Bromine in PDB 4p5a: Crystal Structure of A Ump/Dump Methylase Polb From Streptomyces Cacaoi Bound with 5-Br Ump
Enzymatic activity of Crystal Structure of A Ump/Dump Methylase Polb From Streptomyces Cacaoi Bound with 5-Br Ump
All present enzymatic activity of Crystal Structure of A Ump/Dump Methylase Polb From Streptomyces Cacaoi Bound with 5-Br Ump:
2.1.1.148;
Protein crystallography data
The structure of Crystal Structure of A Ump/Dump Methylase Polb From Streptomyces Cacaoi Bound with 5-Br Ump, PDB code: 4p5a
was solved by
Y.Li,
W.Chen,
J.Li,
Z.Xia,
Z.Deng,
J.Zhou,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
50.00 /
1.76
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
62.897,
94.160,
91.948,
90.00,
98.30,
90.00
|
R / Rfree (%)
|
15.4 /
19.3
|
Bromine Binding Sites:
The binding sites of Bromine atom in the Crystal Structure of A Ump/Dump Methylase Polb From Streptomyces Cacaoi Bound with 5-Br Ump
(pdb code 4p5a). This binding sites where shown within
5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the
Crystal Structure of A Ump/Dump Methylase Polb From Streptomyces Cacaoi Bound with 5-Br Ump, PDB code: 4p5a:
Jump to Bromine binding site number:
1;
2;
3;
4;
Bromine binding site 1 out
of 4 in 4p5a
Go back to
Bromine Binding Sites List in 4p5a
Bromine binding site 1 out
of 4 in the Crystal Structure of A Ump/Dump Methylase Polb From Streptomyces Cacaoi Bound with 5-Br Ump
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 A Ump/Dump Methylase Polb From Streptomyces Cacaoi Bound with 5-Br Ump within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Br302
b:17.4
occ:1.00
|
BR
|
A:5BU302
|
0.0
|
17.4
|
1.0
|
C5
|
A:5BU302
|
1.9
|
11.3
|
1.0
|
C6
|
A:5BU302
|
2.8
|
12.0
|
1.0
|
C4
|
A:5BU302
|
2.9
|
15.0
|
1.0
|
O4
|
A:5BU302
|
3.1
|
16.8
|
1.0
|
OH
|
B:TYR124
|
3.3
|
32.7
|
1.0
|
N5
|
B:FAD302
|
3.3
|
14.5
|
1.0
|
OG
|
A:SER96
|
3.3
|
15.2
|
1.0
|
C5X
|
B:FAD302
|
3.6
|
16.9
|
1.0
|
C6
|
B:FAD302
|
3.6
|
16.5
|
1.0
|
CD
|
A:ARG98
|
3.6
|
12.2
|
1.0
|
OP2
|
A:5BU302
|
3.6
|
15.2
|
1.0
|
NH1
|
A:ARG98
|
3.8
|
13.6
|
1.0
|
CZ
|
B:TYR124
|
3.9
|
31.2
|
1.0
|
C4X
|
B:FAD302
|
4.0
|
12.5
|
1.0
|
CB
|
A:ARG98
|
4.0
|
14.0
|
1.0
|
CB
|
A:SER96
|
4.1
|
11.7
|
1.0
|
N1
|
A:5BU302
|
4.1
|
9.8
|
1.0
|
CG
|
A:ARG98
|
4.1
|
13.5
|
1.0
|
N3
|
A:5BU302
|
4.2
|
12.2
|
1.0
|
O4
|
B:FAD302
|
4.3
|
13.2
|
1.0
|
CE1
|
B:TYR124
|
4.4
|
34.9
|
1.0
|
C4
|
B:FAD302
|
4.4
|
12.1
|
1.0
|
C9A
|
B:FAD302
|
4.5
|
12.0
|
1.0
|
NE
|
A:ARG98
|
4.5
|
12.9
|
1.0
|
C7
|
