Sodium in PDB 8e9a: Crystal Structure of Asfvpolx in Complex with 10-23 Dnazyme and Mg
Enzymatic activity of Crystal Structure of Asfvpolx in Complex with 10-23 Dnazyme and Mg
All present enzymatic activity of Crystal Structure of Asfvpolx in Complex with 10-23 Dnazyme and Mg:
2.7.7.7;
Protein crystallography data
The structure of Crystal Structure of Asfvpolx in Complex with 10-23 Dnazyme and Mg, PDB code: 8e9a
was solved by
E.R.Cramer,
A.R.Robart,
A.I.Kaya,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
69.92 /
2.69
|
|
Space group
|
C 1 2 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
114.829,
48.419,
139.845,
90,
90,
90
|
|
R / Rfree (%)
|
25.5 /
28.9
|
Other elements in 8e9a:
The structure of Crystal Structure of Asfvpolx in Complex with 10-23 Dnazyme and Mg also contains other interesting chemical elements:
Sodium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Sodium atom in the Crystal Structure of Asfvpolx in Complex with 10-23 Dnazyme and Mg
(pdb code 8e9a). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 12 binding sites of Sodium where determined in the
Crystal Structure of Asfvpolx in Complex with 10-23 Dnazyme and Mg, PDB code: 8e9a:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Sodium binding site 1 out
of 12 in 8e9a
Go back to
Sodium Binding Sites List in 8e9a
Sodium binding site 1 out
of 12 in the Crystal Structure of Asfvpolx in Complex with 10-23 Dnazyme and Mg
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Crystal Structure of Asfvpolx in Complex with 10-23 Dnazyme and Mg within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na202
b:97.8
occ:1.00
|
H
|
A:GLN146
|
2.1
|
92.1
|
1.0
|
|
H
|
A:ASN145
|
2.1
|
84.1
|
1.0
|
|
N
|
A:ASN145
|
2.1
|
70.0
|
1.0
|
|
C
|
A:LYS144
|
2.1
|
63.5
|
1.0
|
|
N
|
A:LYS144
|
2.2
|
78.3
|
1.0
|
|
HA
|
A:LYS144
|
2.2
|
70.7
|
1.0
|
|
CA
|
A:LYS144
|
2.2
|
58.9
|
1.0
|
|
H
|
A:LYS144
|
2.3
|
94.1
|
1.0
|
|
N
|
A:GLN146
|
2.7
|
76.7
|
1.0
|
|
O
|
A:HOH310
|
2.7
|
46.7
|
1.0
|
|
C
|
A:PHE143
|
2.8
|
64.7
|
1.0
|
|
H
|
A:THR147
|
3.0
|
75.3
|
1.0
|
|
HB3
|
A:PHE143
|
3.0
|
75.8
|
1.0
|
|
O
|
A:LYS144
|
3.0
|
58.0
|
1.0
|
|
CA
|
A:ASN145
|
3.2
|
64.0
|
1.0
|
|
C
|
A:ASN145
|
3.3
|
62.3
|
1.0
|
|
O
|
A:PHE143
|
3.3
|
55.0
|
1.0
|
|
HA
|
A:ASN145
|
3.5
|
76.9
|
1.0
|
|
HA
|
A:GLN146
|
3.6
|
88.2
|
1.0
|
|
CB
|
A:PHE143
|
3.7
|
63.1
|
1.0
|
|
CA
|
A:GLN146
|
3.7
|
73.5
|
1.0
|
|
CB
|
A:LYS144
|
3.7
|
51.3
|
1.0
|
|
HB2
|
A:PHE143
|
3.7
|
75.8
|
1.0
|
|
N
|
A:THR147
|
3.8
|
62.7
|
1.0
|
|
CA
|
A:PHE143
|
3.8
|
56.5
|
1.0
|
|
HA
|
A:PHE143
|
4.1
|
67.9
|
1.0
|
|
HB3
|
A:LYS144
|
4.1
|
61.6
|
1.0
|
|
O
|
A:THR147
|
