Sodium in PDB 5c3y: Structure of Human Ribokinase Crystallized with Amppnp
Enzymatic activity of Structure of Human Ribokinase Crystallized with Amppnp
All present enzymatic activity of Structure of Human Ribokinase Crystallized with Amppnp:
2.7.1.15;
Protein crystallography data
The structure of Structure of Human Ribokinase Crystallized with Amppnp, PDB code: 5c3y
was solved by
J.Park,
J.Chakrabarti,
B.Singh,
R.S.Gupta,
M.S.Junop,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
51.26 /
2.60
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
80.310,
168.140,
161.500,
90.00,
90.82,
90.00
|
|
R / Rfree (%)
|
20.5 /
23.2
|
Sodium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
20;
Page 3, Binding sites: 21 -
24;
Binding sites:
The binding sites of Sodium atom in the Structure of Human Ribokinase Crystallized with Amppnp
(pdb code 5c3y). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 24 binding sites of Sodium where determined in the
Structure of Human Ribokinase Crystallized with Amppnp, PDB code: 5c3y:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Sodium binding site 1 out
of 24 in 5c3y
Go back to
Sodium Binding Sites List in 5c3y
Sodium binding site 1 out
of 24 in the Structure of Human Ribokinase Crystallized with Amppnp
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Structure of Human Ribokinase Crystallized with Amppnp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na402
b:26.8
occ:1.00
|
O
|
A:HOH526
|
2.4
|
25.2
|
1.0
|
|
O
|
A:HOH507
|
2.4
|
22.4
|
1.0
|
|
O
|
A:ALA304
|
2.4
|
38.6
|
1.0
|
|
O
|
A:SER301
|
2.5
|
34.5
|
1.0
|
|
O
|
A:ASP263
|
2.5
|
40.5
|
1.0
|
|
OG
|
A:SER310
|
2.7
|
31.2
|
1.0
|
|
CB
|
A:SER310
|
3.3
|
32.9
|
1.0
|
|
C
|
A:SER301
|
3.5
|
33.7
|
1.0
|
|
C
|
A:ALA304
|
3.7
|
40.5
|
1.0
|
|
C
|
A:ASP263
|
3.7
|
43.6
|
1.0
|
|
O
|
A:THR265
|
3.8
|
33.9
|
1.0
|
|
CA
|
A:VAL302
|
4.1
|
38.3
|
1.0
|
|
OD2
|
A:ASP263
|
4.1
|
43.6
|
1.0
|
|
CB
|
A:ASP263
|
4.2
|
46.2
|
1.0
|
|
N
|
A:VAL302
|
4.2
|
35.6
|
1.0
|
|
CG
|
A:ASP263
|
4.3
|
45.1
|
1.0
|
|
N
|
A:THR307