B:FAD302
|
4.5
|
19.2
|
1.0
|
C2
|
A:5BU302
|
4.6
|
11.3
|
1.0
|
CZ
|
A:ARG98
|
4.6
|
15.2
|
1.0
|
CE2
|
B:TYR124
|
4.6
|
36.5
|
1.0
|
C10
|
B:FAD302
|
4.8
|
13.8
|
1.0
|
P
|
A:5BU302
|
4.9
|
13.4
|
1.0
|
|
Bromine binding site 2 out
of 4 in 4p5a
Go back to
Bromine Binding Sites List in 4p5a
Bromine binding site 2 out
of 4 in the Crystal Structure of A Ump/Dump Methylase Polb From Streptomyces Cacaoi Bound with 5-Br Ump
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 A Ump/Dump Methylase Polb From Streptomyces Cacaoi Bound with 5-Br Ump within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Br301
b:17.6
occ:1.00
|
BR
|
B:5BU301
|
0.0
|
17.6
|
1.0
|
C5
|
B:5BU301
|
1.9
|
14.0
|
1.0
|
C6
|
B:5BU301
|
2.8
|
11.9
|
1.0
|
C4
|
B:5BU301
|
2.8
|
17.4
|
1.0
|
O4
|
B:5BU301
|
3.1
|
17.5
|
1.0
|
OH
|
A:TYR124
|
3.2
|
28.3
|
1.0
|
N5
|
A:FAD301
|
3.3
|
14.5
|
1.0
|
OG
|
B:SER96
|
3.4
|
16.7
|
1.0
|
C5X
|
A:FAD301
|
3.6
|
16.0
|
1.0
|
C6
|
A:FAD301
|
3.6
|
16.4
|
1.0
|
CD
|
B:ARG98
|
3.6
|
11.1
|
1.0
|
OP3
|
B:5BU301
|
3.7
|
14.8
|
1.0
|
CZ
|
A:TYR124
|
3.7
|
27.1
|
1.0
|
O
|
A:HOH578
|
3.8
|
34.0
|
1.0
|
NH1
|
B:ARG98
|
3.9
|
9.8
|
1.0
|
CB
|
B:ARG98
|
4.0
|
13.3
|
1.0
|
C4X
|
A:FAD301
|
4.0
|
13.8
|
1.0
|
CB
|
B:SER96
|
4.1
|
15.2
|
1.0
|
N3
|
B:5BU301
|
4.1
|
10.9
|
1.0
|
CE1
|
A:TYR124
|
4.1
|
28.2
|
1.0
|
N1
|
B:5BU301
|
4.1
|
9.1
|
1.0
|
CG
|
B:ARG98
|
4.2
|
10.5
|
1.0
|
O4
|
A:FAD301
|
4.2
|
13.8
|
1.0
|
C4
|
A:FAD301
|
4.4
|
13.7
|
1.0
|
CE2
|
A:TYR124
|
4.5
|
29.9
|
1.0
|
C7
|
A:FAD301
|
4.5
|
14.0
|
1.0
|
C9A
|
A:FAD301
|
4.5
|
15.2
|
1.0
|
NE
|
B:ARG98
|
4.5
|
14.5
|
1.0
|
C2
|
B:5BU301
|
4.6
|
13.1
|
1.0
|
CZ
|
B:ARG98
|
4.6
|
12.9
|
1.0
|
C10
|
A:FAD301
|
4.9
|
10.6
|
1.0
|
P
|
B:5BU301
|
4.9
|
13.6
|
1.0
|
O5'
|
B:5BU301
|
5.0
|
12.6
|
1.0
|
|
Bromine binding site 3 out
of 4 in 4p5a
Go back to
Bromine Binding Sites List in 4p5a
Bromine binding site 3 out
of 4 in the Crystal Structure of A Ump/Dump Methylase Polb From Streptomyces Cacaoi Bound with 5-Br Ump
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 A Ump/Dump Methylase Polb From Streptomyces Cacaoi Bound with 5-Br Ump within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Br302
b:15.1
occ:1.00
|
BR
|
C:5BU302
|
0.0
|
15.1
|
1.0
|
C5
|
C:5BU302
|
1.9
|
10.4
|
1.0
|
C6
|
C:5BU302
|
2.8
|
11.9
|
1.0
|
C4
|
C:5BU302
|
2.9
|
12.6
|
1.0
|
O4
|
C:5BU302
|
3.1
|
15.0
|
1.0
|
OH
|
D:TYR124
|
3.2
|
29.6
|
1.0
|
OG
|
C:SER96
|
3.3
|
14.0
|
1.0
|
N5
|
D:FAD302
|
3.3
|
14.4
|
1.0
|
C6
|
D:FAD302
