Bromine in PDB 4my1: Crystal Structure of the Inosine 5'-Monophosphate Dehydrogenase, with A Internal Deletion of Cbs Domain From Bacillus Anthracis Str. Ames Complexed with P68
Enzymatic activity of Crystal Structure of the Inosine 5'-Monophosphate Dehydrogenase, with A Internal Deletion of Cbs Domain From Bacillus Anthracis Str. Ames Complexed with P68
All present enzymatic activity of Crystal Structure of the Inosine 5'-Monophosphate Dehydrogenase, with A Internal Deletion of Cbs Domain From Bacillus Anthracis Str. Ames Complexed with P68:
1.1.1.205;
Protein crystallography data
The structure of Crystal Structure of the Inosine 5'-Monophosphate Dehydrogenase, with A Internal Deletion of Cbs Domain From Bacillus Anthracis Str. Ames Complexed with P68, PDB code: 4my1
was solved by
Y.Kim,
M.Makowska-Grzyska,
M.Gu,
W.F.Anderson,
A.Joachimiak,
Csgid,
Centerfor Structural Genomics Of Infectious Diseases (Csgid),
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
36.25 /
2.60
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
83.220,
89.391,
103.987,
81.13,
89.95,
83.59
|
R / Rfree (%)
|
19.4 /
25.3
|
Bromine Binding Sites:
The binding sites of Bromine atom in the Crystal Structure of the Inosine 5'-Monophosphate Dehydrogenase, with A Internal Deletion of Cbs Domain From Bacillus Anthracis Str. Ames Complexed with P68
(pdb code 4my1). This binding sites where shown within
5.0 Angstroms radius around Bromine atom.
In total 8 binding sites of Bromine where determined in the
Crystal Structure of the Inosine 5'-Monophosphate Dehydrogenase, with A Internal Deletion of Cbs Domain From Bacillus Anthracis Str. Ames Complexed with P68, PDB code: 4my1:
Jump to Bromine binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Bromine binding site 1 out
of 8 in 4my1
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Bromine Binding Sites List in 4my1
Bromine binding site 1 out
of 8 in the Crystal Structure of the Inosine 5'-Monophosphate Dehydrogenase, with A Internal Deletion of Cbs Domain From Bacillus Anthracis Str. Ames Complexed with P68
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 the Inosine 5'-Monophosphate Dehydrogenase, with A Internal Deletion of Cbs Domain From Bacillus Anthracis Str. Ames Complexed with P68 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Br501
b:72.5
occ:0.45
|
BR1
|
A:P68501
|
0.0
|
72.5
|
0.5
|
C8
|
A:P68501
|
1.9
|
59.0
|
1.0
|
C9
|
A:P68501
|
2.8
|
59.0
|
1.0
|
C7
|
A:P68501
|
2.8
|
59.0
|
1.0
|
O
|
C:VAL25
|
3.7
|
66.5
|
1.0
|
O
|
C:GLY444
|
3.8
|
45.8
|
1.0
|
C
|
C:GLY444
|
3.8
|
45.0
|
1.0
|
CA
|
C:GLY444
|
3.9
|
44.2
|
1.0