4.2
|
57.9
|
1.0
|
|
HB2
|
A:LYS144
|
4.2
|
61.6
|
1.0
|
|
C
|
A:GLN146
|
4.3
|
74.6
|
1.0
|
|
HB2
|
A:LYS136
|
4.3
|
69.8
|
1.0
|
|
HA
|
A:TYR135
|
4.3
|
66.1
|
1.0
|
|
H
|
A:LYS136
|
4.3
|
71.3
|
1.0
|
|
O
|
A:ASN145
|
4.4
|
72.4
|
1.0
|
|
HB2
|
A:ASN145
|
4.4
|
75.0
|
1.0
|
|
CB
|
A:ASN145
|
4.4
|
62.4
|
1.0
|
|
HG3
|
A:LYS144
|
4.5
|
68.5
|
1.0
|
|
CG
|
A:LYS144
|
4.6
|
57.0
|
1.0
|
|
HG2
|
A:LYS144
|
4.6
|
68.5
|
1.0
|
|
HB3
|
A:LYS136
|
4.7
|
69.8
|
1.0
|
|
N
|
A:LYS136
|
4.8
|
59.3
|
1.0
|
|
HB
|
A:THR147
|
4.8
|
102.5
|
1.0
|
|
CA
|
A:THR147
|
4.9
|
68.4
|
1.0
|
|
C
|
A:THR147
|
4.9
|
65.5
|
1.0
|
|
CB
|
A:LYS136
|
4.9
|
58.1
|
1.0
|
|
CB
|
A:GLN146
|
5.0
|
77.0
|
1.0
|
|
Sodium binding site 2 out
of 12 in 8e9a
Go back to
Sodium Binding Sites List in 8e9a
Sodium binding site 2 out
of 12 in the Crystal Structure of Asfvpolx in Complex with 10-23 Dnazyme and Mg
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Crystal Structure of Asfvpolx in Complex with 10-23 Dnazyme and Mg within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na203
b:64.2
occ:1.00
|
O
|
A:THR103
|
2.4
|
50.6
|
1.0
|
|
HE2
|
A:PHE116
|
2.9
|
63.6
|
1.0
|
|
HG3
|
A:GLN139
|
3.0
|
89.7
|
1.0
|
|
HZ
|
A:PHE116
|
3.1
|
50.6
|
1.0
|
|
HB2
|
A:ALA104
|
3.4
|
68.7
|
1.0
|
|
HE1
|
A:TYR140
|
3.4
|
85.1
|
1.0
|
|
HD2
|
A:ARG84
|
3.5
|
70.1
|
1.0
|
|
HB2
|
A:GLN139
|
3.5
|
73.2
|
1.0
|
|
HH11
|
A:ARG84
|
3.5
|
87.4
|
1.0
|
|
HA
|
A:ALA104
|
3.6
|
69.6
|
1.0
|
|
C
|
A:THR103
|
3.6
|
56.5
|
1.0
|
|
CE2
|
A:PHE116
|
3.6
|
52.9
|
1.0
|
|
CZ
|
A:PHE116
|
3.7
|
42.1
|
1.0
|
|
HB1
|
A:ALA112
|
3.8
|
76.2
|
1.0
|
|
CG
|
A:GLN139
|
3.9
|
74.7
|
1.0
|
|
HB2
|
A:ALA112
|
3.9
|
76.2
|
1.0
|
|
HE21
|
A:GLN139
|
3.9
|
98.1
|
1.0
|
|
CE1
|
A:TYR140
|
4.0
|
70.8
|
1.0
|
|
NH1
|
A:ARG84
|
4.1
|
72.8
|
1.0
|
|
HB3
|
A:PHE102
|
4.1
|
64.6
|
1.0
|
|
CB
|
A:GLN139
|
4.2
|
60.9
|
1.0
|
|
CA
|
A:ALA104
|
4.2
|
57.9
|
1.0
|
|
CB
|
A:ALA104
|
4.2
|
57.2
|
1.0
|
|
OE2
|
A:GLU108
|
4.2
|
81.7
|
1.0
|
|
H
|
A:THR103
|
4.2
|
62.1
|
1.0
|
|
N
|
A:ALA104
|
4.3
|
53.9
|
1.0
|
|
CB
|
A:ALA112
|
4.3
|
63.4
|
1.0
|
|
HD11
|
A:LEU53
|
4.3
|
64.8
|
1.0
|
|
HH12
|
A:ARG84
|
4.4
|
87.4
|
1.0
|
|
CD
|
A:ARG84
|
4.4
|
58.4
|
1.0
|
|
OH
|
A:TYR140
|
4.4
|
66.9
|
1.0
|
|
HG2
|
A:GLN139
|
4.4
|
89.7
|
1.0
|
|
HB3
|
A:ARG84
|
4.5
|
76.7
|
1.0
|
|
N
|
A:THR103
|
4.5
|
51.6
|
1.0
|
|
HB3
|
A:GLN139
|
4.5
|
73.2
|
1.0
|
|
NE2
|
A:GLN139
|
4.6
|
81.7
|
1.0
|
|
HD3
|
A:ARG84
|
4.6
|
70.1
|
1.0
|
|
HB1
|
A:ALA104
|
4.6
|
68.7
|
1.0
|
|
CZ
|
A:TYR140
|
4.6
|
81.5
|
1.0
|
|
CA
|
A:THR103
|
4.7
|
59.3
|
1.0
|
|
HD13
|
A:LEU53
|
4.7
|
64.8
|
1.0
|
|
CD
|
A:GLN139
|
4.8
|
