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Bromine in PDB 6vhq: Crystal Structure of Bacillus Subtilis Levansucrase (D86A/E342A) in Complex with Oligosaccharides

Protein crystallography data

The structure of Crystal Structure of Bacillus Subtilis Levansucrase (D86A/E342A) in Complex with Oligosaccharides, PDB code: 6vhq was solved by A.Diaz-Vilchis, E.Raga-Carbajal, S.Rojas-Trejo, C.Olvera, E.Rudino-Pinera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.21 / 2.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 69.313, 78.665, 78.732, 90, 93.94, 90
R / Rfree (%) 16.7 / 23.5

Other elements in 6vhq:

The structure of Crystal Structure of Bacillus Subtilis Levansucrase (D86A/E342A) in Complex with Oligosaccharides also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Bromine Binding Sites:

The binding sites of Bromine atom in the Crystal Structure of Bacillus Subtilis Levansucrase (D86A/E342A) in Complex with Oligosaccharides (pdb code 6vhq). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 9 binding sites of Bromine where determined in the Crystal Structure of Bacillus Subtilis Levansucrase (D86A/E342A) in Complex with Oligosaccharides, PDB code: 6vhq:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Bromine binding site 1 out of 9 in 6vhq

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Bromine binding site 1 out of 9 in the Crystal Structure of Bacillus Subtilis Levansucrase (D86A/E342A) in Complex with Oligosaccharides


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of Bacillus Subtilis Levansucrase (D86A/E342A) in Complex with Oligosaccharides within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br502

b:25.6
occ:0.72
 N A:GLU275 3.4 22.7 1.0
O A:HOH800 3.4 29.8 1.0
N A:GLU274 3.4 20.7 1.0
CB A:GLU275 3.6 27.1 1.0
CA A:GLY273 3.7 19.4 1.0
BR A:BR506 3.7 38.5 0.5
C A:GLY273 3.8 18.3 1.0
CA A:GLU275 4.1 15.8 1.0
CA A:GLU274 4.3 21.1 1.0
C A:GLU274 4.3 20.2 1.0
O A:GLN272 4.5 17.8 1.0
CB A:GLU274 4.6 23.2 1.0
O A:GLY273 4.7 21.9 1.0
N A:GLY273 4.9 22.1 1.0
CG A:GLU275 4.9 20.6 1.0

Bromine binding site 2 out of 9 in 6vhq

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Bromine binding site 2 out of 9 in the Crystal Structure of Bacillus Subtilis Levansucrase (D86A/E342A) in Complex with Oligosaccharides


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 Bacillus Subtilis Levansucrase (D86A/E342A) in Complex with Oligosaccharides within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br503

b:24.5
occ:0.74
 NE2 A:GLN230 3.5 13.6 1.0
CG2 A:THR267 3.7 17.6 1.0
CG A:GLN230 3.9 16.2 1.0
O A:HOH794 4.1 28.1 1.0
CD A:GLN230 4.2 17.7 1.0
CE2 A:TYR271 4.3 18.5 1.0
CB A:GLN230 4.7 18.9 1.0
OH A:TYR271 4.7 16.1 1.0
CZ A:TYR271 4.9 15.9 1.0

Bromine binding site 3 out of 9 in 6vhq

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Bromine binding site 3 out of 9 in the Crystal Structure of Bacillus Subtilis Levansucrase (D86A/E342A) in Complex with Oligosaccharides


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 Bacillus Subtilis Levansucrase (D86A/E342A) in Complex with Oligosaccharides within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br504

b:23.0
occ:0.67
 O4 D:FRU3 3.1 39.9 1.0
OG1 A:THR160 3.1 17.2 1.0
NE2 A:GLN161 3.4 15.2 1.0
CB A:THR160 3.6 23.8 1.0
C4 D:FRU3 3.9 52.9 1.0
CA A:GLY184 3.9 18.8 1.0
CG A:ASP117 4.1 31.6 1.0
CB A:ASP117 4.1 30.4 1.0
O3 D:FRU3 4.2 49.6 1.0
CE1 A:PHE182 4.2 15.6 1.0
N A:GLY184 4.3 18.2 1.0
CG A:GLN161 4.3 14.9 1.0
OD2 A:ASP117 4.3 46.3 1.0
CD A:GLN161 4.3 15.2 1.0
CG2 A:THR160 4.4 23.9 1.0
O1 C:FRU3 4.4 41.7 1.0
OD1 A:ASP117 4.4 32.6 1.0
C3 D:FRU3 4.5 44.4 1.0
O A:THR160 4.7 14.7 1.0
CD1 A:PHE182 4.8 13.7 1.0
C A:THR160 4.8 14.8 1.0
CA A:THR160 4.9 13.7 1.0
O A:ASP117 4.9 19.6 1.0

