Bromine in PDB 5wc8: Structure of A Bacterial Polysialyltransferase at 2.75 Angstrom Resolution
Protein crystallography data
The structure of Structure of A Bacterial Polysialyltransferase at 2.75 Angstrom Resolution, PDB code: 5wc8
was solved by
L.J.Worrall,
C.Lizak,
N.C.J.Strynadka,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
61.76 /
2.75
|
Space group
|
P 31 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
78.080,
78.080,
303.290,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
19 /
24.2
|
Bromine Binding Sites:
Bromine binding site 1 out
of 36 in 5wc8
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Bromine Binding Sites List in 5wc8
Bromine binding site 1 out
of 36 in the Structure of A Bacterial Polysialyltransferase at 2.75 Angstrom Resolution
 Mono view
 Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 1 of Structure of A Bacterial Polysialyltransferase at 2.75 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Br501
b:68.4
occ:0.67
|
NZ
|
M:LYS118
|
2.5
|
88.3
|
1.0
|
NZ
|
M:LYS114
|
3.7
|
65.2
|
1.0
|
CE
|
M:LYS118
|
3.7
|
92.7
|
1.0
|
CE
|
M:LYS114
|
3.8
|
66.3
|
1.0
|
CD
|
M:LYS118
|
5.0
|
80.2
|
1.0
|
|
Bromine binding site 2 out
of 36 in 5wc8
Go back to
Bromine Binding Sites List in 5wc8
Bromine binding site 2 out
of 36 in the Structure of A Bacterial Polysialyltransferase at 2.75 Angstrom Resolution
 Mono view
 Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 2 of Structure of A Bacterial Polysialyltransferase at 2.75 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Br502
b:66.2
occ:0.66
|
CG
|
M:GLU213
|
3.3
|
97.7
|
1.0
|
CB
|
M:GLU213
|
3.4
|
84.1
|
1.0
|
N
|
M:GLU213
|
3.4
|
69.4
|
1.0
|
CA
|
M:PHE211
|
3.5
|
60.2
|
1.0
|
C
|
M:PHE211
|
3.6
|
59.4
|
1.0
|
CD
|
M:PRO212
|
3.7
|
60.0
|
1.0
|
N
|
M:PRO212
|
3.7
|
59.1
|
1.0
|
CB
|
M:PHE211
|
3.8
|
62.7
|
1.0
|
CA
|
M:GLU213
|
4.0
|
71.8
|
1.0
|
O
|
M:PHE211
|
4.3
|
59.1
|
1.0
|
CD1
|
M:PHE211
|
4.4
|
61.9
|
1.0
|
C
|
M:PRO212
|
4.4
|
66.5
|
1.0
|
CA
|
M:PRO212
|
4.6
|
60.2
|
1.0
|
CG
|
M:PHE211
|
4.6
|
62.9
|
1.0
|
CD
|
M:GLU213
|
4.7
|
0.4
|
1.0
|
O
|
M:ALA210
|
4.7
|
59.3
|
1.0
|
N
|
M:LYS214
|
4.7
|
64.8
|
1.0
|
N
|
M:PHE211
|
4.8
|
62.5
|
1.0
|
CG
|
M:PRO212
|
4.8
|
59.1
|
1.0
|
C
|
M:GLU213
|
4.8
|
66.9
|
1.0
|
CB
|
M:PRO212
|
5.0
|
58.8
|
1.0
|
|
Bromine binding site 3 out
of 36 in 5wc8
Go back to
Bromine Binding Sites List in 5wc8
Bromine binding site 3 out