73.9
|
1.0
|
|
CD1
|
A:TYR140
|
4.8
|
69.4
|
1.0
|
|
CZ
|
A:ARG84
|
4.8
|
65.0
|
1.0
|
|
HD1
|
A:TYR140
|
4.9
|
83.3
|
1.0
|
|
HB3
|
A:ALA104
|
4.9
|
68.7
|
1.0
|
|
CD2
|
A:PHE116
|
4.9
|
60.2
|
1.0
|
|
O
|
A:GLN139
|
4.9
|
78.2
|
1.0
|
|
CD1
|
A:LEU53
|
4.9
|
53.9
|
1.0
|
|
HB2
|
A:PHE102
|
5.0
|
64.6
|
1.0
|
|
CB
|
A:PHE102
|
5.0
|
53.8
|
1.0
|
|
NE
|
A:ARG84
|
5.0
|
56.1
|
1.0
|
|
HA
|
A:ALA112
|
5.0
|
62.7
|
1.0
|
|
HB3
|
A:ALA112
|
5.0
|
76.2
|
1.0
|
|
Sodium binding site 3 out
of 12 in 8e9a
Go back to
Sodium Binding Sites List in 8e9a
Sodium binding site 3 out
of 12 in the Crystal Structure of Asfvpolx in Complex with 10-23 Dnazyme and Mg
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Crystal Structure of Asfvpolx in Complex with 10-23 Dnazyme and Mg within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na204
b:80.1
occ:1.00
|
O
|
A:LEU62
|
2.2
|
89.5
|
1.0
|
|
O
|
A:GLU83
|
2.4
|
57.9
|
1.0
|
|
HG21
|
A:THR103
|
2.6
|
51.9
|
1.0
|
|
H
|
A:LEU66
|
2.7
|
79.9
|
1.0
|
|
HB
|
A:VAL65
|
2.8
|
92.9
|
1.0
|
|
HG
|
A:LEU66
|
3.0
|
66.2
|
1.0
|
|
HD12
|
A:LEU62
|
3.1
|
86.3
|
1.0
|
|
HG1
|
A:THR103
|
3.1
|
76.8
|
1.0
|
|
C
|
A:LEU62
|
3.3
|
77.0
|
1.0
|
|
HA
|
A:LEU62
|
3.4
|
100.6
|
1.0
|
|
HB2
|
A:LEU66
|
3.4
|
68.2
|
1.0
|
|
H
|
A:VAL65
|
3.4
|
88.5
|
1.0
|
|
HG
|
A:LEU62
|
3.4
|
92.1
|
1.0
|
|
HA
|
A:GLU83
|
3.4
|
88.2
|
1.0
|
|
HD3
|
A:PRO67
|
3.5
|
90.5
|
1.0
|
|
C
|
A:GLU83
|
3.5
|
71.6
|
1.0
|
|
N
|
A:LEU66
|
3.5
|
66.5
|
1.0
|
|
HG2
|
A:GLU83
|
3.5
|
97.6
|
1.0
|
|
CG2
|
A:THR103
|
3.5
|
43.2
|
1.0
|
|
CB
|
A:VAL65
|
3.8
|
77.3
|
1.0
|
|
CD1
|
A:LEU62
|
3.8
|
71.8
|
1.0
|
|
HG23
|
A:THR103
|
3.8
|
51.9
|
1.0
|
|
OG1
|
A:THR103
|
3.8
|
63.9
|
1.0
|
|
CA
|
A:LEU62
|
3.8
|
83.8
|
1.0
|
|
CG
|
A:LEU66
|
3.9
|
55.1
|
1.0
|
|
HD11
|
A:LEU62
|
3.9
|
86.3
|
1.0
|
|
CB
|
A:LEU66
|
4.0
|
56.8
|
1.0
|
|
CA
|
A:GLU83
|
4.0
|
73.5
|
1.0
|
|
CG
|
A:LEU62
|
4.0
|
76.7
|
1.0
|
|
N
|
A:VAL65
|
4.0
|
73.7
|
1.0
|
|
HD2
|
A:PRO67
|
4.1
|
90.5
|
1.0
|
|
HG3
|
A:GLU83
|
4.1
|
97.6
|
1.0
|
|
CB
|
A:THR103
|
4.2
|
57.1
|
1.0
|
|
HG22
|
A:THR103
|
4.2
|
51.9
|
1.0
|
|
HG23
|
A:VAL65
|
4.2
|
87.1
|
1.0
|
|
CD
|
A:PRO67
|
4.2
|
75.4
|
1.0
|
|
CG
|
A:GLU83
|
4.2
|
81.3
|
1.0
|
|
HB
|
A:THR103
|
4.2
|
68.6
|
1.0
|
|
CA
|
A:VAL65
|
4.3
|
64.6
|
1.0
|
|
CA
|
A:LEU66
|
4.4
|
66.3
|
1.0
|
|
C
|
A:VAL65
|
4.4
|
64.1
|
1.0
|
|
HA
|
A:ARG84
|
4.4
|
76.9
|
1.0
|
|
HA
|
A:LYS63
|
4.4
|
105.8
|
1.0
|
|
N
|
A:LYS63
|
4.4
|
75.8
|
1.0
|
|
HD12
|
A:LEU66
|
4.4
|
73.8
|
1.0
|
|
CG2
|
A:VAL65
|
4.5
|
72.5
|
1.0
|
|
CB
|
A:LEU62
|
4.5
|
86.8
|
1.0
|
|
HG12
|
A:VAL65
|
4.5
|
77.2
|
1.0
|
|
C
|
A:LYS63
|
4.6
|
89.5
|