|
4.4
|
34.1
|
1.0
|
|
C
|
A:ALA305
|
4.4
|
39.3
|
1.0
|
|
OG
|
A:SER301
|
4.5
|
30.3
|
1.0
|
|
N
|
A:ALA304
|
4.5
|
41.1
|
1.0
|
|
CA
|
A:ALA305
|
4.5
|
41.8
|
1.0
|
|
CA
|
A:ASP263
|
4.5
|
46.9
|
1.0
|
|
CA
|
A:SER301
|
4.5
|
31.4
|
1.0
|
|
C
|
A:VAL302
|
4.5
|
40.6
|
1.0
|
|
N
|
A:ALA305
|
4.5
|
41.9
|
1.0
|
|
N
|
A:GLY306
|
4.6
|
38.7
|
1.0
|
|
CB
|
A:SER301
|
4.6
|
29.5
|
1.0
|
|
CA
|
A:ALA304
|
4.7
|
41.3
|
1.0
|
|
N
|
A:THR264
|
4.7
|
44.2
|
1.0
|
|
N
|
A:THR265
|
4.7
|
39.5
|
1.0
|
|
O
|
A:ALA305
|
4.7
|
38.4
|
1.0
|
|
O
|
A:THR307
|
4.8
|
29.7
|
1.0
|
|
CA
|
A:THR307
|
4.8
|
32.0
|
1.0
|
|
O
|
A:VAL302
|
4.8
|
42.9
|
1.0
|
|
CA
|
A:SER310
|
4.8
|
31.8
|
1.0
|
|
CA
|
A:THR264
|
4.9
|
42.3
|
1.0
|
|
C
|
A:THR265
|
4.9
|
34.9
|
1.0
|
|
C
|
A:THR264
|
4.9
|
40.1
|
1.0
|
|
N
|
A:ASP263
|
5.0
|
49.1
|
1.0
|
|
Sodium binding site 2 out
of 24 in 5c3y
Go back to
Sodium Binding Sites List in 5c3y
Sodium binding site 2 out
of 24 in the Structure of Human Ribokinase Crystallized with Amppnp
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Structure of Human Ribokinase Crystallized with Amppnp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na403
b:31.7
occ:1.00
|
O
|
A:HOH512
|
2.3
|
41.0
|
1.0
|
|
O
|
A:HOH505
|
2.3
|
21.3
|
1.0
|
|
O
|
A:HOH535
|
2.4
|
43.8
|
1.0
|
|
O
|
A:HOH536
|
2.5
|
19.5
|
1.0
|
|
O
|
A:HOH519
|
2.7
|
44.0
|
1.0
|
|
CA
|
A:GLY268
|
3.8
|
32.9
|
1.0
|
|
OD1
|
A:ASP269
|
4.0
|
29.9
|
1.0
|
|
NZ
|
A:LYS54
|
4.0
|
25.2
|
1.0
|
|
C
|
A:GLY268
|
4.0
|
30.8
|
1.0
|
|
ND2
|
A:ASN177
|
4.3
|
35.0
|
1.0
|
|
N
|
A:ASP269
|
4.3
|
29.1
|
1.0
|
|
OD1
|
A:ASN177
|
4.3
|
31.9
|
1.0
|
|
O
|
A:GLY268
|
4.5
|
31.0
|
1.0
|
|
ND2
|
A:ASN199
|
4.5
|
58.4
|
1.0
|
|
OE2
|
A:GLU202
|
4.7
|
56.0
|
1.0
|
|
CG
|
A:ASP269
|
4.7
|
28.9
|
1.0
|
|
N
|
A:GLY268
|
4.7
|
33.0
|
1.0
|
|
CB
|
A:ALA179
|
4.7
|
38.5
|
1.0
|
|
CG
|
A:ASN177
|
4.7
|
33.7
|
1.0
|
|
OE1
|
A:GLU202
|
4.8
|
56.8
|
1.0
|
|
N3B
|
A:AN2401
|
4.8
|
42.5
|
1.0
|
|
O2B
|
A:AN2401
|
4.9
|
38.5
|
1.0
|
|
Sodium binding site 3 out
of 24 in 5c3y
Go back to
