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Bromine in PDB 4lsi: Ion Selectivity of Ompf Porin Soaked in 0.3M Kbr

Protein crystallography data

The structure of Ion Selectivity of Ompf Porin Soaked in 0.3M Kbr, PDB code: 4lsi was solved by D.Balasundaresan, L.Blachowicz, B.Roux, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.74 / 2.09
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 202.094, 116.559, 53.592, 90.00, 97.00, 90.00
R / Rfree (%) 19 / 24.5

Other elements in 4lsi:

The structure of Ion Selectivity of Ompf Porin Soaked in 0.3M Kbr also contains other interesting chemical elements:

Magnesium (Mg) 8 atoms

Bromine Binding Sites:

The binding sites of Bromine atom in the Ion Selectivity of Ompf Porin Soaked in 0.3M Kbr (pdb code 4lsi). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 9 binding sites of Bromine where determined in the Ion Selectivity of Ompf Porin Soaked in 0.3M Kbr, PDB code: 4lsi:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Bromine binding site 1 out of 9 in 4lsi

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Bromine binding site 1 out of 9 in the Ion Selectivity of Ompf Porin Soaked in 0.3M Kbr


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Ion Selectivity of Ompf Porin Soaked in 0.3M Kbr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br408

b:40.8
occ:0.61
 O A:HOH599 3.3 35.6 1.0
N A:SER125 3.5 24.1 1.0
NH2 A:ARG167 3.5 24.8 1.0
O A:HOH513 3.8 43.5 1.0
CA A:TYR124 3.9 28.5 1.0
OG A:SER125 4.1 36.0 1.0
CB A:TYR124 4.2 29.1 1.0
C A:TYR124 4.2 27.1 1.0
CD1 A:TYR124 4.2 30.0 1.0
CB A:SER125 4.3 31.0 1.0
O1 A:PEG401 4.3 50.9 1.0
CA A:SER125 4.4 27.2 1.0
O A:SER125 4.6 26.0 1.0
CG A:TYR124 4.7 28.6 1.0
C1 A:PEG401 4.7 55.8 1.0
CZ A:ARG167 4.9 25.9 1.0
O B:HOH540 4.9 30.5 1.0

Bromine binding site 2 out of 9 in 4lsi

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Bromine binding site 2 out of 9 in the Ion Selectivity of Ompf Porin Soaked in 0.3M Kbr


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Ion Selectivity of Ompf Porin Soaked in 0.3M Kbr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br409

b:33.9
occ:0.45
 O A:HOH514 3.1 36.4 1.0
O A:HOH646 3.3 47.1 1.0
CD A:LYS16 3.7 32.5 1.0
CG A:LYS16 3.8 28.8 1.0
CD1 A:TYR14 3.9 29.6 1.0
CE1 A:TYR14 4.1 32.1 1.0
C A:GLY15 4.1 26.9 1.0
CB A:ARG42 4.2 27.9 1.0
CE A:LYS16 4.2 35.2 1.0
O A:GLY15 4.3 27.2 1.0
CA A:GLY15 4.3 27.5 1.0
CB A:LYS16 4.3 25.0 1.0
N A:LYS16 4.4 23.0 1.0
O A:HOH558 4.5 54.7 1.0
N A:GLY15 4.6 25.1 1.0
CG A:ARG42 4.6 26.6 1.0
NZ A:LYS16 4.8 38.4 1.0

Bromine binding site 3 out of 9 in 4lsi

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Bromine binding site 3 out of 9 in the Ion Selectivity of Ompf Porin Soaked in 0.3M Kbr


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Ion Selectivity of Ompf Porin Soaked in 0.3M Kbr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br410