Bromine binding site 4 out of 9 in 6vhq

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Bromine binding site 4 out of 9 in the Crystal Structure of Bacillus Subtilis Levansucrase (D86A/E342A) in Complex with Oligosaccharides


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 Bacillus Subtilis Levansucrase (D86A/E342A) in Complex with Oligosaccharides within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br505

b:25.4
occ:1.00
 N A:ASP438 3.3 17.0 1.0
CB A:ASP438 3.6 26.5 1.0
CA A:ASP438 3.9 19.9 1.0
N A:ALA437 4.0 18.6 1.0
CD2 A:TYR436 4.0 38.5 1.0
CB A:TYR436 4.0 17.8 1.0
O A:HOH702 4.0 37.4 1.0
N A:LYS439 4.3 16.8 1.0
C A:ALA437 4.3 16.1 1.0
C A:ASP438 4.4 24.1 1.0
CB A:ALA437 4.4 18.3 1.0
CG A:LYS439 4.4 24.5 1.0
CG A:ASP438 4.4 26.5 1.0
CA A:ALA437 4.5 19.1 1.0
C A:TYR436 4.5 21.2 1.0
CG A:TYR436 4.5 27.2 1.0
CA A:TYR436 4.6 18.6 1.0
CD A:LYS439 4.6 34.8 1.0
CE A:LYS439 4.7 34.6 1.0
OD2 A:ASP438 4.7 31.8 1.0

Bromine binding site 5 out of 9 in 6vhq

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Bromine binding site 5 out of 9 in the Crystal Structure of Bacillus Subtilis Levansucrase (D86A/E342A) in Complex with Oligosaccharides


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 Bacillus Subtilis Levansucrase (D86A/E342A) in Complex with Oligosaccharides within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br506

b:38.5
occ:0.53
 O A:HOH690 2.9 47.2 1.0
N A:GLU274 3.2 20.7 1.0
BR A:BR502 3.7 25.6 0.7
NH1 A:ARG304 3.7 27.1 1.0
CB A:GLU274 3.8 23.2 1.0
CA A:GLY273 3.9 19.4 1.0
C A:GLY273 4.1 18.3 1.0
CA A:GLU274 4.1 21.1 1.0
O A:HOH865 4.2 33.5 1.0
CZ A:ARG304 4.7 29.8 1.0
NH2 A:ARG304 4.8 26.6 1.0
OE1 A:GLU307 4.8 21.3 1.0

Bromine binding site 6 out of 9 in 6vhq

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Bromine binding site 6 out of 9 in the Crystal Structure of Bacillus Subtilis Levansucrase (D86A/E342A) in Complex with Oligosaccharides


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 Bacillus Subtilis Levansucrase (D86A/E342A) in Complex with Oligosaccharides within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br507

b:79.4
occ:1.00
 N A:ASP145 2.9 18.6 1.0
O A:HOH842 3.1 16.0 1.0
CB A:LYS144 3.4 24.4 1.0
CA A:LYS144 3.5 20.5 1.0
CG A:ASP145 3.7 29.3 1.0
C A:LYS144 3.7 15.9 1.0
OD1 A:ASP145 3.7 29.5 1.0
CB A:ASP145 3.7 31.2 1.0
CA A:ASP145 3.9 21.7 1.0
NH2 A:ARG141 3.9 48.4 1.0
NH1 A:ARG141 4.1 39.4 1.0
OD2 A:ASP145 4.3 35.1 1.0
CZ A:ARG141 4.5 49.3 1.0
CG A:LYS144 4.9 27.4 1.0
N A:LYS144 4.9 19.9 1.0
N A:SER146 4.9 19.2 1.0
O A:LYS144 5.0 15.2 1.0

Bromine binding site 7 out of 9 in 6vhq

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Bromine binding site 7 out of 9 in the Crystal Structure of Bacillus Subtilis Levansucrase (D86A/E342A) in Complex with Oligosaccharides