Sodium Binding Sites List in 5c3y
Sodium binding site 3 out
of 24 in the Structure of Human Ribokinase Crystallized with Amppnp
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Structure of Human Ribokinase Crystallized with Amppnp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na402
b:22.4
occ:1.00
|
O
|
B:HOH510
|
2.3
|
26.3
|
1.0
|
|
O
|
B:SER301
|
2.4
|
29.4
|
1.0
|
|
O
|
B:HOH529
|
2.4
|
23.0
|
1.0
|
|
O
|
B:ALA304
|
2.5
|
31.3
|
1.0
|
|
O
|
B:ASP263
|
2.6
|
30.1
|
1.0
|
|
OG
|
B:SER310
|
2.6
|
25.1
|
1.0
|
|
CB
|
B:SER310
|
3.3
|
26.0
|
1.0
|
|
C
|
B:SER301
|
3.4
|
28.5
|
1.0
|
|
C
|
B:ALA304
|
3.7
|
32.3
|
1.0
|
|
C
|
B:ASP263
|
3.8
|
32.7
|
1.0
|
|
O
|
B:THR265
|
3.8
|
28.5
|
1.0
|
|
CA
|
B:VAL302
|
4.0
|
30.6
|
1.0
|
|
N
|
B:VAL302
|
4.1
|
29.2
|
1.0
|
|
OD2
|
B:ASP263
|
4.3
|
35.2
|
1.0
|
|
CB
|
B:ASP263
|
4.3
|
34.9
|
1.0
|
|
CA
|
B:SER301
|
4.3
|
27.9
|
1.0
|
|
OG
|
B:SER301
|
4.3
|
27.8
|
1.0
|
|
CG
|
B:ASP263
|
4.4
|
34.8
|
1.0
|
|
CB
|
B:SER301
|
4.4
|
26.8
|
1.0
|
|
N
|
B:THR307
|
4.4
|
27.3
|
1.0
|
|
N
|
B:ALA304
|
4.5
|
32.5
|
1.0
|
|
C
|
B:ALA305
|
4.5
|
30.8
|
1.0
|
|
C
|
B:VAL302
|
4.5
|
32.3
|
1.0
|
|
CA
|
B:ASP263
|
4.6
|
35.0
|
1.0
|
|
CA
|
B:ALA305
|
4.6
|
32.4
|
1.0
|
|
N
|
B:ALA305
|
4.6
|
32.9
|
1.0
|
|
N
|
B:THR265
|
4.7
|
30.1
|
1.0
|
|
N
|
B:GLY306
|
4.7
|
30.0
|
1.0
|
|
CA
|
B:ALA304
|
4.7
|
32.8
|
1.0
|
|
O
|
B:THR307
|
4.7
|
24.7
|
1.0
|
|
CA
|
B:SER310
|
4.7
|
25.3
|
1.0
|
|
N
|
B:THR264
|
4.7
|
32.5
|
1.0
|
|
O
|
B:ALA305
|
4.8
|
30.2
|
1.0
|
|
CA
|
B:THR307
|
4.8
|
25.9
|
1.0
|
|
O
|
B:VAL302
|
4.8
|
33.7
|
1.0
|
|
C
|
B:THR265
|
4.9
|
28.2
|
1.0
|
|
C
|
B:THR264
|
4.9
|
29.8
|
1.0
|
|
CA
|
B:THR264
|
4.9
|
30.9
|
1.0
|
|
Sodium binding site 4 out
of 24 in 5c3y
Go back to
Sodium Binding Sites List in 5c3y
Sodium binding site 4 out
of 24 in the Structure of Human Ribokinase Crystallized with Amppnp
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Structure of Human Ribokinase Crystallized with Amppnp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na403