|
CD
|
C:PRO27
|
3.9
|
60.7
|
1.0
|
C10
|
A:P68501
|
4.1
|
59.0
|
1.0
|
CD2
|
A:HIS254
|
4.1
|
50.5
|
1.0
|
C6
|
A:P68501
|
4.1
|
58.9
|
1.0
|
CB
|
A:HIS254
|
4.3
|
50.9
|
1.0
|
N
|
C:TYR445
|
4.4
|
45.0
|
1.0
|
CG
|
C:PRO27
|
4.4
|
58.9
|
1.0
|
OG
|
C:SER23
|
4.4
|
56.2
|
1.0
|
CG
|
A:HIS254
|
4.6
|
50.2
|
1.0
|
C5
|
A:P68501
|
4.6
|
59.0
|
1.0
|
CA
|
C:LEU26
|
4.7
|
66.1
|
1.0
|
C
|
C:VAL25
|
4.8
|
67.3
|
1.0
|
CB
|
C:SER23
|
4.9
|
57.0
|
1.0
|
OG
|
A:SER257
|
4.9
|
61.4
|
1.0
|
N
|
C:PRO27
|
4.9
|
60.1
|
1.0
|
|
Bromine binding site 2 out
of 8 in 4my1
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Bromine Binding Sites List in 4my1
Bromine binding site 2 out
of 8 in the Crystal Structure of the Inosine 5'-Monophosphate Dehydrogenase, with A Internal Deletion of Cbs Domain From Bacillus Anthracis Str. Ames Complexed with P68
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 the Inosine 5'-Monophosphate Dehydrogenase, with A Internal Deletion of Cbs Domain From Bacillus Anthracis Str. Ames Complexed with P68 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Br501
b:0.8
occ:1.00
|
BR1
|
B:P68501
|
0.0
|
0.8
|
1.0
|
C8
|
B:P68501
|
1.9
|
56.2
|
1.0
|
C9
|
B:P68501
|
2.8
|
56.1
|
1.0
|
C7
|
B:P68501
|
2.8
|
56.1
|
1.0
|
O
|
A:GLY444
|
3.6
|
50.1
|
1.0
|
C
|
A:GLY444
|
3.7
|
49.5
|
1.0
|
CB
|
B:HIS254
|
3.8
|
51.5
|
1.0
|
O
|
A:VAL25
|
3.9
|
69.4
|
1.0
|
CA
|
A:GLY444
|
3.9
|
49.7
|
1.0
|
CD
|
A:PRO27
|
4.0
|
60.8
|
1.0
|
CD2
|
B:HIS254
|
4.1
|
51.5
|
1.0
|
C10
|
B:P68501
|
4.1
|
56.0
|
1.0
|
C6
|
B:P68501
|
4.1
|
56.0
|
1.0
|
CG
|
B:HIS254
|
4.3
|
51.1
|
1.0
|
N
|
A:TYR445
|
4.4
|
48.8
|
1.0
|
OG
|
A:SER23
|
4.5
|
64.0
|
1.0
|
CG
|
A:PRO27
|
4.6
|
60.0
|
1.0
|
C5
|
B:P68501
|
4.6
|
56.0
|
1.0
|
CA
|
A:LEU26
|
4.6
|
64.3
|
1.0
|
CD2
|
A:LEU26
|
4.7
|
60.5
|
1.0
|
N
|
A:PRO27
|
4.9
|
61.6
|
1.0
|
C
|
A:VAL25
|
4.9
|
70.3
|
1.0
|
|
Bromine binding site 3 out
of 8 in 4my1
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Bromine Binding Sites List in 4my1
Bromine binding site 3 out
of 8 in the Crystal Structure of the Inosine 5'-Monophosphate Dehydrogenase, with A Internal Deletion of Cbs Domain From Bacillus Anthracis Str. Ames Complexed with P68
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 the Inosine 5'-Monophosphate Dehydrogenase, with A Internal Deletion of Cbs Domain From Bacillus Anthracis Str. Ames Complexed with P68 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Br501
b:0.1
occ:1.00
|
BR1
|
C:P68501
|
0.0
|
0.1
|
1.0
|
C8
|
C:P68501
|
1.9
|
55.6
|
1.0
|
C7
|
C:P68501
|
2.9
|
55.6
|
1.0
|
C9
|
C:P68501
|
2.9
|
55.6
|
1.0
|
O
|
D:GLY444