1.0
|
|
HG21
|
A:VAL65
|
4.6
|
87.1
|
1.0
|
|
HD13
|
A:LEU62
|
4.6
|
86.3
|
1.0
|
|
CD1
|
A:LEU66
|
4.6
|
61.5
|
1.0
|
|
N
|
A:ARG84
|
4.7
|
67.0
|
1.0
|
|
O
|
A:GLY82
|
4.7
|
67.8
|
1.0
|
|
CB
|
A:GLU83
|
4.7
|
76.5
|
1.0
|
|
CG1
|
A:VAL65
|
4.7
|
64.3
|
1.0
|
|
CA
|
A:LYS63
|
4.7
|
88.0
|
1.0
|
|
HD23
|
A:LEU66
|
4.7
|
74.3
|
1.0
|
|
HD11
|
A:LEU66
|
4.8
|
73.8
|
1.0
|
|
HG21
|
A:VAL56
|
4.8
|
82.6
|
1.0
|
|
O
|
A:LEU61
|
4.8
|
84.5
|
1.0
|
|
H
|
A:HIS64
|
4.8
|
107.2
|
1.0
|
|
O
|
A:LYS63
|
4.8
|
76.9
|
1.0
|
|
N
|
A:HIS64
|
4.8
|
89.2
|
1.0
|
|
HB3
|
A:LEU66
|
4.8
|
68.2
|
1.0
|
|
CD2
|
A:LEU66
|
4.9
|
61.9
|
1.0
|
|
HG11
|
A:VAL65
|
4.9
|
77.2
|
1.0
|
|
Sodium binding site 4 out
of 12 in 8e9a
Go back to
Sodium Binding Sites List in 8e9a
Sodium binding site 4 out
of 12 in the Crystal Structure of Asfvpolx in Complex with 10-23 Dnazyme and Mg
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Crystal Structure of Asfvpolx in Complex with 10-23 Dnazyme and Mg within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na205
b:84.2
occ:1.00
|
HZ3
|
A:LYS144
|
1.8
|
84.8
|
1.0
|
|
HZ1
|
A:LYS144
|
1.8
|
84.8
|
1.0
|
|
NZ
|
A:LYS144
|
2.1
|
70.6
|
1.0
|
|
HZ2
|
A:LYS144
|
2.7
|
84.8
|
1.0
|
|
HG13
|
A:VAL149
|
3.3
|
74.5
|
1.0
|
|
CE
|
A:LYS144
|
3.3
|
61.2
|
1.0
|
|
HE2
|
A:LYS144
|
3.4
|
73.6
|
1.0
|
|
HE3
|
A:LYS144
|
3.6
|
73.6
|
1.0
|
|
HG11
|
A:VAL149
|
3.7
|
74.5
|
1.0
|
|
CG1
|
A:VAL149
|
3.9
|
62.0
|
1.0
|
|
OH
|
A:TYR135
|
4.3
|
76.3
|
1.0
|
|
HG22
|
A:VAL149
|
4.4
|
76.5
|
1.0
|
|
HG12
|
A:VAL149
|
4.5
|
74.5
|
1.0
|
|
HG21
|
A:VAL149
|
4.6
|
76.5
|
1.0
|
|
CD
|
A:LYS144
|
4.6
|
64.7
|
1.0
|
|
HD3
|
A:LYS144
|
4.6
|
77.7
|
1.0
|
|
HH
|
A:TYR135
|
4.6
|
91.7
|
1.0
|
|
CG2
|
A:VAL149
|
4.8
|
63.7
|
1.0
|
|
HD2
|
A:LYS144
|
4.9
|
77.7
|
1.0
|
|
CB
|
A:VAL149
|
5.0
|
70.6
|
1.0
|
|
Sodium binding site 5 out
of 12 in 8e9a
Go back to
Sodium Binding Sites List in 8e9a
Sodium binding site 5 out
of 12 in the Crystal Structure of Asfvpolx in Complex with 10-23 Dnazyme and Mg
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Crystal Structure of Asfvpolx in Complex with 10-23 Dnazyme and Mg within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na206
b:76.8
occ:1.00
|
O
|
A:THR166
|
2.4
|
61.4
|
1.0
|
|
HD2
|
A:ARG168
|
2.9
|
93.7
|
1.0
|
|
OH
|
A:TYR122
|
3.2
|
58.9
|
1.0
|
|
HB3
|
A:PHE165
|
3.2
|
81.5
|
1.0
|
|
HB
|
A:THR166
|
3.3
|
90.7
|
1.0
|
|
HD3
|
A:ARG168
|
3.3
|
93.7
|
1.0
|
|
HE1
|
A:TYR122
|
3.4
|
79.0
|
1.0
|
|
C
|
A:THR166
|
3.4
|
66.5
|
1.0
|
|
H
|
A:THR166
|
3.5
|
97.5
|
1.0
|
|
HH11
|
A:ARG168
|
3.5
|
119.0
|
1.0
|
|
CD
|
A:ARG168
|
3.5
|
78.0
|
1.0
|
|
N
|
A:THR166
|