b:31.2
occ:1.00
|
O
|
B:HOH542
|
2.1
|
30.1
|
1.0
|
|
O
|
B:HOH511
|
2.3
|
26.0
|
1.0
|
|
O
|
B:HOH519
|
2.4
|
19.8
|
1.0
|
|
O
|
B:HOH504
|
2.6
|
20.6
|
1.0
|
|
O
|
B:HOH571
|
2.7
|
35.9
|
1.0
|
|
O
|
B:HOH574
|
2.8
|
24.4
|
1.0
|
|
ND2
|
B:ASN199
|
3.9
|
33.0
|
1.0
|
|
CA
|
B:GLY268
|
4.1
|
25.6
|
1.0
|
|
NZ
|
B:LYS54
|
4.1
|
21.3
|
1.0
|
|
OE2
|
B:GLU202
|
4.3
|
35.1
|
1.0
|
|
C
|
B:GLY268
|
4.4
|
23.8
|
1.0
|
|
ND2
|
B:ASN177
|
4.5
|
25.5
|
1.0
|
|
OE1
|
B:GLU202
|
4.5
|
36.0
|
1.0
|
|
O
|
B:HOH524
|
4.5
|
23.2
|
1.0
|
|
OD1
|
B:ASP269
|
4.5
|
21.3
|
1.0
|
|
O3A
|
B:AN2401
|
4.7
|
38.2
|
1.0
|
|
OD1
|
B:ASN177
|
4.7
|
24.1
|
1.0
|
|
N
|
B:ASP269
|
4.7
|
22.6
|
1.0
|
|
O2B
|
B:AN2401
|
4.7
|
28.4
|
1.0
|
|
CB
|
B:ALA179
|
4.7
|
28.0
|
1.0
|
|
CD
|
B:GLU202
|
4.8
|
36.5
|
1.0
|
|
CG
|
B:ASN199
|
4.9
|
34.4
|
1.0
|
|
O
|
B:GLY268
|
4.9
|
23.3
|
1.0
|
|
N
|
B:GLY268
|
4.9
|
26.1
|
1.0
|
|
CB
|
B:ASN199
|
5.0
|
34.0
|
1.0
|
|
Sodium binding site 5 out
of 24 in 5c3y
Go back to
Sodium Binding Sites List in 5c3y
Sodium binding site 5 out
of 24 in the Structure of Human Ribokinase Crystallized with Amppnp
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Structure of Human Ribokinase Crystallized with Amppnp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na402
b:29.1
occ:1.00
|
O
|
C:HOH505
|
2.3
|
35.4
|
1.0
|
|
O
|
C:HOH512
|
2.5
|
46.9
|
1.0
|
|
O
|
C:ALA304
|
2.5
|
42.4
|
1.0
|
|
O
|
C:SER301
|
2.6
|
36.2
|
1.0
|
|
O
|
C:ASP263
|
2.6
|
42.1
|
1.0
|
|
OG
|
C:SER310
|
2.7
|
32.7
|
1.0
|
|
CB
|
C:SER310
|
3.3
|
34.5
|
1.0
|
|
C
|
C:SER301
|
3.6
|
35.5
|
1.0
|
|
C
|
C:ALA304
|
3.7
|
43.3
|
1.0
|
|
C
|
C:ASP263
|
3.8
|
43.9
|
1.0
|
|
O
|
C:THR265
|
3.8
|
34.9
|
1.0
|
|
OD2
|
C:ASP263
|
4.1
|
46.0
|
1.0
|
|
CB
|
C:ASP263
|
4.2
|
47.8
|
1.0
|
|
CA
|
C:VAL302
|
4.2
|
39.3
|
1.0
|
|
N
|
C:THR307
|
4.2
|
35.4
|
1.0
|
|
CG
|
C:ASP263
|
4.2
|
46.7
|
1.0
|
|
N
|
C:VAL302
|
4.3
|
36.7
|
1.0
|
|
C
|
C:ALA305
|
4.4
|
42.3
|
1.0
|
|
CA
|
C:ALA305
|
4.4
|
44.3
|
1.0
|
|
N
|
C:ALA305
|
4.5
|
44.9
|
1.0
|
|
CA
|
C:ASP263
|
4.5
