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:
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
Go back to
Bromine Binding Sites List in 6vhq
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 Sites List in 6vhq
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
Go back to
Bromine Binding Sites List in 6vhq
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 Sites List in 6vhq
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 Sites List in 6vhq
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 Sites List in 6vhq
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
Go back to
Bromine Binding Sites List in 6vhq
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
Go back to
Bromine Binding Sites List in 6vhq
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
Go back to
Bromine Binding Sites List in 6vhq
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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