|
3.6
|
49.4
|
1.0
|
ND1
|
C:HIS254
|
3.7
|
54.5
|
1.0
|
C
|
D:GLY444
|
3.7
|
48.9
|
1.0
|
CB
|
C:HIS254
|
3.9
|
54.2
|
1.0
|
O
|
D:VAL25
|
4.0
|
60.2
|
1.0
|
CA
|
D:GLY444
|
4.0
|
48.8
|
1.0
|
C6
|
C:P68501
|
4.2
|
55.6
|
1.0
|
C10
|
C:P68501
|
4.2
|
55.6
|
1.0
|
OG
|
D:SER23
|
4.2
|
59.2
|
1.0
|
CG
|
C:HIS254
|
4.2
|
53.5
|
1.0
|
OG
|
C:SER257
|
4.3
|
62.0
|
1.0
|
N
|
D:TYR445
|
4.3
|
48.8
|
1.0
|
CD
|
D:PRO27
|
4.5
|
63.0
|
1.0
|
CD2
|
D:LEU26
|
4.5
|
60.9
|
1.0
|
C5
|
C:P68501
|
4.7
|
55.6
|
1.0
|
CB
|
D:SER23
|
4.7
|
59.2
|
1.0
|
CE1
|
C:HIS254
|
4.8
|
54.0
|
1.0
|
CB
|
C:SER257
|
4.8
|
59.9
|
1.0
|
CA
|
D:TYR445
|
4.8
|
49.2
|
1.0
|
CG
|
D:PRO27
|
4.9
|
62.6
|
1.0
|
CA
|
D:LEU26
|
4.9
|
61.5
|
1.0
|
|
Bromine binding site 4 out
of 8 in 4my1
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Bromine Binding Sites List in 4my1
Bromine binding site 4 out
of 8 in the Crystal Structure of the Inosine 5'-Monophosphate Dehydrogenase, with A Internal Deletion of Cbs Domain From Bacillus Anthracis Str. Ames Complexed with P68
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 the Inosine 5'-Monophosphate Dehydrogenase, with A Internal Deletion of Cbs Domain From Bacillus Anthracis Str. Ames Complexed with P68 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Br501
b:0.1
occ:1.00
|
BR1
|
D:P68501
|
0.0
|
0.1
|
1.0
|
C8
|
D:P68501
|
1.9
|
61.9
|
1.0
|
C9
|
D:P68501
|
2.8
|
61.9
|
1.0
|
C7
|
D:P68501
|
2.9
|
61.8
|
1.0
|
O
|
B:GLY444
|
3.8
|
49.5
|
1.0
|
O
|
B:VAL25
|
3.9
|
59.8
|
1.0
|
CB
|
D:HIS254
|
3.9
|
63.3
|
1.0
|
C
|
B:GLY444
|
4.0
|
49.0
|
1.0
|
CD2
|
D:HIS254
|
4.0
|
63.3
|
1.0
|
CD
|
B:PRO27
|
4.1
|
57.5
|
1.0
|
CA
|
B:GLY444
|
4.1
|
49.3
|
1.0
|
C10
|
D:P68501
|
4.1
|
61.8
|
1.0
|
C6
|
D:P68501
|
4.2
|
61.7
|
1.0
|
CG
|
D:HIS254
|
4.3
|
62.7
|
1.0
|
CD2
|
B:LEU26
|
4.4
|
65.7
|
1.0
|
OG
|
B:SER23
|
4.5
|
60.9
|
1.0
|
N
|
B:TYR445
|
4.6
|
48.1
|
1.0
|
C5
|
D:P68501
|
4.7
|
61.6
|
1.0
|
CA
|
B:LEU26
|
4.8
|
60.2
|
1.0
|
|
Bromine binding site 5 out
of 8 in 4my1
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Bromine Binding Sites List in 4my1
Bromine binding site 5 out
of 8 in the Crystal Structure of the Inosine 5'-Monophosphate Dehydrogenase, with A Internal Deletion of Cbs Domain From Bacillus Anthracis Str. Ames Complexed with P68
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 the Inosine 5'-Monophosphate Dehydrogenase, with A Internal Deletion of Cbs Domain From Bacillus Anthracis Str. Ames Complexed with P68 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Br502
b:0.8
occ:1.00
|
BR1
|
E:P68502
|
0.0
|
0.8
|
1.0
|
C8
|
E:P68502
|