|
47.2
|
1.0
|
|
OG
|
C:SER301
|
4.5
|
31.0
|
1.0
|
|
N
|
C:GLY306
|
4.5
|
41.5
|
1.0
|
|
CA
|
C:SER301
|
4.6
|
33.3
|
1.0
|
|
N
|
C:ALA304
|
4.6
|
43.5
|
1.0
|
|
N
|
C:THR265
|
4.6
|
38.3
|
1.0
|
|
CB
|
C:SER301
|
4.6
|
31.0
|
1.0
|
|
C
|
C:VAL302
|
4.6
|
42.2
|
1.0
|
|
O
|
C:ALA305
|
4.7
|
41.8
|
1.0
|
|
CA
|
C:THR307
|
4.7
|
32.5
|
1.0
|
|
O
|
C:THR307
|
4.7
|
30.9
|
1.0
|
|
CA
|
C:ALA304
|
4.7
|
44.3
|
1.0
|
|
N
|
C:THR264
|
4.7
|
42.8
|
1.0
|
|
CA
|
C:SER310
|
4.8
|
33.8
|
1.0
|
|
C
|
C:THR265
|
4.8
|
35.1
|
1.0
|
|
C
|
C:THR264
|
4.9
|
38.2
|
1.0
|
|
O
|
C:VAL302
|
4.9
|
44.6
|
1.0
|
|
CA
|
C:THR264
|
5.0
|
40.0
|
1.0
|
|
OD1
|
C:ASP263
|
5.0
|
47.0
|
1.0
|
|
Sodium binding site 6 out
of 24 in 5c3y
Go back to
Sodium Binding Sites List in 5c3y
Sodium binding site 6 out
of 24 in the Structure of Human Ribokinase Crystallized with Amppnp
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 6 of Structure of Human Ribokinase Crystallized with Amppnp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na403
b:28.6
occ:1.00
|
O
|
C:HOH502
|
2.2
|
17.4
|
1.0
|
|
O
|
C:HOH540
|
2.3
|
25.5
|
1.0
|
|
O
|
C:HOH550
|
2.4
|
29.5
|
1.0
|
|
O
|
C:HOH524
|
2.4
|
18.6
|
1.0
|
|
O
|
C:HOH561
|
2.6
|
24.2
|
1.0
|
|
O
|
C:HOH501
|
2.7
|
18.7
|
1.0
|
|
CA
|
C:GLY268
|
3.8
|
28.6
|
1.0
|
|
C
|
C:GLY268
|
3.9
|
26.3
|
1.0
|
|
OD1
|
C:ASP269
|
4.0
|
23.7
|
1.0
|
|
NZ
|
C:LYS54
|
4.0
|
26.3
|
1.0
|
|
OD1
|
C:ASN177
|
4.2
|
22.5
|
1.0
|
|
O
|
C:HOH546
|
4.2
|
14.1
|
1.0
|
|
ND2
|
C:ASN177
|
4.2
|
23.9
|
1.0
|
|
N
|
C:ASP269
|
4.3
|
25.4
|
1.0
|
|
O
|
C:GLY268
|
4.4
|
25.6
|
1.0
|
|
ND2
|
C:ASN199
|
4.6
|
34.8
|
1.0
|
|
CG
|
C:ASN177
|
4.7
|
22.8
|
1.0
|
|
CB
|
C:ALA179
|
4.7
|
27.4
|
1.0
|
|
CG
|
C:ASP269
|
4.7
|
24.3
|
1.0
|
|
OE2
|
C:GLU202
|
4.7
|
33.1
|
1.0
|
|
N
|
C:GLY268
|
4.8
|
29.8
|
1.0
|
|
OE1
|
C:GLU202
|
4.8
|
33.8
|
1.0
|
|
O3A
|
C:AN2401
|
4.9
|
36.0
|
1.0
|
|
N3B
|
C:AN2401
|
5.0
|
35.7
|
1.0
|
|
O2B
|
C:AN2401
|
5.0
|
29.7
|
1.0
|
|
Sodium binding site 7 out
of 24 in 5c3y
Go back to
Sodium Binding Sites List in 5c3y