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 Bacillus Subtilis Levansucrase (D86A/E342A) in Complex with Oligosaccharides within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br502

b:45.5
occ:0.63
 O B:HOH831 2.2 29.6 1.0
NZ B:LYS399 3.1 36.0 1.0
O A:HOH818 3.1 36.0 1.0
NE2 B:GLN64 3.8 28.8 1.0
CA B:LYS59 4.0 29.8 1.0
CE B:LYS399 4.0 23.6 1.0
CG B:LYS59 4.0 28.5 1.0
OD2 B:ASP401 4.1 29.7 1.0
O A:LYS452 4.2 35.0 1.0
CA A:GLY453 4.3 27.3 1.0
C A:LYS452 4.3 28.5 1.0
N A:GLY453 4.3 37.7 1.0
O B:GLN58 4.4 24.9 1.0
CB B:LYS59 4.5 24.3 1.0
N B:LYS59 4.6 25.6 1.0
CG B:GLN58 4.7 27.6 1.0
C B:GLN58 4.7 30.2 1.0
O B:HOH657 4.7 35.3 1.0
O B:HOH624 4.8 37.4 1.0
CB A:LYS452 4.8 40.1 1.0
CE A:LYS452 4.8 55.9 1.0
CD B:GLN64 5.0 36.3 1.0

Bromine binding site 8 out of 9 in 6vhq

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Bromine binding site 8 out of 9 in the Crystal Structure of Bacillus Subtilis Levansucrase (D86A/E342A) in Complex with Oligosaccharides


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 Bacillus Subtilis Levansucrase (D86A/E342A) in Complex with Oligosaccharides within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br503

b:38.4
occ:0.67
 OG1 B:THR160 2.9 23.9 1.0
O B:HOH846 3.0 52.7 1.0
NE2 B:GLN161 3.3 26.0 1.0
CB B:THR160 3.7 25.7 1.0
CG B:ASP117 4.1 67.7 1.0
CA B:GLY184 4.1 23.5 1.0
CE2 B:PHE182 4.1 25.4 1.0
OD2 B:ASP117 4.1 66.2 1.0
CB B:ASP117 4.2 54.2 1.0
CG B:GLN161 4.2 23.1 1.0
CD B:GLN161 4.3 27.8 1.0
N B:GLY184 4.3 29.9 1.0
OD1 B:ASP117 4.5 62.0 1.0
O B:ASP117 4.6 48.8 1.0
CG2 B:THR160 4.6 31.2 1.0
CD2 B:PHE182 4.6 21.8 1.0
O B:THR160 4.7 25.6 1.0
C B:THR160 4.8 29.8 1.0
CA B:THR160 4.9 22.3 1.0
CA B:ASP117 5.0 55.0 1.0

Bromine binding site 9 out of 9 in 6vhq

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Bromine binding site 9 out of 9 in the Crystal Structure of Bacillus Subtilis Levansucrase (D86A/E342A) in Complex with Oligosaccharides


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 9 of Crystal Structure of Bacillus Subtilis Levansucrase (D86A/E342A) in Complex with Oligosaccharides within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br504

b:34.9
occ:0.53
 O B:HOH841 2.7 38.8 1.0
N B:LYS329 3.4 18.5 1.0
CB B:MET328 3.6 15.1 1.0
CA B:MET328 3.7 21.7 1.0
CG B:LYS329 3.9 25.4 1.0
C B:MET328 4.0 20.1 1.0
CG B:MET328 4.1 24.5 1.0
O B:HOH644 4.3 22.6 1.0
CE B:MET328 4.3 23.6 1.0
CB B:LYS329 4.4 22.2 1.0
CA B:LYS329 4.5 19.9 1.0
CD B:LYS329 4.5 40.2 1.0
CE B:LYS329 4.6 35.7 1.0
O B:VAL327 4.8 22.8 1.0
N B:MET328 5.0 20.1 1.0

Reference:

E.Raga-Carbajal, A.Diaz-Vilchis, S.Rojas-Trejo, E.Rudino-Pinera, C.Olvera. Crystal Structure of Bacillus Subtilis Levansucrase in Complex with Oligosaccharides To Be Published.
Page generated: Thu Jul 11 03:01:38 2024

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