of 36 in the Structure of A Bacterial Polysialyltransferase at 2.75 Angstrom Resolution
 Mono view
 Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 3 of Structure of A Bacterial Polysialyltransferase at 2.75 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Br503
b:53.1
occ:0.52
|
CA
|
M:SER97
|
3.4
|
61.2
|
1.0
|
N
|
M:MET99
|
3.4
|
47.6
|
1.0
|
C
|
M:SER97
|
3.5
|
54.1
|
1.0
|
N
|
M:PRO98
|
3.5
|
47.9
|
1.0
|
CD
|
M:PRO98
|
3.5
|
49.3
|
1.0
|
CB
|
M:MET99
|
3.6
|
52.9
|
1.0
|
CG
|
M:MET99
|
3.8
|
59.9
|
1.0
|
CA
|
M:MET99
|
4.0
|
50.4
|
1.0
|
CB
|
M:SER97
|
4.0
|
59.8
|
1.0
|
O
|
M:SER97
|
4.1
|
53.3
|
1.0
|
CG
|
M:PRO98
|
4.4
|
48.1
|
1.0
|
OG
|
M:SER97
|
4.4
|
59.6
|
1.0
|
C
|
M:PRO98
|
4.4
|
45.2
|
1.0
|
N
|
M:ARG100
|
4.4
|
55.2
|
1.0
|
CA
|
M:PRO98
|
4.5
|
48.2
|
1.0
|
N
|
M:SER97
|
4.5
|
60.0
|
1.0
|
C
|
M:MET99
|
4.6
|
50.9
|
1.0
|
CG
|
M:ARG100
|
4.8
|
89.5
|
1.0
|
|
Bromine binding site 4 out
of 36 in 5wc8
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Bromine Binding Sites List in 5wc8
Bromine binding site 4 out
of 36 in the Structure of A Bacterial Polysialyltransferase at 2.75 Angstrom Resolution
 Mono view
 Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 4 of Structure of A Bacterial Polysialyltransferase at 2.75 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Br504
b:67.5
occ:0.58
|
OG1
|
M:THR67
|
3.1
|
55.8
|
1.0
|
N
|
M:SER97
|
3.7
|
60.0
|
1.0
|
CG2
|
M:THR67
|
3.8
|
52.8
|
1.0
|
CB
|
M:THR67
|
3.8
|
55.1
|
1.0
|
CB
|
M:ALA69
|
4.0
|
62.3
|
1.0
|
CD
|
M:PRO98
|
4.2
|
49.3
|
1.0
|
CA
|
M:SER97
|
4.3
|
61.2
|
1.0
|
CG
|
M:LYS96
|
4.6
|
97.3
|
1.0
|
CA
|
M:LYS96
|
4.6
|
75.5
|
1.0
|
C
|
M:LYS96
|
4.7
|
66.9
|
1.0
|
OG
|
M:SER97
|
4.9
|
59.6
|
1.0
|
|
Bromine binding site 5 out
of 36 in 5wc8
Go back to
Bromine Binding Sites List in 5wc8
Bromine binding site 5 out
of 36 in the Structure of A Bacterial Polysialyltransferase at 2.75 Angstrom Resolution
 Mono view
 Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 5 of Structure of A Bacterial Polysialyltransferase at 2.75 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Br505
b:59.8
occ:0.59
|
N
|
M:LYS58
|
3.5
|
73.2
|
1.0
|
ND2
|
M:ASN35
|
3.5
|
51.9
|
1.0
|
CA
|
M:LEU57
|
3.9
|
77.9
|
1.0
|
O
|
M:LYS58
|
3.9
|
64.9
|
1.0
|
CD2
|
M:LEU57
|
4.1
|
74.4
|
1.0
|
CG2
|
M:THR34
|
4.1
|
67.7
|
1.0
|
C
|
M:LEU57
|
4.2
|
77.2
|
1.0
|
CA
|
M:LYS58
|
4.3
|
79.8
|
1.0
|
CB
|
M:LYS58
|
4.4
|
85.6