Sodium binding site 7 out
of 24 in the Structure of Human Ribokinase Crystallized with Amppnp
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 7 of Structure of Human Ribokinase Crystallized with Amppnp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na402
b:26.7
occ:1.00
|
O
|
D:HOH517
|
2.3
|
16.2
|
1.0
|
|
O
|
D:SER301
|
2.3
|
31.0
|
1.0
|
|
O
|
D:ASP263
|
2.4
|
36.1
|
1.0
|
|
O
|
D:HOH516
|
2.4
|
19.7
|
1.0
|
|
O
|
D:ALA304
|
2.5
|
37.5
|
1.0
|
|
OG
|
D:SER310
|
2.8
|
28.1
|
1.0
|
|
C
|
D:SER301
|
3.4
|
30.3
|
1.0
|
|
CB
|
D:SER310
|
3.4
|
29.7
|
1.0
|
|
C
|
D:ASP263
|
3.6
|
37.8
|
1.0
|
|
C
|
D:ALA304
|
3.7
|
38.5
|
1.0
|
|
CA
|
D:VAL302
|
3.9
|
33.2
|
1.0
|
|
O
|
D:THR265
|
3.9
|
28.9
|
1.0
|
|
N
|
D:VAL302
|
4.0
|
31.0
|
1.0
|
|
CB
|
D:ASP263
|
4.1
|
40.4
|
1.0
|
|
OD2
|
D:ASP263
|
4.2
|
39.3
|
1.0
|
|
C
|
D:VAL302
|
4.3
|
35.7
|
1.0
|
|
CG
|
D:ASP263
|
4.3
|
39.6
|
1.0
|
|
CA
|
D:ASP263
|
4.4
|
40.5
|
1.0
|
|
OG
|
D:SER301
|
4.4
|
26.9
|
1.0
|
|
N
|
D:ALA304
|
4.4
|
38.3
|
1.0
|
|
CA
|
D:SER301
|
4.4
|
28.7
|
1.0
|
|
CB
|
D:SER301
|
4.5
|
27.1
|
1.0
|
|
N
|
D:THR264
|
4.5
|
37.3
|
1.0
|
|
N
|
D:ALA305
|
4.6
|
40.2
|
1.0
|
|
C
|
D:ALA305
|
4.6
|
38.0
|
1.0
|
|
N
|
D:THR307
|
4.6
|
32.0
|
1.0
|
|
CA
|
D:ALA305
|
4.6
|
39.7
|
1.0
|
|
CA
|
D:ALA304
|
4.6
|
39.5
|
1.0
|
|
N
|
D:THR265
|
4.6
|
33.3
|
1.0
|
|
O
|
D:VAL302
|
4.6
|
37.3
|
1.0
|
|
CA
|
D:THR264
|
4.7
|
35.1
|
1.0
|
|
C
|
D:THR264
|
4.8
|
33.2
|
1.0
|
|
N
|
D:GLY306
|
4.8
|
36.9
|
1.0
|
|
N
|
D:ASP263
|
4.8
|
42.3
|
1.0
|
|
O
|
D:ALA305
|
4.9
|
37.7
|
1.0
|
|
CA
|
D:SER310
|
4.9
|
29.6
|
1.0
|
|
O
|
D:THR307
|
4.9
|
28.1
|
1.0
|
|
N
|
D:GLN303
|
4.9
|
36.4
|
1.0
|
|
C
|
D:THR265
|
4.9
|
29.3
|
1.0
|
|
CA
|
D:THR307
|
5.0
|
29.8
|
1.0
|
|
Sodium binding site 8 out
of 24 in 5c3y
Go back to
Sodium Binding Sites List in 5c3y
Sodium binding site 8 out
of 24 in the Structure of Human Ribokinase Crystallized with Amppnp
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 8 of Structure of Human Ribokinase Crystallized with Amppnp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na403