1.9
|
68.6
|
1.0
|
C9
|
E:P68502
|
2.8
|
68.6
|
1.0
|
C7
|
E:P68502
|
2.8
|
68.6
|
1.0
|
CB
|
E:HIS254
|
3.6
|
63.0
|
1.0
|
ND1
|
E:HIS254
|
3.7
|
63.6
|
1.0
|
O
|
E:HOH606
|
4.0
|
46.6
|
1.0
|
CG
|
E:HIS254
|
4.1
|
62.5
|
1.0
|
C6
|
E:P68502
|
4.1
|
68.5
|
1.0
|
C10
|
E:P68502
|
4.1
|
68.5
|
1.0
|
C
|
G:GLY444
|
4.2
|
54.2
|
1.0
|
O
|
G:GLY444
|
4.2
|
55.2
|
1.0
|
CA
|
G:GLY444
|
4.3
|
53.7
|
1.0
|
O
|
G:VAL25
|
4.5
|
72.3
|
1.0
|
CD
|
G:PRO27
|
4.6
|
67.2
|
1.0
|
N
|
G:TYR445
|
4.6
|
53.8
|
1.0
|
C5
|
E:P68502
|
4.6
|
68.5
|
1.0
|
CG
|
G:PRO27
|
4.8
|
65.7
|
1.0
|
OG
|
E:SER257
|
4.9
|
82.9
|
1.0
|
CE1
|
E:HIS254
|
4.9
|
62.9
|
1.0
|
CA
|
E:HIS254
|
4.9
|
62.5
|
1.0
|
CB
|
E:SER257
|
4.9
|
80.3
|
1.0
|
|
Bromine binding site 6 out
of 8 in 4my1
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Bromine Binding Sites List in 4my1
Bromine binding site 6 out
of 8 in the Crystal Structure of the Inosine 5'-Monophosphate Dehydrogenase, with A Internal Deletion of Cbs Domain From Bacillus Anthracis Str. Ames Complexed with P68
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 the Inosine 5'-Monophosphate Dehydrogenase, with A Internal Deletion of Cbs Domain From Bacillus Anthracis Str. Ames Complexed with P68 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Br503
b:0.1
occ:1.00
|
BR1
|
E:P68503
|
0.0
|
0.1
|
1.0
|
C8
|
E:P68503
|
1.9
|
61.1
|
1.0
|
C9
|
E:P68503
|
2.9
|
61.1
|
1.0
|
C7
|
E:P68503
|
2.9
|
61.1
|
1.0
|
C
|
E:GLY444
|
3.4
|
63.8
|
1.0
|
O
|
E:GLY444
|
3.5
|
66.6
|
1.0
|
CA
|
E:GLY444
|
3.5
|
63.4
|
1.0
|
CD2
|
F:HIS254
|
3.8
|
57.0
|
1.0
|
O
|
E:VAL25
|
3.8
|
72.1
|
1.0
|
OG
|
E:SER23
|
3.9
|
79.4
|
1.0
|
N
|
E:TYR445
|
4.0
|
61.6
|
1.0
|
CB
|
F:HIS254
|
4.1
|
57.9
|
1.0
|
C10
|
E:P68503
|
4.2
|
61.2
|
1.0
|
C6
|
E:P68503
|
4.2
|
61.2
|
1.0
|
CG
|
F:HIS254
|
4.3
|
56.8
|
1.0
|
CD
|
E:PRO27
|
4.5
|
67.0
|
1.0
|
CB
|
E:SER23
|
4.5
|
79.1
|
1.0
|
CD2
|
E:LEU26
|
4.6
|
70.1
|
1.0
|
C5
|
E:P68503
|
4.7
|
61.3
|
1.0
|
CA
|
E:TYR445
|
4.7
|
62.6
|
1.0
|
CG
|
E:PRO27
|
4.9
|
65.8
|
1.0
|
N
|
E:GLY444
|
4.9
|
60.8
|
1.0
|
NE2
|
F:HIS254
|
5.0
|
56.9
|
1.0
|
C
|
E:VAL25
|
5.0
|
73.0
|
1.0
|
|
Bromine binding site 7 out
of 8 in 4my1
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Bromine Binding Sites List in 4my1
Bromine binding site 7 out
of 8 in the Crystal Structure of the Inosine 5'-Monophosphate Dehydrogenase, with A Internal Deletion of Cbs Domain From Bacillus Anthracis Str. Ames Complexed with P68
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 the Inosine 5'-Monophosphate Dehydrogenase, with A Internal Deletion of Cbs Domain From Bacillus Anthracis Str. Ames Complexed with P68 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Br501