|
1.0
|
CG
|
M:ASN35
|
4.4
|
56.6
|
1.0
|
CB
|
M:LEU57
|
4.4
|
78.7
|
1.0
|
OD1
|
M:ASN35
|
4.5
|
55.7
|
1.0
|
C
|
M:LYS58
|
4.6
|
75.3
|
1.0
|
O
|
M:LYS56
|
4.6
|
81.0
|
1.0
|
CB
|
M:THR34
|
4.7
|
65.8
|
1.0
|
CG
|
M:LEU57
|
4.9
|
76.6
|
1.0
|
|
Bromine binding site 6 out
of 36 in 5wc8
Go back to
Bromine Binding Sites List in 5wc8
Bromine binding site 6 out
of 36 in the Structure of A Bacterial Polysialyltransferase at 2.75 Angstrom Resolution
 Mono view
 Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 6 of Structure of A Bacterial Polysialyltransferase at 2.75 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Br506
b:57.2
occ:0.52
|
O
|
M:HOH618
|
3.0
|
51.3
|
1.0
|
NE2
|
M:HIS133
|
3.2
|
40.8
|
1.0
|
OH
|
M:TYR134
|
3.4
|
47.9
|
1.0
|
CG
|
M:PRO98
|
3.7
|
48.1
|
1.0
|
CE2
|
M:TYR134
|
3.8
|
43.4
|
1.0
|
CE1
|
M:HIS133
|
4.0
|
44.8
|
1.0
|
CZ
|
M:TYR134
|
4.0
|
44.2
|
1.0
|
SD
|
M:MET99
|
4.2
|
63.2
|
1.0
|
CD2
|
M:HIS133
|
4.3
|
39.1
|
1.0
|
CG
|
M:MET99
|
4.4
|
59.9
|
1.0
|
CB
|
M:PRO98
|
4.6
|
49.6
|
1.0
|
CD1
|
M:LEU94
|
4.6
|
55.2
|
1.0
|
CD
|
M:PRO98
|
4.8
|
49.3
|
1.0
|
CB
|
M:SER40
|
4.8
|
52.6
|
1.0
|
CD2
|
M:TYR134
|
5.0
|
41.8
|
1.0
|
|
Bromine binding site 7 out
of 36 in 5wc8
Go back to
Bromine Binding Sites List in 5wc8
Bromine binding site 7 out
of 36 in the Structure of A Bacterial Polysialyltransferase at 2.75 Angstrom Resolution
 Mono view
 Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 7 of Structure of A Bacterial Polysialyltransferase at 2.75 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Br507
b:57.8
occ:0.48
|
N
|
M:ARG259
|
3.3
|
49.7
|
1.0
|
CD2
|
M:HIS291
|
3.7
|
67.9
|
1.0
|
CA
|
M:GLN258
|
3.8
|
42.9
|
1.0
|
CB
|
M:GLN258
|
3.9
|
40.5
|
1.0
|
C
|
M:GLN258
|
4.1
|
44.9
|
1.0
|
O
|
M:ARG259
|
4.1
|
46.5
|
1.0
|
CB
|
M:ARG259
|
4.2
|
64.9
|
1.0
|
CA
|
M:ARG259
|
4.2
|
55.3
|
1.0
|
CG
|
M:GLN258
|
4.2
|
40.9
|
1.0
|
NE
|
M:ARG259
|
4.3
|
95.5
|
1.0
|
NE2
|
M:HIS291
|
4.5
|
71.8
|
1.0
|
CG
|
M:ARG259
|
4.6
|
72.4
|
1.0
|
CG
|
M:HIS291
|
4.6
|
63.7
|
1.0
|
C
|
M:ARG259
|
4.7
|
51.1
|
1.0
|
NH1
|
M:ARG259
|
4.8
|
99.1
|
1.0
|
|
Bromine binding site 8 out
of 36 in 5wc8
Go back to
Bromine Binding Sites List in 5wc8
Bromine binding site 8 out
of 36 in the Structure of A Bacterial Polysialyltransferase at 2.75 Angstrom Resolution
 Mono view
 Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 8 of Structure of A Bacterial Polysialyltransferase at 2.75 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Br508