|
3.5
|
14.9
|
1.0
|
C5X
|
D:FAD302
|
3.5
|
15.4
|
1.0
|
OP1
|
C:5BU302
|
3.7
|
17.2
|
1.0
|
CD
|
C:ARG98
|
3.7
|
12.4
|
1.0
|
CZ
|
D:TYR124
|
3.8
|
30.0
|
1.0
|
NH1
|
C:ARG98
|
3.9
|
10.1
|
1.0
|
C4X
|
D:FAD302
|
4.0
|
10.9
|
1.0
|
CB
|
C:SER96
|
4.0
|
11.8
|
1.0
|
CB
|
C:ARG98
|
4.1
|
13.7
|
1.0
|
N1
|
C:5BU302
|
4.1
|
9.6
|
1.0
|
N3
|
C:5BU302
|
4.1
|
9.9
|
1.0
|
CG
|
C:ARG98
|
4.2
|
12.8
|
1.0
|
CE1
|
D:TYR124
|
4.2
|
26.8
|
1.0
|
O4
|
D:FAD302
|
4.2
|
11.9
|
1.0
|
C4
|
D:FAD302
|
4.4
|
13.0
|
1.0
|
C7
|
D:FAD302
|
4.5
|
16.5
|
1.0
|
C9A
|
D:FAD302
|
4.5
|
10.2
|
1.0
|
NE
|
C:ARG98
|
4.6
|
12.2
|
1.0
|
CE2
|
D:TYR124
|
4.6
|
29.3
|
1.0
|
CZ
|
C:ARG98
|
4.6
|
15.5
|
1.0
|
C2
|
C:5BU302
|
4.6
|
10.9
|
1.0
|
C10
|
D:FAD302
|
4.8
|
9.2
|
1.0
|
P
|
C:5BU302
|
4.9
|
12.5
|
1.0
|
|
Bromine binding site 4 out
of 4 in 4p5a
Go back to
Bromine Binding Sites List in 4p5a
Bromine binding site 4 out
of 4 in the Crystal Structure of A Ump/Dump Methylase Polb From Streptomyces Cacaoi Bound with 5-Br Ump
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 A Ump/Dump Methylase Polb From Streptomyces Cacaoi Bound with 5-Br Ump within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Br301
b:17.1
occ:1.00
|
BR
|
D:5BU301
|
0.0
|
17.1
|
1.0
|
C5
|
D:5BU301
|
2.0
|
10.0
|
1.0
|
C6
|
D:5BU301
|
2.8
|
14.9
|
1.0
|
C4
|
D:5BU301
|
2.9
|
13.2
|
1.0
|
O4
|
D:5BU301
|
3.0
|
15.1
|
1.0
|
OH
|
C:TYR124
|
3.3
|
28.4
|
1.0
|
N5
|
C:FAD301
|
3.3
|
12.9
|
1.0
|
OG
|
D:SER96
|
3.4
|
14.8
|
1.0
|
C5X
|
C:FAD301
|
3.5
|
13.0
|
1.0
|
C6
|
C:FAD301
|
3.5
|
13.8
|
1.0
|
CD
|
D:ARG98
|
3.7
|
11.3
|
1.0
|
OP1
|
D:5BU301
|
3.7
|
17.6
|
1.0
|
NH1
|
D:ARG98
|
3.8
|
11.9
|
1.0
|
CZ
|
C:TYR124
|
4.0
|
28.6
|
1.0
|
CB
|
D:ARG98
|
4.0
|
12.5
|
1.0
|
CB
|
D:SER96
|
4.1
|
16.5
|
1.0
|
C4X
|
C:FAD301
|
4.1
|
13.5
|
1.0
|
N1
|
D:5BU301
|
4.1
|
11.1
|
1.0
|
N3
|
D:5BU301
|
4.1
|
7.2
|
1.0
|
CG
|
D:ARG98
|
4.2
|
11.9
|
1.0
|
O4
|
C:FAD301
|
4.2
|
14.1
|
1.0
|
CE1
|
C:TYR124
|
4.4
|
25.4
|
1.0
|
C7
|
C:FAD301
|
4.4
|
12.3
|
1.0
|
C4
|
C:FAD301
|
4.5
|
13.6
|
1.0
|
NE
|
D:ARG98
|
4.6
|
15.2
|
1.0
|
C9A
|
C:FAD301
|
4.6
|
10.9
|
1.0
|
C2
|
D:5BU301
|
4.6
|
11.7
|
1.0
|
CZ
|
D:ARG98
|
4.6
|
16.6
|
1.0
|
P
|
D:5BU301
|
4.9
|
13.8
|
1.0
|
CE2
|
C:TYR124
|
5.0
|
25.7
|
1.0
|
C10
|
C:FAD301
|
5.0
|
9.1
|
1.0
|
|
Reference:
Y.Li,
W.Chen,
J.Li,
Z.Xia,
Z.Deng,
J.Zhou.
Crystal Structure of A Ump/Dump Methylase Polb From Streptomyces Cacaoi with 5-Br Ump To Be Published.
Page generated: Wed Jul 10 22:13:48 2024
|