b:0.6
occ:1.00
|
BR1
|
G:P68501
|
0.0
|
0.6
|
1.0
|
C8
|
G:P68501
|
1.9
|
60.3
|
1.0
|
C7
|
G:P68501
|
2.8
|
60.3
|
1.0
|
C9
|
G:P68501
|
2.9
|
60.3
|
1.0
|
CD2
|
G:HIS254
|
3.7
|
54.6
|
1.0
|
CB
|
G:HIS254
|
3.8
|
53.7
|
1.0
|
O
|
H:VAL25
|
3.9
|
67.9
|
1.0
|
O
|
H:GLY444
|
3.9
|
55.3
|
1.0
|
C
|
H:GLY444
|
3.9
|
54.0
|
1.0
|
CA
|
H:GLY444
|
4.1
|
53.6
|
1.0
|
CG
|
G:HIS254
|
4.1
|
54.0
|
1.0
|
C6
|
G:P68501
|
4.1
|
60.2
|
1.0
|
C10
|
G:P68501
|
4.1
|
60.2
|
1.0
|
OG
|
H:SER23
|
4.2
|
64.0
|
1.0
|
CD
|
H:PRO27
|
4.3
|
64.6
|
1.0
|
N
|
H:TYR445
|
4.5
|
53.1
|
1.0
|
CG
|
H:PRO27
|
4.6
|
63.2
|
1.0
|
CB
|
H:SER23
|
4.6
|
64.5
|
1.0
|
C5
|
G:P68501
|
4.7
|
60.1
|
1.0
|
CD2
|
H:LEU26
|
4.7
|
67.0
|
1.0
|
CB
|
G:SER257
|
5.0
|
68.2
|
1.0
|
C
|
H:VAL25
|
5.0
|
69.2
|
1.0
|
|
Bromine binding site 8 out
of 8 in 4my1
Go back to
Bromine Binding Sites List in 4my1
Bromine binding site 8 out
of 8 in the Crystal Structure of the Inosine 5'-Monophosphate Dehydrogenase, with A Internal Deletion of Cbs Domain From Bacillus Anthracis Str. Ames Complexed with P68
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 the Inosine 5'-Monophosphate Dehydrogenase, with A Internal Deletion of Cbs Domain From Bacillus Anthracis Str. Ames Complexed with P68 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Br501
b:0.6
occ:1.00
|
BR1
|
H:P68501
|
0.0
|
0.6
|
1.0
|
C8
|
H:P68501
|
1.9
|
56.2
|
1.0
|
C9
|
H:P68501
|
2.8
|
56.2
|
1.0
|
C7
|
H:P68501
|
2.9
|
56.2
|
1.0
|
C
|
F:GLY444
|
3.7
|
47.0
|
1.0
|
CA
|
F:GLY444
|
3.7
|
47.1
|
1.0
|
O
|
F:VAL25
|
3.7
|
58.6
|
1.0
|
CB
|
H:HIS254
|
3.8
|
53.0
|
1.0
|
O
|
F:GLY444
|
3.9
|
47.0
|
1.0
|
CD2
|
H:HIS254
|
3.9
|
49.6
|
1.0
|
CD
|
F:PRO27
|
3.9
|
55.8
|
1.0
|
C10
|
H:P68501
|
4.1
|
56.2
|
1.0
|
N
|
F:TYR445
|
4.1
|
47.0
|
1.0
|
CG
|
H:HIS254
|
4.1
|
50.5
|
1.0
|
C6
|
H:P68501
|
4.1
|
56.1
|
1.0
|
OG
|
F:SER23
|
4.5
|
58.9
|
1.0
|
CD2
|
F:LEU26
|
4.5
|
65.3
|
1.0
|
CA
|
F:LEU26
|
4.6
|
59.5
|
1.0
|
C5
|
H:P68501
|
4.6
|
56.1
|
1.0
|
C
|
F:VAL25
|
4.8
|
60.1
|
1.0
|
CB
|
F:SER23
|
4.9
|
58.7
|
1.0
|
CA
|
F:TYR445
|
4.9
|
47.0
|
1.0
|
N
|
F:PRO27
|
4.9
|
56.1
|
1.0
|
CG
|
F:PRO27
|
4.9
|
55.0
|
1.0
|
|
Reference:
Y.Kim,
M.Makowska-Grzyska,
M.Gu,
W.F.Anderson,
A.Joachimiak,
Csgid.
Crystal Structure of the Inosine 5'-Monophosphate Dehydrogenase, with A Internal Deletion of Cbs Domain From Bacillus Anthracis Str. Ames Complexed with P68 To Be Published 2013.
Page generated: Wed Jul 10 22:04:06 2024
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