b:23.1
occ:0.01
 N A:GLY103 1.8 24.2 1.0
CA A:GLY103 2.0 24.1 1.0
O A:GLY103 2.3 20.2 1.0
C A:GLY103 2.4 21.4 1.0
O A:GLY131 2.7 24.9 1.0
C A:TYR102 2.9 26.2 1.0
O A:PHE129 2.9 25.3 1.0
N A:GLY131 3.2 25.7 1.0
C A:GLY131 3.3 24.7 1.0
CB A:TYR106 3.3 25.8 1.0
C A:VAL130 3.5 25.0 1.0
CA A:TYR102 3.5 26.7 1.0
CA A:GLY131 3.5 23.2 1.0
C A:PHE129 3.6 26.3 1.0
N A:VAL104 3.6 23.3 1.0
O A:TYR102 3.8 20.7 1.0
CB A:TYR102 3.9 25.5 1.0
O A:VAL130 3.9 28.4 1.0
N A:TYR106 4.0 23.7 1.0
N A:VAL130 4.0 27.5 1.0
CA A:VAL130 4.1 29.7 1.0
O A:HOH625 4.2 31.1 1.0
CA A:TYR106 4.3 23.2 1.0
N A:ARG132 4.3 25.9 1.0
CG A:TYR106 4.4 26.7 1.0
CD1 A:TYR102 4.5 28.5 1.0
CA A:PHE129 4.6 27.6 1.0
CA A:VAL104 4.7 26.4 1.0
CG A:TYR102 4.7 27.6 1.0
N A:VAL105 4.8 26.5 1.0
C A:VAL104 4.8 26.7 1.0
O A:HOH501 4.8 25.9 1.0
N A:TYR102 4.9 25.8 1.0
CA A:ARG132 4.9 25.1 1.0

Bromine binding site 4 out of 9 in 4lsi

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Bromine binding site 4 out of 9 in the Ion Selectivity of Ompf Porin Soaked in 0.3M Kbr


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Ion Selectivity of Ompf Porin Soaked in 0.3M Kbr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br411

b:81.9
occ:0.21
 CA A:LEU115 1.8 32.8 1.0
NE2 A:GLN262 2.5 27.6 1.0
CB A:LEU115 2.6 34.9 1.0
O A:MET114 2.6 25.7 1.0
N A:LEU115 2.6 29.1 1.0
CD A:PRO116 2.7 31.3 1.0
C A:LEU115 2.8 31.6 1.0
C A:MET114 2.9 31.5 1.0
CD2 A:LEU115 2.9 37.0 1.0
N A:PRO116 3.1 30.9 1.0
CG A:LEU115 3.2 35.5 1.0
OG A:SER272 3.2 32.6 1.0
CD A:GLN262 3.8 31.9 1.0
CB A:SER272 3.8 33.0 1.0
O A:LEU115 3.9 30.4 1.0
CG A:PRO116 4.1 31.7 1.0
CA A:MET114 4.3 29.0 1.0
CD1 A:LEU115 4.4 39.2 1.0
OE2 A:GLU296 4.4 29.7 1.0
O A:HOH511 4.5 40.2 1.0
CA A:PRO116 4.5 28.9 1.0
OE1 A:GLN262 4.6 31.1 1.0
CB A:MET114 4.7 32.7 1.0
CG A:GLN262 4.7 32.2 1.0
OE1 A:GLU296 4.8 26.7 1.0
N A:MET114 4.9 30.0 1.0
CD A:GLU296 4.9 28.2 1.0

Bromine binding site 5 out of 9 in 4lsi

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Bromine binding site 5 out of 9 in the Ion Selectivity of Ompf Porin Soaked in 0.3M Kbr


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Ion Selectivity of Ompf Porin Soaked in 0.3M Kbr within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br409

b:42.2
occ:0.62
 O B:HOH518 3.1 32.0 1.0
CD1 B:TYR14 3.7 27.7 1.0
CD B:LYS16 3.8 35.7 1.0
CG B:LYS16 3.8 31.3 1.0
CE1 B:TYR14 3.9 30.2 1.0
C B:GLY15 4.0 27.0 1.0
CA B:GLY15 4.1 26.6 1.0
CB B:ARG42 4.2 27.1 1.0
CE B:LYS16 4.2 38.4 1.0
CB B:LYS16 4.2 26.9 1.0
O B:GLY15 4.3 25.2 1.0
N B:LYS16 4.4 24.4 1.0
CG B:ARG42 4.6 26.6 1.0
N B:GLY15 4.6 25.7 1.0
NZ B:LYS16 4.8 39.4 1.0
CA B:LYS16 5.0 24.9 1.0
O B:HOH630 5.0 50.7 1.0

Bromine binding site 6 out of 9 in 4lsi

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Bromine binding site 6 out of 9 in the Ion Selectivity of Ompf Porin Soaked in 0.3M Kbr