3.7
|
81.2
|
1.0
|
|
HH
|
A:TYR122
|
3.7
|
70.8
|
1.0
|
|
HG3
|
A:ARG168
|
3.9
|
94.3
|
1.0
|
|
CA
|
A:THR166
|
3.9
|
79.4
|
1.0
|
|
CB
|
A:THR166
|
4.0
|
75.5
|
1.0
|
|
CB
|
A:PHE165
|
4.1
|
67.8
|
1.0
|
|
HB2
|
A:PHE165
|
4.1
|
81.5
|
1.0
|
|
CZ
|
A:TYR122
|
4.1
|
68.2
|
1.0
|
|
CE1
|
A:TYR122
|
4.1
|
65.8
|
1.0
|
|
HD11
|
A:ILE126
|
4.2
|
73.9
|
1.0
|
|
CG
|
A:ARG168
|
4.2
|
78.5
|
1.0
|
|
HB2
|
A:ARG168
|
4.3
|
83.0
|
1.0
|
|
NH1
|
A:ARG168
|
4.3
|
99.1
|
1.0
|
|
C
|
A:PHE165
|
4.4
|
77.1
|
1.0
|
|
N
|
A:TYR167
|
4.6
|
62.0
|
1.0
|
|
NE
|
A:ARG168
|
4.7
|
98.5
|
1.0
|
|
HA
|
A:TYR167
|
4.7
|
90.3
|
1.0
|
|
OG1
|
A:THR166
|
4.8
|
67.4
|
1.0
|
|
CA
|
A:PHE165
|
4.8
|
78.4
|
1.0
|
|
CB
|
A:ARG168
|
4.8
|
69.1
|
1.0
|
|
HA
|
A:THR166
|
4.9
|
95.4
|
1.0
|
|
HD12
|
A:ILE160
|
4.9
|
80.5
|
1.0
|
|
HD2
|
A:PHE165
|
4.9
|
86.1
|
1.0
|
|
HH12
|
A:ARG168
|
4.9
|
119.0
|
1.0
|
|
C
|
A:TYR167
|
4.9
|
79.2
|
1.0
|
|
HA
|
A:PHE165
|
4.9
|
94.1
|
1.0
|
|
N
|
A:ARG168
|
5.0
|
73.7
|
1.0
|
|
CZ
|
A:ARG168
|
5.0
|
96.9
|
1.0
|
|
CA
|
A:TYR167
|
5.0
|
75.2
|
1.0
|
|
Sodium binding site 6 out
of 12 in 8e9a
Go back to
Sodium Binding Sites List in 8e9a
Sodium binding site 6 out
of 12 in the Crystal Structure of Asfvpolx in Complex with 10-23 Dnazyme and Mg
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 6 of Crystal Structure of Asfvpolx in Complex with 10-23 Dnazyme and Mg within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na202
b:70.6
occ:1.00
|
N
|
B:LYS28
|
2.1
|
63.7
|
1.0
|
|
HB2
|
B:LYS28
|
2.2
|
90.3
|
1.0
|
|
OE1
|
A:GLU21
|
2.5
|
82.2
|
1.0
|
|
HA
|
B:ILE27
|
2.6
|
79.6
|
1.0
|
|
CB
|
B:LYS28
|
2.9
|
75.2
|
1.0
|
|
CA
|
B:LYS28
|
2.9
|
67.9
|
1.0
|
|
HG23
|
B:ILE27
|
3.0
|
92.8
|
1.0
|
|
HH22
|
A:ARG70
|
3.0
|
84.1
|
1.0
|
|
C
|
B:ILE27
|
3.0
|
60.1
|
1.0
|
|
CD
|
A:GLU21
|
3.2
|
91.8
|
1.0
|
|
CA
|
B:ILE27
|
3.2
|
66.3
|
1.0
|
|
OE2
|
A:GLU21
|
3.3
|
85.0
|
1.0
|
|
O
|
B:LYS28
|
3.3
|
60.3
|
1.0
|
|
HD3
|
B:LYS28
|
3.4
|
111.0
|
1.0
|
|
HH21
|
A:ARG70
|
3.4
|
84.1
|
1.0
|
|
NH2
|
A:ARG70
|
3.6
|
70.0
|
1.0
|
|
C
|
B:LYS28
|
3.6
|
64.4
|
1.0
|
|
HG22
|
B:ILE27
|
3.6
|
92.8
|
1.0
|
|
O
|
B:HOH302
|
3.7
|
66.0
|
1.0
|
|
CG2
|
B:ILE27
|
3.7
|
77.2
|
1.0
|
|
HB3
|
B:LYS28
|
3.7
|
90.3
|
1.0
|
|
HG3
|
B:LYS28
|
3.7
|
97.9
|
1.0
|
|
CG
|
B:LYS28
|
3.8
|
81.5
|
1.0
|
|
HA
|
B:LYS28
|
3.8
|
81.6
|
1.0
|
|
OD1
|
A:ASN68
|
3.8
|
80.1
|
1.0
|
|
CD
|
B:LYS28
|
4.0
|
92.4
|
1.0
|
|
CB
|
B:ILE27
|
4.1
|
70.7
|
1.0
|
|
O
|
B:LEU26
|
4.1
|
75.9
|
1.0
|
|
O
|
B:ILE27
|
4.2
|
61.4
|
1.0
|
|
HD13
|
B:ILE27
|
4.2
|
84.0
|
1.0
|
|
N
|
B:ILE27
|
4.4
|
68.6
|
1.0
|
|
HE3
|
B:LYS28
|
4.5
|
92.7
|
1.0
|
|
HB3