b:34.2
occ:1.00
|
O
|
D:HOH511
|
2.2
|
30.9
|
1.0
|
|
O
|
D:HOH527
|
2.2
|
20.7
|
1.0
|
|
O
|
D:HOH547
|
2.2
|
38.5
|
1.0
|
|
O
|
D:HOH560
|
2.4
|
31.4
|
1.0
|
|
O
|
D:HOH512
|
2.4
|
19.8
|
1.0
|
|
O
|
D:HOH558
|
2.9
|
25.1
|
1.0
|
|
CA
|
D:GLY268
|
3.9
|
24.3
|
1.0
|
|
O
|
D:HOH549
|
4.0
|
24.4
|
1.0
|
|
C
|
D:GLY268
|
4.2
|
22.6
|
1.0
|
|
ND2
|
D:ASN177
|
4.2
|
23.3
|
1.0
|
|
ND2
|
D:ASN199
|
4.2
|
32.5
|
1.0
|
|
NZ
|
D:LYS54
|
4.3
|
25.4
|
1.0
|
|
OD1
|
D:ASP269
|
4.4
|
20.9
|
1.0
|
|
OD1
|
D:ASN177
|
4.4
|
22.9
|
1.0
|
|
OE1
|
D:GLU202
|
4.4
|
33.6
|
1.0
|
|
OE2
|
D:GLU202
|
4.5
|
34.8
|
1.0
|
|
N
|
D:ASP269
|
4.6
|
22.1
|
1.0
|
|
O
|
D:GLY268
|
4.6
|
21.8
|
1.0
|
|
CB
|
D:ALA179
|
4.7
|
26.3
|
1.0
|
|
CG
|
D:ASN177
|
4.8
|
22.6
|
1.0
|
|
N
|
D:GLY268
|
4.9
|
25.1
|
1.0
|
|
O2B
|
D:AN2401
|
4.9
|
29.3
|
1.0
|
|
O
|
D:HOH502
|
4.9
|
18.0
|
1.0
|
|
CD
|
D:GLU202
|
4.9
|
34.5
|
1.0
|
|
Sodium binding site 9 out
of 24 in 5c3y
Go back to
Sodium Binding Sites List in 5c3y
Sodium binding site 9 out
of 24 in the Structure of Human Ribokinase Crystallized with Amppnp
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 9 of Structure of Human Ribokinase Crystallized with Amppnp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Na402
b:25.5
occ:1.00
|
O
|
E:HOH519
|
2.3
|
32.2
|
1.0
|
|
O
|
E:SER301
|
2.5
|
27.4
|
1.0
|
|
O
|
E:HOH517
|
2.5
|
26.3
|
1.0
|
|
O
|
E:ALA304
|
2.5
|
31.1
|
1.0
|
|
O
|
E:ASP263
|
2.5
|
33.1
|
1.0
|
|
OG
|
E:SER310
|
2.7
|
24.5
|
1.0
|
|
CB
|
E:SER310
|
3.3
|
26.1
|
1.0
|
|
C
|
E:SER301
|
3.5
|
27.0
|
1.0
|
|
C
|
E:ASP263
|
3.7
|
34.8
|
1.0
|
|
C
|
E:ALA304
|
3.7
|
32.9
|
1.0
|
|
O
|
E:THR265
|
3.8
|
26.1
|
1.0
|
|
CA
|
E:VAL302
|
4.1
|
30.5
|
1.0
|
|
OD2
|
E:ASP263
|
4.2
|
37.2
|
1.0
|
|
CB
|
E:ASP263
|
4.2
|
37.8
|
1.0
|
|
N
|
E:VAL302
|
4.2
|
28.3
|
1.0
|
|
CG
|
E:ASP263
|
4.3
|
37.1
|
1.0
|
|
N
|
E:THR307
|
4.4
|
29.1
|
1.0
|
|
C
|
E:ALA305
|
4.4
|
32.8
|
1.0
|
|
OG
|
E:SER301
|
4.4
|
23.5
|
1.0
|
|
CA
|
E:SER301
|
4.5
|
25.4
|
1.0
|
|
CA
