Bromine in PDB 6pky: Guinea Pig N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) Catalytic Domain Auto-Inhibited By Pro- Peptide
Protein crystallography data
The structure of Guinea Pig N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) Catalytic Domain Auto-Inhibited By Pro- Peptide, PDB code: 6pky
was solved by
A.Gorelik,
K.Illes,
B.Nagar,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
47.23 /
3.00
|
Space group
|
P 41
|
Cell size a, b, c (Å), α, β, γ (°)
|
72.622,
72.622,
240.691,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
21.3 /
25.8
|
Other elements in 6pky:
The structure of Guinea Pig N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) Catalytic Domain Auto-Inhibited By Pro- Peptide also contains other interesting chemical elements:
Bromine Binding Sites:
The binding sites of Bromine atom in the Guinea Pig N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) Catalytic Domain Auto-Inhibited By Pro- Peptide
(pdb code 6pky). This binding sites where shown within
5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the
Guinea Pig N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) Catalytic Domain Auto-Inhibited By Pro- Peptide, PDB code: 6pky:
Jump to Bromine binding site number:
1;
2;
3;
4;
Bromine binding site 1 out
of 4 in 6pky
Go back to
Bromine Binding Sites List in 6pky
Bromine binding site 1 out
of 4 in the Guinea Pig N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) Catalytic Domain Auto-Inhibited By Pro- Peptide
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 1 of Guinea Pig N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) Catalytic Domain Auto-Inhibited By Pro- Peptide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Br402
b:70.7
occ:1.00
|
H
|
A:ARG44
|
2.2
|
62.2
|
1.0
|
HD3
|
A:ARG44
|
2.9
|
56.1
|
1.0
|
HB2
|
A:ARG44
|
3.0
|
63.7
|
1.0
|
N
|
A:ARG44
|
3.1
|
51.8
|
1.0
|
HA
|
A:ALA43
|
3.1
|
62.7
|
1.0
|
HD13
|
A:LEU149
|
3.2
|
86.8
|
1.0
|
CB
|
A:ARG44
|
3.7
|
53.1
|
1.0
|
HG3
|
A:ARG44
|
3.7
|
53.0
|
1.0
|
CD
|
A:ARG44
|
3.7
|
46.8
|
1.0
|
HD1
|
A:TYR40
|
3.8
|
62.8
|
1.0
|
CA
|
A:ARG44
|
3.9
|
44.3
|
1.0
|
CG
|
A:ARG44
|
3.9
|
44.2
|
1.0
|
CD1
|
A:LEU149
|
3.9
|
72.3
|
1.0
|
CA
|
A:ALA43
|
3.9
|
52.3
|
1.0
|
HD11
|
A:LEU149
|
4.0
|
86.8
|
1.0
|
C
|
A:ALA43
|
4.0
|
58.5
|
1.0
|
O
|
A:ARG44
|
4.1
|
54.9
|
1.0
|
HB1
|
A:ALA43
|
4.1
|
57.3
|
1.0
|
HD12
|
A:LEU149
|
4.1
|
86.8
|
1.0
|
HE
|
A:ARG44
|
4.1
|
54.8
|
1.0
|
HB2
|
A:TYR40
|
4.2
|
51.8
|
1.0
|
NE
|
A:ARG44
|
4.4
|
45.7
|
1.0
|
HD2
|
A:ARG44
|
4.4
|
56.1
|
1.0
|
C
|
A:ARG44
|
4.4
|
50.5
|
1.0
|
CD1
|
A:TYR40
|
4.5
|
52.4
|
1.0
|
CB
|
A:ALA43
|
4.5
|
47.8
|
1.0
|
HB3
|
A:ARG44
|
4.5
|
63.7
|
1.0
|
HE
|
A:ARG142
|
4.5
|
80.6
|
1.0
|
HA
|
A:ARG44
|
4.7
|
53.1
|
1.0
|
O
|
A:ARG42
|
4.8
|
66.4
|
1.0
|
HB2
|
A:ALA43
|
4.8
|
57.3
|
1.0
|
HG2
|
A:ARG44
|
4.9
|
53.0
|
1.0
|
O
