Sodium in PDB 8vn7: Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH8.0 (Tris) with 500 Um MG2+ For 20S
Protein crystallography data
The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH8.0 (Tris) with 500 Um MG2+ For 20S, PDB code: 8vn7
was solved by
C.Chang,
Y.Gao,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
42.99 /
1.67
|
Space group
|
P 31 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
113.65,
113.65,
88.31,
90,
90,
120
|
R / Rfree (%)
|
17.7 /
19.6
|
Other elements in 8vn7:
The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH8.0 (Tris) with 500 Um MG2+ For 20S also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH8.0 (Tris) with 500 Um MG2+ For 20S
(pdb code 8vn7). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the
Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH8.0 (Tris) with 500 Um MG2+ For 20S, PDB code: 8vn7:
Jump to Sodium binding site number:
1;
2;
Sodium binding site 1 out
of 2 in 8vn7
Go back to
Sodium Binding Sites List in 8vn7
Sodium binding site 1 out
of 2 in the Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH8.0 (Tris) with 500 Um MG2+ For 20S
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH8.0 (Tris) with 500 Um MG2+ For 20S within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
c:Na502
b:16.4
occ:0.65
|
MG
|
c:MG501
|
0.0
|
16.3
|
0.3
|
O
|
B:HOH606
|
2.2
|
22.5
|
1.0
|
OD1
|
B:ASN319
|
2.2
|
17.2
|
1.0
|
O
|
B:HOH504
|
2.3
|
21.2
|
1.0
|
O
|
B:HOH528
|
2.3
|
16.5
|
1.0
|
O3'
|
C:DA413
|
2.4
|
17.2
|
0.7
|
OP2
|
c:DG414
|
2.4
|
17.1
|
0.7
|
O3'
|
C:DA413
|
2.5
|
17.2
|
0.3
|
P
|
c:DG414
|
2.9
|
17.9
|
0.7
|
CG
|
B:ASN319
|
3.3
|
16.8
|
1.0
|
P
|
c:DG414
|
3.4
|
16.1
|
0.3
|
C3'
|
C:DA413
|
3.6
|
17.6
|
0.7
|
C3'
|
C:DA413
|
3.7
|
17.6
|
0.3
|
O
|
B:ASN319
|
3.8
|
15.3
|
1.0
|
O5'
|
c:DG414
|
3.8
|
17.0
|
0.7
|
OP1
|
c:DG414
|
3.8
|
18.5
|
0.3
|
N
|
B:HIS298
|
3.9
|
17.5
|
1.0
|
O5'
|
c:DG414
|
4.0
|
17.3
|
0.3
|
ND2
|
B:ASN319
|
4.0
|
16.5
|
1.0
|
C4'
|
C:DA413
|
4.0
|
17.8
|
0.7
|
OG
|
B:SER297
|
4.0
|
19.3
|
1.0
|
C4'
|
C:DA413
|
4.1
|
17.8
|
0.3
|
OP1
|
c:DG414
|
4.2
|
19.1
|
0.7
|
O
|
B:HIS298
|
4.2
|
16.9
|
1.0
|
O
|
c:HOH614
|
4.2
|
26.5
|
1.0
|
C
|
B:ASN319
|
4.2
|
18.4
|
1.0
|
C2'
|
C:DA413
|
4.3
|
16.5
|
0.7
|
C2'
|
C:DA413
|
4.3
|
16.6
|
0.3
|
CA
|
B:SER297
|
4.5
|
17.1
|
1.0
|
OD1
|
B:ASN323
|
4.5
|
15.9
|
1.0
|
CB
|
B:ASN319
|
4.6
|
16.5
|
1.0
|
OP2
|
c:DG414
|
4.6
|
22.1
|
0.3
|
