Sodium in PDB 4tpy: High Throughput Screening Using Acoustic Droplet Ejection to Combine Protein Crystals and Chemical Libraries on Crystallization Plates at High Density
Enzymatic activity of High Throughput Screening Using Acoustic Droplet Ejection to Combine Protein Crystals and Chemical Libraries on Crystallization Plates at High Density
All present enzymatic activity of High Throughput Screening Using Acoustic Droplet Ejection to Combine Protein Crystals and Chemical Libraries on Crystallization Plates at High Density:
3.4.21.4;
Protein crystallography data
The structure of High Throughput Screening Using Acoustic Droplet Ejection to Combine Protein Crystals and Chemical Libraries on Crystallization Plates at High Density, PDB code: 4tpy
was solved by
E.Teplitsky,
K.Joshi,
J.D.Mullen,
A.S.Soares,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
43.95 /
1.30
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
53.677,
58.443,
66.670,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
14.2 /
17.2
|
Other elements in 4tpy:
The structure of High Throughput Screening Using Acoustic Droplet Ejection to Combine Protein Crystals and Chemical Libraries on Crystallization Plates at High Density also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the High Throughput Screening Using Acoustic Droplet Ejection to Combine Protein Crystals and Chemical Libraries on Crystallization Plates at High Density
(pdb code 4tpy). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the
High Throughput Screening Using Acoustic Droplet Ejection to Combine Protein Crystals and Chemical Libraries on Crystallization Plates at High Density, PDB code: 4tpy:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
Sodium binding site 1 out
of 6 in 4tpy
Go back to
Sodium Binding Sites List in 4tpy
Sodium binding site 1 out
of 6 in the High Throughput Screening Using Acoustic Droplet Ejection to Combine Protein Crystals and Chemical Libraries on Crystallization Plates at High Density
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of High Throughput Screening Using Acoustic Droplet Ejection to Combine Protein Crystals and Chemical Libraries on Crystallization Plates at High Density within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na302
b:17.4
occ:1.00
|
O
|
A:HOH742
|
1.2
|
20.3
|
1.0
|
O
|
A:HOH637
|
2.5
|
23.3
|
1.0
|
OG1
|
A:THR80
|
3.2
|
9.8
|
1.0
|
O
|
A:HOH680
|
3.4
|
38.5
|
1.0
|
ND2
|
A:ASN82
|
3.6
|
11.3
|
1.0
|
CB
|
A:ASN82
|
3.6
|
8.2
|
1.0
|
ND2
|
A:ASN77
|
3.8
|
13.8
|
1.0
|
O
|
A:HOH673
|
3.9
|
35.7
|
1.0
|
CB
|
A:ASN77
|
3.9
|
9.0
|
1.0
|
CG2
|
A:THR80
|
4.0
|
10.4
|
1.0
|
O
|
A:HOH763
|
4.0
|
20.4
|
0.5
|
CB
|
A:THR80
|
4.1
|
10.1
|
1.0
|
CG
|
A:ASN77
|
4.1
|
10.8
|
1.0
|
CG
|
A:ASN82
|
4.2
|
9.3
|
1.0
|
O
|
A:HOH749
|
4.5
|
42.5
|
1.0
|
CA
|
A:ASN82
|
5.0
|
7.5
|
1.0
|
OD1
|
A:ASN77
|
5.0
|
10.0
|
1.0
|
|
Sodium binding site 2 out
of 6 in 4tpy
Go back to
Sodium Binding Sites List in 4tpy
Sodium binding site 2 out