|
A:ASN68
|
4.5
|
82.5
|
1.0
|
|
HG21
|
B:ILE27
|
4.5
|
92.8
|
1.0
|
|
HB3
|
A:GLU21
|
4.6
|
93.0
|
1.0
|
|
HG2
|
B:LYS28
|
4.7
|
97.9
|
1.0
|
|
C
|
B:LEU26
|
4.7
|
69.8
|
1.0
|
|
CG
|
A:GLU21
|
4.7
|
85.5
|
1.0
|
|
CE
|
B:LYS28
|
4.8
|
77.2
|
1.0
|
|
CG
|
A:ASN68
|
4.8
|
74.4
|
1.0
|
|
HB
|
B:ILE27
|
4.8
|
85.0
|
1.0
|
|
HD2
|
B:LYS28
|
4.8
|
111.0
|
1.0
|
|
HD23
|
B:LEU26
|
4.9
|
86.9
|
1.0
|
|
CZ
|
A:ARG70
|
4.9
|
78.3
|
1.0
|
|
N
|
B:ILE29
|
4.9
|
77.4
|
1.0
|
|
HE2
|
B:LYS28
|
5.0
|
92.7
|
1.0
|
|
Sodium binding site 7 out
of 12 in 8e9a
Go back to
Sodium Binding Sites List in 8e9a
Sodium binding site 7 out
of 12 in the Crystal Structure of Asfvpolx in Complex with 10-23 Dnazyme and Mg
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 7 of Crystal Structure of Asfvpolx in Complex with 10-23 Dnazyme and Mg within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na203
b:72.6
occ:1.00
|
O
|
B:HOH304
|
2.5
|
56.3
|
1.0
|
|
HB3
|
B:ARG84
|
2.6
|
99.8
|
1.0
|
|
O
|
B:ARG84
|
2.6
|
61.8
|
1.0
|
|
H4'
|
D:DG4
|
2.6
|
76.8
|
1.0
|
|
HB2
|
B:LYS85
|
3.0
|
100.7
|
1.0
|
|
HZ
|
B:PHE116
|
3.0
|
79.4
|
1.0
|
|
HB2
|
B:ARG84
|
3.2
|
99.8
|
1.0
|
|
C
|
B:ARG84
|
3.2
|
74.4
|
1.0
|
|
CB
|
B:ARG84
|
3.3
|
83.1
|
1.0
|
|
HD1
|
B:PHE102
|
3.3
|
86.1
|
1.0
|
|
H5''
|
D:DG4
|
3.4
|
73.2
|
1.0
|
|
HE21
|
B:GLN139
|
3.4
|
82.7
|
1.0
|
|
C4'
|
D:DG4
|
3.5
|
64.0
|
1.0
|
|
HB3
|
B:PHE102
|
3.5
|
89.6
|
1.0
|
|
O
|
D:HOH207
|
3.8
|
79.2
|
1.0
|
|
C5'
|
D:DG4
|
3.8
|
61.0
|
1.0
|
|
H5'
|
D:DG4
|
3.8
|
73.2
|
1.0
|
|
CB
|
B:LYS85
|
3.9
|
83.8
|
1.0
|
|
CA
|
B:ARG84
|
3.9
|
78.1
|
1.0
|
|
CZ
|
B:PHE116
|
3.9
|
66.1
|
1.0
|
|
NE2
|
B:GLN139
|
4.0
|
68.8
|
1.0
|
|
N
|
B:LYS85
|
4.0
|
77.3
|
1.0
|
|
CD1
|
B:PHE102
|
4.0
|
71.7
|
1.0
|
|
HE22
|
B:GLN139
|
4.0
|
82.7
|
1.0
|
|
HB3
|
B:LYS85
|
4.1
|
100.7
|
1.0
|
|
HA
|
B:LYS85
|
4.1
|
82.7
|
1.0
|
|
CA
|
B:LYS85
|
4.2
|
68.9
|
1.0
|
|
HA
|
B:ARG84
|
4.3
|
93.8
|
1.0
|
|
HE1
|
B:PHE116
|
4.4
|
83.4
|
1.0
|
|
CB
|
B:PHE102
|
4.4
|
74.6
|
1.0
|
|
O4'
|
D:DG4
|
4.4
|
62.4
|
1.0
|
|
O3'
|
D:DG4
|
4.4
|
61.1
|
1.0
|
|
C3'
|
D:DG4
|
4.5
|
73.3
|
1.0
|
|
CG
|
B:ARG84
|
4.5
|
91.0
|
1.0
|
|
HD2
|
B:ARG84
|
4.6
|
85.7
|
1.0
|
|
HA
|
B:PHE102
|
4.6
|
86.4
|
1.0
|
|
CG
|
B:PHE102
|
4.6
|
67.6
|
1.0
|
|
HG3
|
B:ARG84
|
4.6
|
109.2
|
1.0
|
|
H
|
B:THR103
|
4.6
|
83.8
|
1.0
|
|
CE1
|
B:PHE116
|
4.6
|
69.4
|
1.0
|
|
H
|
B:LYS85
|
4.7
|
92.9
|
1.0
|
|
OH
|
B:TYR140
|
4.7
|
63.4
|
1.0
|
|
H3'
|
D:DG4
|
4.7
|
88.1
|
1.0
|
|
HG3
|
B:GLN139
|
4.8
|
94.2
|
1.0
|
|
HE2
|
B:PHE116
|
4.8
|
75.3
|
1.0
|
|
CE1
|
B:PHE102
|
4.9
|
59.9
|
1.0
|
|
HE1
|
B:PHE102
|
4.9
|
72.0
|
1.0
|
|
CE2
|