C
|
B:SER297
|
4.7
|
17.4
|
1.0
|
CA
|
B:ASN319
|
4.7
|
14.5
|
1.0
|
C5'
|
C:DA413
|
4.7
|
16.8
|
0.7
|
CA
|
B:HIS298
|
4.7
|
16.7
|
1.0
|
ND1
|
B:HIS301
|
4.7
|
16.8
|
1.0
|
CB
|
B:HIS298
|
4.7
|
16.7
|
1.0
|
C5'
|
C:DA413
|
4.7
|
16.9
|
0.3
|
CB
|
B:SER297
|
4.8
|
16.7
|
1.0
|
C
|
B:HIS298
|
4.8
|
15.4
|
1.0
|
CE1
|
B:HIS301
|
4.9
|
20.6
|
1.0
|
N
|
B:LYS320
|
5.0
|
13.3
|
1.0
|
|
Sodium binding site 2 out
of 2 in 8vn7
Go back to
Sodium Binding Sites List in 8vn7
Sodium binding site 2 out
of 2 in the Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH8.0 (Tris) with 500 Um MG2+ For 20S
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH8.0 (Tris) with 500 Um MG2+ For 20S within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na604
b:16.7
occ:0.75
|
MG
|
A:MG603
|
0.0
|
16.6
|
0.2
|
OD1
|
A:ASN119
|
2.2
|
17.0
|
1.0
|
O
|
A:HOH722
|
2.3
|
16.9
|
1.0
|
O
|
A:HOH813
|
2.3
|
20.9
|
1.0
|
O
|
A:HOH710
|
2.3
|
21.9
|
1.0
|
O3'
|
D:DA513
|
2.4
|
16.9
|
0.8
|
O3'
|
D:DA513
|
2.4
|
16.9
|
0.2
|
OP1
|
d:DG514
|
2.5
|
16.6
|
0.8
|
P
|
d:DG514
|
3.0
|
15.3
|
0.8
|
CG
|
A:ASN119
|
3.4
|
15.7
|
1.0
|
P
|
d:DG514
|
3.6
|
15.9
|
0.2
|
C3'
|
D:DA513
|
3.6
|
17.8
|
0.8
|
C3'
|
D:DA513
|
3.7
|
17.7
|
0.2
|
O
|
A:ASN119
|
3.7
|
15.1
|
1.0
|
O5'
|
d:DG514
|
3.9
|
15.1
|
0.8
|
N
|
A:HIS98
|
3.9
|
14.9
|
1.0
|
C4'
|
D:DA513
|
3.9
|
16.2
|
0.8
|
OP2
|
d:DG514
|
3.9
|
18.4
|
0.2
|
ND2
|
A:ASN119
|
4.0
|
15.7
|
1.0
|
C4'
|
D:DA513
|
4.0
|
16.3
|
0.2
|
O5'
|
d:DG514
|
4.1
|
16.2
|
0.2
|
OG
|
A:SER97
|
4.2
|
18.5
|
1.0
|
C
|
A:ASN119
|
4.2
|
14.7
|
1.0
|
O
|
A:HIS98
|
4.2
|
16.4
|
1.0
|
OP2
|
d:DG514
|
4.3
|
17.6
|
0.8
|
C2'
|
D:DA513
|
4.3
|
15.8
|
0.8
|
C2'
|
D:DA513
|
4.3
|
15.9
|
0.2
|
OD1
|
A:ASN123
|
4.5
|
16.4
|
1.0
|
O
|
d:HOH606
|
4.5
|
33.5
|
1.0
|
CA
|
A:SER97
|
4.5
|
13.9
|
1.0
|
CB
|
A:ASN119
|
4.6
|
13.2
|
1.0
|
C5'
|
D:DA513
|
4.6
|
17.9
|
0.8
|
C
|
A:SER97
|
4.6
|
12.6
|
1.0
|
CA
|
A:ASN119
|
4.6
|
14.5
|
1.0
|
C5'
|
D:DA513
|
4.7
|
17.9
|
0.2
|
CB
|
A:HIS98
|
4.7
|
17.3
|
1.0
|
CA
|
A:HIS98
|
4.7
|
17.4
|
1.0
|
OP1
|
d:DG514
|
4.7
|
19.4
|
0.2
|
ND1
|
A:HIS101
|
4.7
|
17.1
|
1.0
|
CB
|
A:SER97
|
4.8
|
15.4
|
1.0
|
C
|
A:HIS98
|
4.9
|
15.4
|
1.0
|
CE1
|
A:HIS101
|
4.9
|
15.5
|
1.0
|
N
|
A:LYS120
|
4.9
|
13.1
|
1.0
|
|
Reference:
C.Chang,
Y.Gao.
Homing Endonuclease I-Ppoi-Dna Complex:Reaction with 500 Um MG2+ For 160S To Be Published.
Page generated: Wed Oct 9 14:07:51 2024
|