of 6 in the High Throughput Screening Using Acoustic Droplet Ejection to Combine Protein Crystals and Chemical Libraries on Crystallization Plates at High Density
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of High Throughput Screening Using Acoustic Droplet Ejection to Combine Protein Crystals and Chemical Libraries on Crystallization Plates at High Density within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na303
b:29.3
occ:1.00
|
O
|
A:HOH669
|
3.2
|
32.9
|
1.0
|
OE1
|
A:GLN115
|
3.3
|
36.1
|
1.0
|
CG
|
A:GLN115
|
3.3
|
18.2
|
1.0
|
O
|
A:HOH527
|
3.6
|
37.0
|
1.0
|
N
|
A:PRO141
|
3.6
|
11.1
|
1.0
|
CB
|
A:GLN115
|
3.7
|
15.7
|
1.0
|
C
|
A:ALA140
|
3.7
|
10.0
|
1.0
|
CD
|
A:PRO141
|
3.7
|
11.8
|
1.0
|
CD
|
A:GLN115
|
3.8
|
24.6
|
1.0
|
CB
|
A:PRO141
|
4.0
|
12.4
|
1.0
|
CA
|
A:GLN115
|
4.0
|
13.7
|
1.0
|
CA
|
A:ALA140
|
4.1
|
11.2
|
1.0
|
CA
|
A:PRO141
|
4.1
|
11.1
|
1.0
|
OH
|
A:TYR165
|
4.2
|
18.0
|
1.0
|
CG
|
A:PRO141
|
4.2
|
12.9
|
1.0
|
N
|
A:ALA140
|
4.3
|
10.4
|
1.0
|
O
|
A:ALA140
|
4.3
|
10.5
|
1.0
|
C
|
A:LYS139
|
4.6
|
10.3
|
1.0
|
O
|
A:HOH479
|
4.7
|
42.9
|
1.0
|
O
|
A:LYS139
|
4.7
|
11.5
|
1.0
|
N
|
A:GLN115
|
4.9
|
12.6
|
1.0
|
|
Sodium binding site 3 out
of 6 in 4tpy
Go back to
Sodium Binding Sites List in 4tpy
Sodium binding site 3 out
of 6 in the High Throughput Screening Using Acoustic Droplet Ejection to Combine Protein Crystals and Chemical Libraries on Crystallization Plates at High Density
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of High Throughput Screening Using Acoustic Droplet Ejection to Combine Protein Crystals and Chemical Libraries on Crystallization Plates at High Density within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na304
b:18.2
occ:1.00
|
O
|
A:HOH689
|
2.4
|
50.7
|
1.0
|
OD1
|
A:ASP133
|
2.4
|
15.0
|
0.3
|
N
|
A:ASP133
|
3.2
|
12.1
|
0.3
|
N
|
A:ASP133
|
3.3
|
11.6
|
0.7
|
O
|
A:HOH420
|
3.3
|
35.1
|
1.0
|
O
|
A:HOH474
|
3.4
|
31.1
|
0.5
|
CG
|
A:ASP133
|
3.5
|
14.2
|
0.3
|
CA
|
A:PRO132
|
3.8
|
13.1
|
1.0
|
N
|
A:VAL134
|
3.8
|
10.3
|
1.0
|
CB
|
A:PRO132
|
3.9
|
13.1
|
1.0
|
CG2
|
A:VAL134
|
4.0
|
12.7
|
1.0
|
C
|
A:PRO132
|
4.0
|
11.9
|
1.0
|
CA
|
A:ASP133
|
4.1
|
12.5
|
0.3
|
CA
|
A:ASP133
|
4.2
|
13.2
|
0.7
|
CB
|
A:ASP133
|
4.2
|
14.6
|
0.7
|
OD2
|
A:ASP133
|
4.2
|
15.9
|
0.3
|
CB
|
A:ASP133
|
4.3
|
13.4
|
0.3
|
C
|
A:ASP133
|
4.5
|
11.2
|
0.3
|
OD2
|
A:ASP133
|
4.5
|
18.9
|
0.7
|
C
|
A:ASP133
|
4.5
|
10.7
|
0.7
|
CE
|
A:LYS136
|
4.7
|
17.8
|
1.0
|
CG
|
A:ASP133
|
4.7
|
16.2
|
0.7
|
CB
|
A:VAL134
|
4.7
|
10.8
|
1.0
|
CA
|
A:VAL134
|
4.8
|
9.3
|
1.0
|
CG1
|
A:VAL134
|
4.9
|
11.4
|
1.0
|
BR
|
A:BR324
|
5.0
|
29.5
|
0.4
|
O
|
A:HOH750
|
5.0
|
43.4
|
1.0
|
|
Sodium binding site 4 out
of 6 in 4tpy
Go back to
Sodium Binding Sites List in 4tpy
Sodium binding site 4 out
of 6 in the High Throughput Screening Using Acoustic Droplet Ejection to Combine Protein Crystals and Chemical Libraries on Crystallization Plates at High Density