|
A:HOH506
|
4.9
|
35.3
|
1.0
|
|
Bromine binding site 2 out
of 4 in 6pky
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Bromine Binding Sites List in 6pky
Bromine binding site 2 out
of 4 in the Guinea Pig N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) Catalytic Domain Auto-Inhibited By Pro- Peptide
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 2 of Guinea Pig N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) Catalytic Domain Auto-Inhibited By Pro- Peptide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Br404
b:75.2
occ:1.00
|
HH21
|
B:ARG44
|
2.3
|
83.2
|
1.0
|
HE
|
B:ARG44
|
2.7
|
88.0
|
1.0
|
HD1
|
B:TYR40
|
2.7
|
77.6
|
1.0
|
NH2
|
B:ARG44
|
3.1
|
69.4
|
1.0
|
NE
|
B:ARG44
|
3.3
|
73.4
|
1.0
|
HB2
|
B:TYR40
|
3.4
|
89.2
|
1.0
|
H
|
B:ARG44
|
3.4
|
97.2
|
1.0
|
CD1
|
B:TYR40
|
3.5
|
64.7
|
1.0
|
HA
|
B:ALA43
|
3.5
|
92.4
|
1.0
|
HD13
|
B:LEU149
|
3.6
|
61.6
|
1.0
|
CZ
|
B:ARG44
|
3.6
|
71.3
|
1.0
|
HH22
|
B:ARG44
|
3.7
|
83.2
|
1.0
|
HE
|
B:ARG142
|
3.8
|
51.8
|
1.0
|
HH21
|
B:ARG142
|
4.2
|
81.5
|
1.0
|
CB
|
B:TYR40
|
4.2
|
74.4
|
1.0
|
HE1
|
B:TYR40
|
4.3
|
85.3
|
1.0
|
N
|
B:ARG44
|
4.3
|
81.0
|
1.0
|
CG
|
B:TYR40
|
4.3
|
67.8
|
1.0
|
HD11
|
B:LEU149
|
4.3
|
61.6
|
1.0
|
CE1
|
B:TYR40
|
4.3
|
71.1
|
1.0
|
CD1
|
B:LEU149
|
4.4
|
51.4
|
1.0
|
HG3
|
B:ARG44
|
4.5
|
99.7
|
1.0
|
HB2
|
B:ARG44
|
4.5
|
95.7
|
1.0
|
CA
|
B:ALA43
|
4.5
|
77.0
|
1.0
|
O
|
B:TYR40
|
4.5
|
87.3
|
1.0
|
CD
|
B:ARG44
|
4.6
|
74.0
|
1.0
|
NE
|
B:ARG142
|
4.6
|
43.2
|
1.0
|
HD12
|
B:LEU149
|
4.7
|
61.6
|
1.0
|
HB3
|
B:TYR40
|
4.8
|
89.2
|
1.0
|
HD3
|
B:ARG44
|
4.8
|
88.8
|
1.0
|
HB1
|
B:ALA43
|
4.9
|
90.4
|
1.0
|
NH2
|
B:ARG142
|
4.9
|
68.0
|
1.0
|
H
|
B:TYR40
|
4.9
|
85.0
|
1.0
|
NH1
|
B:ARG44
|
4.9
|
63.7
|
1.0
|
CG
|
B:ARG44
|
4.9
|
83.1
|
1.0
|
O
|
B:ARG42
|
4.9
|
78.2
|
1.0
|
C
|
B:ALA43
|
5.0
|
81.2
|
1.0
|
|
Bromine binding site 3 out
of 4 in 6pky
Go back to
Bromine Binding Sites List in 6pky
Bromine binding site 3 out
of 4 in the Guinea Pig N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) Catalytic Domain Auto-Inhibited By Pro- Peptide
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 3 of Guinea Pig N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) Catalytic Domain Auto-Inhibited By Pro- Peptide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Br402
b:97.3
occ:1.00
|
HH21
|
C:ARG142
|
2.8
|
66.2
|
1.0
|
H
|
C:ARG44
|
3.1
|
91.1
|
1.0
|
HA
|
C:ALA43
|
3.1
|
60.2
|
1.0
|
HB1
|
C:ALA43
|
3.1
|
71.9
|
1.0
|
HD13
|
C:LEU149
|
3.2
|
78.9
|
1.0
|
NH2
|
C:ARG142
|
3.4
|
55.2
|
1.0
|
HG2
|
C:ARG44
|
3.5
|
90.2
|
1.0
|
N
|
C:ARG44
|
3.6
|
75.9
|
1.0
|
HH22
|
C:ARG142
|
3.7
|
66.2
|
1.0
|
O
|
C:ARG44
|
3.7
|
80.9
|
1.0
|
HD22
|
C:LEU149
|
3.7
|
72.7
|
1.0
|
CA
|
C:ALA43
|
3.7
|
50.2
|
1.0
|
CB
|
C:ALA43
|
3.8
|
60.0
|
1.0
|
HD11
|
C:LEU149
|
3.9
|
78.9
|
1.0
|
CD1
|
C:LEU149
|