|
E:ASP263
|
4.5
|
37.9
|
1.0
|
|
CB
|
E:SER301
|
4.5
|
23.5
|
1.0
|
|
N
|
E:ALA304
|
4.5
|
33.6
|
1.0
|
|
CA
|
E:ALA305
|
4.5
|
34.5
|
1.0
|
|
C
|
E:VAL302
|
4.6
|
32.8
|
1.0
|
|
N
|
E:GLY306
|
4.6
|
33.0
|
1.0
|
|
N
|
E:THR265
|
4.6
|
29.7
|
1.0
|
|
N
|
E:ALA305
|
4.6
|
34.3
|
1.0
|
|
N
|
E:THR264
|
4.7
|
34.3
|
1.0
|
|
CA
|
E:ALA304
|
4.7
|
33.6
|
1.0
|
|
O
|
E:THR307
|
4.7
|
25.9
|
1.0
|
|
CA
|
E:THR307
|
4.8
|
26.7
|
1.0
|
|
O
|
E:ALA305
|
4.8
|
31.7
|
1.0
|
|
CA
|
E:SER310
|
4.8
|
25.7
|
1.0
|
|
C
|
E:THR264
|
4.8
|
29.7
|
1.0
|
|
C
|
E:THR265
|
4.8
|
26.3
|
1.0
|
|
O
|
E:VAL302
|
4.8
|
34.7
|
1.0
|
|
CA
|
E:THR264
|
4.9
|
31.9
|
1.0
|
|
N
|
E:ASP263
|
5.0
|
39.9
|
1.0
|
|
Sodium binding site 10 out
of 24 in 5c3y
Go back to
Sodium Binding Sites List in 5c3y
Sodium binding site 10 out
of 24 in the Structure of Human Ribokinase Crystallized with Amppnp
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 10 of Structure of Human Ribokinase Crystallized with Amppnp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Na403
b:26.7
occ:1.00
|
O
|
E:HOH534
|
2.0
|
24.8
|
1.0
|
|
O
|
E:HOH531
|
2.2
|
15.0
|
1.0
|
|
O
|
E:HOH560
|
2.4
|
7.7
|
1.0
|
|
O
|
E:HOH542
|
2.5
|
30.3
|
1.0
|
|
O
|
E:HOH577
|
2.6
|
19.4
|
1.0
|
|
O
|
E:HOH553
|
2.7
|
19.6
|
1.0
|
|
OD1
|
E:ASN177
|
4.0
|
21.0
|
1.0
|
|
OD1
|
E:ASP269
|
4.0
|
18.7
|
1.0
|
|
ND2
|
E:ASN177
|
4.0
|
21.4
|
1.0
|
|
NZ
|
E:LYS54
|
4.0
|
23.5
|
1.0
|
|
CA
|
E:GLY268
|
4.1
|
20.4
|
1.0
|
|
C
|
E:GLY268
|
4.2
|
18.8
|
1.0
|
|
O
|
E:HOH558
|
4.3
|
17.5
|
1.0
|
|
CG
|
E:ASN177
|
4.4
|
20.7
|
1.0
|
|
CB
|
E:ALA179
|
4.4
|
22.6
|
1.0
|
|
N
|
E:ASP269
|
4.5
|
18.4
|
1.0
|
|
OE2
|
E:GLU202
|
4.5
|
30.3
|
1.0
|
|
O
|
E:GLY268
|
4.6
|
18.2
|
1.0
|
|
O
|
E:HOH529
|
4.6
|
20.6
|
1.0
|
|
ND2
|
E:ASN199
|
4.6
|
27.8
|
1.0
|
|
OE1
|
E:GLU202
|
4.6
|
29.5
|
1.0
|
|
CG
|
E:ASP269
|
4.8
|
19.1
|
1.0
|
|
Reference:
J.Park,
J.Chakrabarti,
B.Singh,
R.S.Gupta,
M.S.Junop.
Structure of Human Ribokinase Crystallized with Amppnp To Be Published.
Page generated: Tue Dec 15 10:37:19 2020
|