b:49.5
occ:0.36
|
OG
|
M:SER269
|
3.1
|
57.3
|
1.0
|
CG
|
M:GLU266
|
3.9
|
65.0
|
1.0
|
CA
|
M:GLU266
|
4.0
|
59.6
|
1.0
|
CB
|
M:SER269
|
4.0
|
51.6
|
1.0
|
CG
|
M:ARG265
|
4.1
|
86.0
|
1.0
|
CD
|
M:LYS368
|
4.1
|
56.4
|
1.0
|
O
|
M:ARG265
|
4.1
|
58.5
|
1.0
|
N
|
M:GLU266
|
4.3
|
58.8
|
1.0
|
C
|
M:ARG265
|
4.3
|
60.8
|
1.0
|
NZ
|
M:LYS368
|
4.4
|
64.3
|
1.0
|
CB
|
M:GLU266
|
4.5
|
60.4
|
1.0
|
CD
|
M:GLU266
|
4.7
|
66.0
|
1.0
|
CE
|
M:LYS368
|
4.7
|
58.4
|
1.0
|
CD
|
M:ARG265
|
4.9
|
93.0
|
1.0
|
CB
|
M:ARG265
|
4.9
|
72.4
|
1.0
|
|
Bromine binding site 9 out
of 36 in 5wc8
Go back to
Bromine Binding Sites List in 5wc8
Bromine binding site 9 out
of 36 in the Structure of A Bacterial Polysialyltransferase at 2.75 Angstrom Resolution
 Mono view
 Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 9 of Structure of A Bacterial Polysialyltransferase at 2.75 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Br509
b:73.4
occ:0.35
|
O
|
M:HOH609
|
2.4
|
49.7
|
1.0
|
NH1
|
M:ARG332
|
3.4
|
99.3
|
1.0
|
NZ
|
M:LYS251
|
3.5
|
99.3
|
1.0
|
NH2
|
M:ARG332
|
3.7
|
0.4
|
1.0
|
CZ
|
M:ARG332
|
3.7
|
0.6
|
1.0
|
CE
|
M:LYS251
|
4.3
|
0.7
|
1.0
|
NE
|
M:ARG332
|
4.7
|
0.1
|
1.0
|
|
Bromine binding site 10 out
of 36 in 5wc8
Go back to
Bromine Binding Sites List in 5wc8
Bromine binding site 10 out
of 36 in the Structure of A Bacterial Polysialyltransferase at 2.75 Angstrom Resolution
 Mono view
 Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 10 of Structure of A Bacterial Polysialyltransferase at 2.75 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Br510
b:95.0
occ:0.78
|
N
|
M:LYS96
|
3.3
|
70.3
|
1.0
|
CA
|
M:PRO95
|
3.6
|
54.9
|
1.0
|
C
|
M:PRO95
|
3.9
|
61.5
|
1.0
|
CB
|
M:PRO95
|
4.1
|
54.2
|
1.0
|
CB
|
M:LYS96
|
4.2
|
83.8
|
1.0
|
CA
|
M:LYS96
|
4.3
|
75.5
|
1.0
|
CD
|
M:LYS96
|
4.7
|
98.8
|
1.0
|
CG
|
M:LYS96
|
4.8
|
97.3
|
1.0
|
O
|
M:LEU94
|
4.8
|
64.1
|
1.0
|
N
|
M:PRO95
|
4.8
|
50.6
|
1.0
|
|
Reference:
C.Lizak,
L.J.Worrall,
L.Baumann,
M.M.Pfleiderer,
G.Volkers,
T.Sun,
L.Sim,
W.Wakarchuk,
S.G.Withers,
N.C.J.Strynadka.
X-Ray Crystallographic Structure of A Bacterial Polysialyltransferase Provides Insight Into the Biosynthesis of Capsular Polysialic Acid. Sci Rep V. 7 5842 2017.
ISSN: ESSN 2045-2322
PubMed: 28724897
DOI: 10.1038/S41598-017-05627-Z
Page generated: Thu Jul 11 01:15:29 2024
|