4.0
|
65.8
|
1.0
|
HB2
|
C:ALA43
|
4.0
|
71.9
|
1.0
|
C
|
C:ALA43
|
4.1
|
64.5
|
1.0
|
HD2
|
C:TYR40
|
4.2
|
66.0
|
1.0
|
HG3
|
C:ARG44
|
4.2
|
90.2
|
1.0
|
HE
|
C:ARG142
|
4.2
|
70.4
|
1.0
|
CG
|
C:ARG44
|
4.3
|
75.2
|
1.0
|
HD21
|
C:LEU149
|
4.3
|
72.7
|
1.0
|
CD2
|
C:LEU149
|
4.4
|
60.6
|
1.0
|
CZ
|
C:ARG142
|
4.4
|
65.9
|
1.0
|
C
|
C:ARG44
|
4.5
|
81.3
|
1.0
|
CA
|
C:ARG44
|
4.5
|
75.8
|
1.0
|
HB3
|
C:ALA43
|
4.6
|
71.9
|
1.0
|
HD12
|
C:LEU149
|
4.6
|
78.9
|
1.0
|
NE
|
C:ARG142
|
4.7
|
58.7
|
1.0
|
HB2
|
C:TYR40
|
4.7
|
69.0
|
1.0
|
HE
|
C:ARG44
|
4.8
|
76.5
|
1.0
|
CG
|
C:LEU149
|
4.8
|
60.5
|
1.0
|
O
|
C:HOH516
|
4.8
|
33.9
|
1.0
|
HB3
|
C:LEU149
|
4.9
|
68.3
|
1.0
|
CD2
|
C:TYR40
|
4.9
|
55.0
|
1.0
|
CB
|
C:ARG44
|
5.0
|
75.5
|
1.0
|
|
Bromine binding site 4 out
of 4 in 6pky
Go back to
Bromine Binding Sites List in 6pky
Bromine binding site 4 out
of 4 in the Guinea Pig N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) Catalytic Domain Auto-Inhibited By Pro- Peptide
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 4 of Guinea Pig N-Acetylglucosamine-1-Phosphodiester Alpha-N- Acetylglucosaminidase (Nagpa) Catalytic Domain Auto-Inhibited By Pro- Peptide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Br401
b:1.0
occ:1.00
|
HH21
|
D:ARG44
|
2.9
|
75.0
|
1.0
|
O
|
D:HOH533
|
2.9
|
33.7
|
1.0
|
HD2
|
D:TYR40
|
3.1
|
89.6
|
1.0
|
HE
|
D:ARG44
|
3.2
|
77.2
|
1.0
|
HA
|
D:ALA43
|
3.3
|
82.1
|
1.0
|
HD13
|
D:LEU149
|
3.3
|
40.1
|
1.0
|
HB2
|
D:TYR40
|
3.3
|
80.0
|
1.0
|
H
|
D:ARG44
|
3.6
|
87.7
|
1.0
|
NH2
|
D:ARG44
|
3.6
|
62.6
|
1.0
|
NE
|
D:ARG44
|
3.9
|
64.3
|
1.0
|
CD2
|
D:TYR40
|
4.0
|
74.7
|
1.0
|
HD11
|
D:LEU149
|
4.0
|
40.1
|
1.0
|
O
|
D:TYR40
|
4.0
|
69.6
|
1.0
|
CD1
|
D:LEU149
|
4.0
|
33.5
|
1.0
|
CZ
|
D:ARG44
|
4.2
|
57.2
|
1.0
|
HH21
|
D:ARG46
|
4.2
|
30.8
|
1.0
|
CB
|
D:TYR40
|
4.2
|
66.7
|
1.0
|
CA
|
D:ALA43
|
4.2
|
68.4
|
1.0
|
HH22
|
D:ARG44
|
4.2
|
75.0
|
1.0
|
HE
|
D:ARG142
|
4.3
|
58.5
|
1.0
|
N
|
D:ARG44
|
4.4
|
73.1
|
1.0
|
HD12
|
D:LEU149
|
4.5
|
40.1
|
1.0
|
CG
|
D:TYR40
|
4.6
|
74.7
|
1.0
|
HB1
|
D:ALA43
|
4.6
|
72.0
|
1.0
|
H
|
D:TYR40
|
4.7
|
77.8
|
1.0
|
HD22
|
D:LEU149
|
4.7
|
48.0
|
1.0
|
HB2
|
D:ALA43
|
4.7
|
72.0
|
1.0
|
HD21
|
D:LEU149
|
4.7
|
48.0
|
1.0
|
HG3
|
D:ARG44
|
4.7
|
86.4
|
1.0
|
HB3
|
D:TYR40
|
4.8
|
80.0
|
1.0
|
O
|
D:ARG42
|
4.8
|
76.2
|
1.0
|
CB
|
D:ALA43
|
4.8
|
60.0
|
1.0
|
C
|
D:ALA43
|
4.9
|
71.8
|
1.0
|
C
|
D:TYR40
|
4.9
|
65.2
|
1.0
|
HB2
|
D:ARG44
|
4.9
|
74.7
|
1.0
|
HE2
|
D:TYR40
|
4.9
|
83.7
|
1.0
|
CE2
|
D:TYR40
|
4.9
|
69.8
|
1.0
|
NH2
|
D:ARG46
|
5.0
|
25.7
|
1.0
|
CL
|
D:CL405
|
5.0
|
17.0
|
1.0
|
|
Reference:
A.Gorelik,
K.Illes,
B.Nagar.
Guinea Pig N-Acetylglucosamine-1-Phosphodiester Alpha-N-Acetylglucosaminidase (Nagpa) Catalytic Domain Auto-Inhibited By Pro-Peptide To Be Published.
Page generated: Thu Jul 11 02:24:09 2024
|