B:PHE116
|
4.9
|
62.7
|
1.0
|
|
HD2
|
B:LYS85
|
4.9
|
100.2
|
1.0
|
|
Sodium binding site 8 out
of 12 in 8e9a
Go back to
Sodium Binding Sites List in 8e9a
Sodium binding site 8 out
of 12 in the Crystal Structure of Asfvpolx in Complex with 10-23 Dnazyme and Mg
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 8 of Crystal Structure of Asfvpolx in Complex with 10-23 Dnazyme and Mg within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na204
b:81.4
occ:1.00
|
OE2
|
B:GLU83
|
2.4
|
96.1
|
1.0
|
|
OE1
|
B:GLU83
|
2.5
|
95.4
|
1.0
|
|
CD
|
B:GLU83
|
2.8
|
98.4
|
1.0
|
|
HD23
|
B:LEU62
|
3.9
|
107.0
|
1.0
|
|
HB3
|
B:LEU62
|
4.0
|
117.6
|
1.0
|
|
CG
|
B:GLU83
|
4.3
|
99.1
|
1.0
|
|
HD22
|
B:LEU62
|
4.6
|
107.0
|
1.0
|
|
HB2
|
B:LEU62
|
4.6
|
117.6
|
1.0
|
|
HG3
|
B:GLU83
|
4.6
|
119.0
|
1.0
|
|
CD2
|
B:LEU62
|
4.7
|
89.1
|
1.0
|
|
HE2
|
B:LYS63
|
4.7
|
130.9
|
1.0
|
|
CB
|
B:LEU62
|
4.7
|
98.0
|
1.0
|
|
HG2
|
B:GLU83
|
4.7
|
119.0
|
1.0
|
|
HB3
|
B:GLU83
|
4.8
|
106.9
|
1.0
|
|
Sodium binding site 9 out
of 12 in 8e9a
Go back to
Sodium Binding Sites List in 8e9a
Sodium binding site 9 out
of 12 in the Crystal Structure of Asfvpolx in Complex with 10-23 Dnazyme and Mg
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 9 of Crystal Structure of Asfvpolx in Complex with 10-23 Dnazyme and Mg within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na205
b:71.3
occ:1.00
|
OP1
|
D:DC52
|
2.3
|
71.9
|
1.0
|
|
OG
|
B:SER39
|
2.4
|
84.0
|
1.0
|
|
OD2
|
B:ASP51
|
2.5
|
71.2
|
1.0
|
|
H
|
B:SER39
|
2.5
|
75.6
|
1.0
|
|
OD1
|
B:ASP49
|
2.8
|
75.9
|
1.0
|
|
NA
|
D:NA104
|
2.9
|
69.2
|
1.0
|
|
HB3
|
B:SER39
|
3.3
|
78.8
|
1.0
|
|
OD2
|
B:ASP49
|
3.3
|
67.3
|
1.0
|
|
N
|
B:SER39
|
3.3
|
63.0
|
1.0
|
|
CB
|
B:SER39
|
3.4
|
65.6
|
1.0
|
|
CG
|
B:ASP49
|
3.4
|
73.4
|
1.0
|
|
H5''
|
D:DC52
|
3.5
|
93.3
|
1.0
|
|
P
|
D:DC52
|
3.6
|
86.2
|
1.0
|
|
CG
|
B:ASP51
|
3.6
|
67.6
|
1.0
|
|
HA3
|
B:GLY38
|
3.8
|
99.3
|
1.0
|
|
O
|
B:HOH303
|
3.9
|
60.9
|
1.0
|
|
O5'
|
D:DC52
|
3.9
|
74.4
|
1.0
|
|
CA
|
B:SER39
|
4.0
|
68.4
|
1.0
|
|
C5'
|
D:DC52
|
4.2
|
77.6
|
1.0
|
|
HB2
|
B:SER39
|
4.2
|
78.8
|
1.0
|
|
OD1
|
B:ASP51
|
4.2
|
72.0
|
1.0
|
|
C
|
B:GLY38
|
4.3
|
72.7
|
1.0
|
|
CA
|
B:GLY38
|
4.4
|
82.7
|
1.0
|
|
NH2
|
B:ARG42
|
4.4
|
81.4
|
1.0
|
|
HA2
|
B:GLY38
|
4.4
|
99.3
|
1.0
|
|
OP2
|
D:DC52
|
4.4
|
75.3
|
1.0
|
|
O
|
B:ASP49
|
4.4
|
64.2
|
1.0
|
|
HH21
|
B:ARG42
|
4.5
|
97.8
|
1.0
|
|
HB3
|
B:ASN48
|
4.5
|
100.2
|
1.0
|
|
H
|
B:ASP49
|
4.5
|
94.0
|
1.0
|
|
H5'
|
D:DC52
|
4.6
|
93.3
|
1.0
|
|
HA
|
B:SER39
|
4.6
|
82.1
|
1.0
|
|
HB2
|
B:ASP51
|
4.7
|
80.9
|
1.0
|
|
O
|
D:HOH202
|
4.7
|
69.7
|
1.0
|
|
H
|
B:LEU40
|
