5
occ:1.00
 OG1 D:THR126 2.9 38.7 1.0
O D:HOH502 3.3 49.5 1.0
OG D:SER130 3.3 44.2 1.0
CB D:THR126 3.6 36.5 1.0
NZ D:LYS256 3.7 45.8 1.0
CE D:LYS256 3.7 48.7 1.0
CB D:SER130 3.8 40.9 1.0
CD1 D:TRP127 3.8 40.1 1.0
O D:THR126 3.9 33.4 1.0
C D:THR126 3.9 34.2 1.0
CB D:SER81 3.9 38.9 1.0
O D:HOH504 4.1 46.3 1.0
OG D:SER81 4.1 36.7 1.0
CA D:SER78 4.2 43.5 1.0
N D:TRP127 4.2 33.9 1.0
CG1 D:VAL77 4.2 40.0 1.0
O D:VAL77 4.4 40.8 1.0
CA D:THR126 4.4 35.8 1.0
N D:SER78 4.4 41.4 1.0
NE1 D:TRP127 4.5 40.6 1.0
C D:VAL77 4.5 40.4 1.0
CA D:TRP127 4.5 35.2 1.0
O D:HOH503 4.6 38.1 1.0
CB D:SER78 4.7 42.9 1.0
C15 D:RET292 4.7 46.7 1.0
OG D:SER78 4.7 44.0 1.0
CG2 D:THR126 4.8 33.4 1.0
CB D:VAL77 4.9 39.5 1.0
CG D:TRP127 4.9 40.9 1.0
O D:ARG123 5.0 43.5 1.0

Reference:

S.Kanada, Y.Takeguchi, M.Murakami, K.Ihara, T.Kouyama. Crystal Structures of An O-Like Blue Form and An Anion-Free Yellow Form of Pharaonis Halorhodopsin J.Mol.Biol. V. 413 162 2011.
ISSN: ISSN 0022-2836
PubMed: 21871461
DOI: 10.1016/J.JMB.2011.08.021
Page generated: Mon Jul 7 05:50:15 2025

Last articles

Br in 7EVU
Br in 7F30
Br in 7EOT
Br in 7EX4
Br in 7EUW
Br in 7EJC
Br in 7END
Br in 7ECK
Br in 7ECL
Br in 7EN9
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy