Sodium in PDB 3fc3: Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I
Protein crystallography data
The structure of Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I, PDB code: 3fc3
was solved by
M.Sokolowska,
H.Czapinska,
M.Bochtler,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.71 /
1.75
|
Space group
|
H 3 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
90.089,
90.089,
334.254,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
18.1 /
20.5
|
Other elements in 3fc3:
The structure of Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I
(pdb code 3fc3). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the
Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I, PDB code: 3fc3:
Jump to Sodium binding site number:
1;
2;
3;
Sodium binding site 1 out
of 3 in 3fc3
Go back to
Sodium Binding Sites List in 3fc3
Sodium binding site 1 out
of 3 in the Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I
![](/pictures/NA/pdb/fc/3fc3-NA-sphere_01.jpg) Mono view
![](/pictures/NA/pdb/fc/3fc3-NA-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na305
b:26.8
occ:1.00
|
OD1
|
A:ASP148
|
2.2
|
22.4
|
1.0
|
OD1
|
A:ASN165
|
2.3
|
21.4
|
1.0
|
O
|
A:HOH439
|
2.4
|
23.1
|
1.0
|
OP1
|
C:DT3
|
2.4
|
27.9
|
0.5
|
O3'
|
D:DG2
|
2.5
|
20.5
|
0.5
|
O
|
A:HOH516
|
2.6
|
31.6
|
1.0
|
OP1
|
D:DA3
|
2.7
|
21.5
|
0.5
|
O3'
|
C:DG2
|
2.8
|
27.3
|
0.5
|
P
|
C:DT3
|
3.1
|
28.7
|
0.5
|
P
|
D:DA3
|
3.1
|
22.9
|
0.5
|
CG
|
A:ASP148
|
3.3
|
23.6
|
1.0
|
CG
|
A:ASN165
|
3.3
|
20.0
|
1.0
|
C3'
|
C:DG2
|
3.5
|
26.1
|
0.5
|
C3'
|
D:DG2
|
3.6
|
21.0
|
0.5
|
O5'
|
C:DT3
|
3.7
|
29.8
|
0.5
|
ND2
|
A:ASN165
|
3.8
|
20.6
|
1.0
|
C4'
|
C:DG2
|
3.9
|
24.7
|
0.5
|
O5'
|
D:DA3
|
3.9
|
23.4
|
0.5
|
C4'
|
D:DG2
|
3.9
|
21.1
|
0.5
|
NH2
|
A:ARG157
|
3.9
|
24.8
|
1.0
|
CB
|
A:ASP148
|
4.0
|
24.3
|
1.0
|
N
|
A:HIS149
|
4.1
|
23.8
|
1.0
|
CA
|
A:ASP148
|
4.1
|
24.1
|
1.0
|
O
|
A:HIS149
|
4.1
|
23.5
|
1.0
|
OD2
|
A:ASP148
|
4.3
|
21.5
|
1.0
|
OD2
|
A:ASP173
|
4.4
|
32.4
|
1.0
|
OP2
|
C:DT3
|
4.4
|
28.7
|
0.5
|
OP2
|
D:DA3
|
4.4
|
19.9
|
0.5
|
O
|
A:HOH515
|
4.6
|
36.3
|
1.0
|
C
|
A:ASP148
|
4.6
|
23.8
|
1.0
|
O
|
A:ASN165
|
4.6
|
20.3
|
1.0
|
CB
|
A:ASN165
|
4.6
|
17.9
|
1.0
|
CD1
|
A:LEU168
|
4.7
|
25.9
|
1.0
|
C5'
|
C:DG2
|
4.7
|
24.1
|
0.5
|
C5'
|
D:DG2
|
4.8
|
21.7
|
0.5
|
OD1
|
A:ASP173
|
4.9
|
32.7
|
1.0
|
C2'
|
D:DG2
|
4.9
|
19.4
|
0.5
|
O4'
|
D:DG2
|
4.9
|
20.0
|
0.5
|
CA
|
A:ASN165
|
4.9
|
18.9
|
1.0
|
O4'
|
C:DG2
|
4.9
|
24.9
|
0.5
|
C2'
|
C:DG2
|
5.0
|
25.7
|
0.5
|
|
Sodium binding site 2 out
of 3 in 3fc3
Go back to
Sodium Binding Sites List in 3fc3
Sodium binding site 2 out
of 3 in the Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I
![](/pictures/NA/pdb/fc/3fc3-NA-sphere_02.jpg) Mono view
![](/pictures/NA/pdb/fc/3fc3-NA-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na306
b:26.3
occ:1.00
|
OD1
|
B:ASP148
|
2.3
|
22.1
|
1.0
|
OD1
|
B:ASN165
|
2.3
|
21.7
|
1.0
|
O
|
B:HOH208
|
2.3
|
24.9
|
1.0
|
OP1
|
C:DT3
|
2.4
|
27.9
|
0.5
|
O3'
|
D:DG2
|
2.4
|
20.5
|
0.5
|
O
|
B:HOH466
|
2.5
|
27.3
|
1.0
|
OP1
|
D:DA3
|
2.6
|
21.5
|
0.5
|
O3'
|
C:DG2
|
2.7
|
27.3
|
0.5
|
P
|
C:DT3
|
3.0
|
28.7
|
0.5
|
P
|
D:DA3
|
3.1
|
22.9
|
0.5
|
CG
|
B:ASN165
|
3.3
|
18.8
|
1.0
|
CG
|
B:ASP148
|
3.4
|
24.1
|
1.0
|
C3'
|
C:DG2
|
3.5
|
26.1
|
0.5
|
C3'
|
D:DG2
|
3.6
|
21.0
|
0.5
|
O5'
|
C:DT3
|
3.7
|
29.8
|
0.5
|
ND2
|
B:ASN165
|
3.7
|
18.9
|
1.0
|
O5'
|
D:DA3
|
3.8
|
23.4
|
0.5
|
C4'
|
C:DG2
|
3.8
|
24.7
|
0.5
|
C4'
|
D:DG2
|
3.9
|
21.1
|
0.5
|
NH2
|
B:ARG157
|
4.0
|
23.9
|
1.0
|
CA
|
B:ASP148
|
4.1
|
23.8
|
1.0
|
CB
|
B:ASP148
|
4.1
|
23.5
|
1.0
|
N
|
B:HIS149
|
4.1
|
23.4
|
1.0
|
O
|
B:HIS149
|
4.1
|
22.5
|
1.0
|
OD2
|
B:ASP148
|
4.3
|
22.1
|
1.0
|
OP2
|
C:DT3
|
4.4
|
28.7
|
0.5
|
OP2
|
D:DA3
|
4.4
|
19.9
|
0.5
|
OD2
|
B:ASP173
|
4.4
|
30.9
|
1.0
|
O
|
C:HOH212
|
4.5
|
41.2
|
1.0
|
O
|
B:ASN165
|
4.6
|
20.2
|
1.0
|
CB
|
B:ASN165
|
4.6
|
19.6
|
1.0
|
C
|
B:ASP148
|
4.6
|
23.4
|
1.0
|
C5'
|
C:DG2
|
4.7
|
24.1
|
0.5
|
OD1
|
B:ASP173
|
4.8
|
28.9
|
1.0
|
C5'
|
D:DG2
|
4.8
|
21.7
|
0.5
|
CD1
|
B:LEU168
|
4.9
|
26.2
|
1.0
|
C2'
|
D:DG2
|
4.9
|
19.4
|
0.5
|
C2'
|
C:DG2
|
4.9
|
25.7
|
0.5
|
O4'
|
D:DG2
|
4.9
|
20.0
|
0.5
|
CA
|
B:ASN165
|
4.9
|
19.0
|
1.0
|
O4'
|
C:DG2
|
5.0
|
24.9
|
0.5
|
|
Sodium binding site 3 out
of 3 in 3fc3
Go back to
Sodium Binding Sites List in 3fc3
Sodium binding site 3 out
of 3 in the Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I
![](/pictures/NA/pdb/fc/3fc3-NA-sphere_03.jpg) Mono view
![](/pictures/NA/pdb/fc/3fc3-NA-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Crystal Structure of the Beta-Beta-Alpha-Me Type II Restriction Endonuclease HPY99I within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na307
b:30.5
occ:1.00
|
O
|
B:TYR57
|
2.3
|
22.0
|
1.0
|
O
|
B:HOH198
|
2.4
|
32.6
|
1.0
|
OH
|
B:TYR63
|
2.4
|
17.2
|
1.0
|
CZ
|
B:TYR63
|
3.4
|
17.2
|
1.0
|
C
|
B:TYR57
|
3.5
|
20.9
|
1.0
|
CE2
|
B:TYR63
|
3.6
|
17.6
|
1.0
|
CB
|
B:TYR57
|
4.1
|
21.5
|
1.0
|
CA
|
B:TYR57
|
4.3
|
21.1
|
1.0
|
N
|
B:ARG58
|
4.4
|
19.4
|
1.0
|
CA
|
B:ARG58
|
4.6
|
19.5
|
1.0
|
CE1
|
B:TYR63
|
4.6
|
16.2
|
1.0
|
CG
|
B:ARG58
|
4.9
|
20.2
|
1.0
|
O
|
B:HOH482
|
4.9
|
23.5
|
1.0
|
CD2
|
B:TYR63
|
5.0
|
17.6
|
1.0
|
|
Reference:
M.Sokolowska,
H.Czapinska,
M.Bochtler.
Crystal Structure of the Beta Beta Alpha-Me Type II Restriction Endonuclease HPY99I with Target Dna. Nucleic Acids Res. V. 37 3799 2009.
ISSN: ISSN 0305-1048
PubMed: 19380375
DOI: 10.1093/NAR/GKP228
Page generated: Tue Dec 15 06:10:32 2020
|