4.7
|
103.8
|
1.0
|
|
O3'
|
D:DG51
|
4.8
|
70.5
|
1.0
|
|
CB
|
B:ASP49
|
4.8
|
71.5
|
1.0
|
|
CB
|
B:ASP51
|
4.8
|
67.4
|
1.0
|
|
C
|
B:ASP49
|
4.9
|
68.6
|
1.0
|
|
N
|
B:ASP49
|
4.9
|
78.3
|
1.0
|
|
H
|
B:ASN48
|
5.0
|
93.0
|
1.0
|
|
Sodium binding site 10 out
of 12 in 8e9a
Go back to
Sodium Binding Sites List in 8e9a
Sodium binding site 10 out
of 12 in the Crystal Structure of Asfvpolx in Complex with 10-23 Dnazyme and Mg
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 10 of Crystal Structure of Asfvpolx in Complex with 10-23 Dnazyme and Mg within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na102
b:85.8
occ:1.00
|
H5''
|
C:DT37
|
1.6
|
106.0
|
1.0
|
|
H5'
|
C:DT37
|
2.3
|
106.0
|
1.0
|
|
C5'
|
C:DT37
|
2.3
|
88.3
|
1.0
|
|
O
|
C:HOH205
|
2.4
|
87.0
|
1.0
|
|
O3'
|
C:DC36
|
2.6
|
103.2
|
1.0
|
|
H3'
|
C:DT37
|
2.7
|
107.0
|
1.0
|
|
H4'
|
C:DC36
|
3.0
|
127.5
|
1.0
|
|
O5'
|
C:DT37
|
3.4
|
103.3
|
1.0
|
|
C4'
|
C:DT37
|
3.4
|
86.7
|
1.0
|
|
C3'
|
C:DT37
|
3.4
|
89.1
|
1.0
|
|
H2''
|
C:DC36
|
3.5
|
129.5
|
1.0
|
|
C3'
|
C:DC36
|
3.5
|
106.5
|
1.0
|
|
OP2
|
C:DC39
|
3.6
|
127.2
|
1.0
|
|
P
|
C:DT37
|
3.6
|
104.2
|
1.0
|
|
OP2
|
C:DA38
|
3.6
|
103.1
|
1.0
|
|
C4'
|
C:DC36
|
3.7
|
106.2
|
1.0
|
|
H5'
|
C:DC39
|
3.7
|
110.0
|
1.0
|
|
H4'
|
C:DA38
|
3.9
|
147.6
|
1.0
|
|
H4'
|
C:DT37
|
3.9
|
104.2
|
1.0
|
|
H2'
|
C:DT37
|
3.9
|
102.2
|
1.0
|
|
H5
|
C:DC39
|
4.0
|
94.5
|
1.0
|
|
H6
|
C:DC39
|
4.0
|
75.8
|
1.0
|
|
C2'
|
C:DC36
|
4.0
|
107.9
|
1.0
|
|
H1'
|
C:DA38
|
4.1
|
145.5
|
1.0
|
|
H5''
|
C:DC36
|
4.1
|
118.7
|
1.0
|
|
OP1
|
C:DT37
|
4.1
|
95.7
|
1.0
|
|
C2'
|
C:DT37
|
4.3
|
85.1
|
1.0
|
|
H3'
|
C:DC36
|
4.4
|
127.9
|
1.0
|
|
O4'
|
C:DT37
|
4.5
|
80.7
|
1.0
|
|
O3'
|
C:DT37
|
4.5
|
94.9
|
1.0
|
|
C5'
|
C:DC36
|
4.5
|
98.9
|
1.0
|
|
C5'
|
C:DC39
|
4.5
|
91.6
|
1.0
|
|
C5
|
C:DC39
|
4.5
|
78.7
|
1.0
|
|
C6
|
C:DC39
|
4.6
|
63.1
|
1.0
|
|
H5''
|
C:DC39
|
4.6
|
110.0
|
1.0
|
|
O4'
|
C:DA38
|
4.6
|
114.7
|
1.0
|
|
P
|
C:DA38
|
4.6
|
97.7
|
1.0
|
|
C4'
|
C:DA38
|
4.7
|
122.9
|
1.0
|
|
H1'
|
C:DC36
|
4.7
|
130.0
|
1.0
|
|
H2'
|
C:DC36
|
4.8
|
129.5
|
1.0
|
|
O4'
|
C:DC36
|
4.8
|
112.3
|
1.0
|
|
OP2
|
C:DT37
|
4.8
|
91.3
|
1.0
|
|
C1'
|
C:DC36
|
4.8
|
108.3
|
1.0
|
|
C1'
|
C:DA38
|
4.8
|
121.2
|
1.0
|
|
P
|
C:DC39
|
4.8
|
122.4
|
1.0
|
|
O5'
|
C:DC39
|
4.9
|
97.6
|
1.0
|
|
H2''
|
C:DT37
|
5.0
|
102.2
|
1.0
|
|
Reference:
E.R.Cramer,
S.A.Starcovic,
R.M.Avey,
A.I.Kaya,
A.R.Robart.
Structure of A 10-23 Deoxyribozyme Exhibiting A Homodimer Conformation. Commun Chem V. 6 119 2023.
ISSN: ESSN 2399-3669
PubMed: 37301907
DOI: 10.1038/S42004-023-00924-3
Page generated: Fri Jul 28 03:23:41 2023
|