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Ion Selectivity of Ompf Porin Soaked in 0.3M Kbr within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br410

b:37.8
occ:0.56
 O B:HOH605 3.4 35.5 1.0
N B:SER125 3.4 22.8 1.0
NH2 B:ARG167 3.6 30.6 1.0
CA B:TYR124 3.9 25.3 1.0
OG B:SER125 3.9 27.2 1.0
C B:TYR124 4.2 23.3 1.0
CB B:SER125 4.2 24.7 1.0
CB B:TYR124 4.3 25.0 1.0
CA B:SER125 4.3 25.1 1.0
CD1 B:TYR124 4.4 31.2 1.0
O B:SER125 4.4 25.7 1.0
O C:HOH560 4.8 36.4 1.0
CG B:TYR124 4.8 26.0 1.0
CZ B:ARG167 4.8 28.1 1.0
C B:SER125 4.9 24.3 1.0

Bromine binding site 7 out of 9 in 4lsi

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Bromine binding site 7 out of 9 in the Ion Selectivity of Ompf Porin Soaked in 0.3M Kbr


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of Ion Selectivity of Ompf Porin Soaked in 0.3M Kbr within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br411

b:72.1
occ:0.23
 O B:ILE51 3.2 34.0 1.0
C B:ILE51 4.3 35.1 1.0
CB C:ASN304 4.5 30.7 1.0
O C:PHE303 4.5 35.3 1.0
CA B:ILE51 4.7 33.0 1.0
O B:HOH666 4.8 52.1 1.0
ND2 C:ASN304 4.9 27.3 1.0

Bromine binding site 8 out of 9 in 4lsi

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Bromine binding site 8 out of 9 in the Ion Selectivity of Ompf Porin Soaked in 0.3M Kbr


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of Ion Selectivity of Ompf Porin Soaked in 0.3M Kbr within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br410

b:40.4
occ:0.61
 O C:HOH506 3.0 31.0 1.0
O C:HOH600 3.0 42.0 1.0
O C:HOH613 3.6 53.4 1.0
CD C:LYS16 3.7 32.2 1.0
CE C:LYS16 3.8 36.6 1.0
CD1 C:TYR14 3.9 24.6 1.0
CG C:LYS16 3.9 30.9 1.0
CE1 C:TYR14 4.0 25.2 1.0
CB C:ARG42 4.1 25.1 1.0
C C:GLY15 4.2 27.4 1.0
CA C:GLY15 4.2 29.1 1.0
N C:LYS16 4.4 26.1 1.0
CB C:LYS16 4.5 25.1 1.0
O C:GLY15 4.5 28.7 1.0
CG C:ARG42 4.6 24.6 1.0
NZ C:LYS16 4.7 38.3 1.0
N C:GLY15 4.7 27.5 1.0

Bromine binding site 9 out of 9 in 4lsi

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Bromine binding site 9 out of 9 in the Ion Selectivity of Ompf Porin Soaked in 0.3M Kbr


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 9 of Ion Selectivity of Ompf Porin Soaked in 0.3M Kbr within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br411

b:34.7
occ:0.57
 O C:HOH595 3.4 36.6 1.0
N C:SER125 3.5 22.7 1.0
NH2 C:ARG167 3.5 29.2 1.0
CA C:TYR124 3.9 25.2 1.0
O1 C:PEG408 4.1 58.6 1.0
OG C:SER125 4.1 29.6 1.0
CB C:SER125 4.2 25.1 1.0
C C:TYR124 4.2 23.8 1.0
CD1 C:TYR124 4.2 28.9 1.0
CB C:TYR124 4.3 25.6 1.0
CA C:SER125 4.3 23.7 1.0
O C:SER125 4.5 23.1 1.0
CG C:TYR124 4.7 24.8 1.0
O A:HOH521 4.8 30.1 1.0
CZ C:ARG167 4.8 29.7 1.0
C1 C:PEG408 4.9 61.7 1.0
C C:SER125 4.9 24.2 1.0

Reference:

B.Dhakshnamoorthy, B.K.Ziervogel, L.Blachowicz, B.Roux. A Structural Study of Ion Permeation in Ompf Porin From Anomalous X-Ray Diffraction and Molecular Dynamics Simulations. J.Am.Chem.Soc. V. 135 16561 2013.
ISSN: ISSN 0002-7863
PubMed: 24106986
DOI: 10.1021/JA407783A
Page generated: Sat Dec 12 02:21:19 2020

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