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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: Sat Dec 12 02:14:50 2020

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