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of High Throughput Screening Using Acoustic Droplet Ejection to Combine Protein Crystals and Chemical Libraries on Crystallization Plates at High Density within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na305
b:15.9
occ:1.00
|
O
|
A:HOH518
|
2.9
|
34.1
|
1.0
|
OH
|
A:TYR76
|
2.9
|
9.1
|
1.0
|
O
|
A:HOH461
|
3.0
|
14.1
|
1.0
|
O
|
A:HOH512
|
3.5
|
27.5
|
1.0
|
CB
|
A:SER78
|
3.6
|
11.2
|
1.0
|
CA
|
A:HIS40
|
3.8
|
7.7
|
1.0
|
O
|
A:HOH642
|
3.8
|
25.9
|
1.0
|
CE2
|
A:TYR76
|
3.9
|
7.7
|
1.0
|
CB
|
A:HIS40
|
3.9
|
8.9
|
1.0
|
CZ
|
A:TYR76
|
3.9
|
7.6
|
1.0
|
O
|
A:HIS40
|
4.3
|
10.3
|
1.0
|
C
|
A:HIS40
|
4.5
|
9.0
|
1.0
|
OG
|
A:SER78
|
4.6
|
13.0
|
1.0
|
CA
|
A:SER78
|
4.6
|
8.7
|
1.0
|
O
|
A:ALA39
|
4.7
|
7.8
|
1.0
|
O
|
A:HOH575
|
4.7
|
50.6
|
1.0
|
N
|
A:HIS40
|
4.7
|
7.1
|
1.0
|
O
|
A:HOH484
|
4.7
|
22.0
|
1.0
|
|
Sodium binding site 5 out
of 6 in 4tpy
Go back to
Sodium Binding Sites List in 4tpy
Sodium binding site 5 out
of 6 in the High Throughput Screening Using Acoustic Droplet Ejection to Combine Protein Crystals and Chemical Libraries on Crystallization Plates at High Density
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of High Throughput Screening Using Acoustic Droplet Ejection to Combine Protein Crystals and Chemical Libraries on Crystallization Plates at High Density within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na306
b:22.8
occ:1.00
|
O
|
A:HOH743
|
2.5
|
39.6
|
1.0
|
O
|
A:HOH775
|
2.6
|
26.5
|
0.5
|
O1
|
A:EDO338
|
2.8
|
31.8
|
1.0
|
N
|
A:PHE64
|
3.2
|
8.4
|
1.0
|
O
|
A:HOH691
|
3.2
|
35.5
|
1.0
|
C1
|
A:EDO338
|
3.4
|
26.3
|
1.0
|
O
|
A:PHE64
|
3.7
|
11.8
|
1.0
|
CA
|
A:GLN63
|
3.8
|
9.0
|
1.0
|
C
|
A:GLN63
|
4.0
|
9.1
|
1.0
|
CA
|
A:PHE64
|
4.1
|
9.3
|
1.0
|
CB
|
A:PHE64
|
4.2
|
8.9
|
1.0
|
C
|
A:PHE64
|
4.3
|
9.5
|
1.0
|
O
|
A:GLU62
|
4.3
|
10.9
|
1.0
|
CB
|
A:GLN63
|
4.5
|
9.7
|
1.0
|
CG
|
A:PHE64
|
4.7
|
9.6
|
1.0
|
N
|
A:GLN63
|
4.7
|
8.7
|
1.0
|
C2
|
A:EDO338
|
4.8
|
24.3
|
1.0
|
O
|
A:HOH780
|
4.8
|
28.6
|
0.5
|
C
|
A:GLU62
|
4.9
|
9.3
|
1.0
|
O
|
A:HOH648
|
5.0
|
23.4
|
1.0
|
CG
|
A:GLN63
|
5.0
|
10.3
|
1.0
|
|
Sodium binding site 6 out
of 6 in 4tpy
Go back to
Sodium Binding Sites List in 4tpy
Sodium binding site 6 out
of 6 in the High Throughput Screening Using Acoustic Droplet Ejection to Combine Protein Crystals and Chemical Libraries on Crystallization Plates at High Density
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 6 of High Throughput Screening Using Acoustic Droplet Ejection to Combine Protein Crystals and Chemical Libraries on Crystallization Plates at High Density within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na307
b:28.4
occ:1.00
|
O
|
A:HOH631
|
3.3
|
23.1
|
1.0
|
N
|
A:SER158
|
3.3
|
11.3
|
1.0
|
CB
|
A:THR157
|
3.7
|
11.5
|
1.0
|
CA
|
A:THR157
|
3.7
|
10.6
|
1.0
|
OG
|
A:SER158
|
3.8
|
21.9
|
1.0
|
O
|
A:HOH749
|
3.8
|
42.5
|
1.0
|
C
|
A:THR157
|
4.0
|
10.6
|
1.0
|
CB
|
A:SER158
|
4.1
|
14.9
|
1.0
|
CA
|
A:SER158
|
4.3
|
12.8
|
1.0
|
CG2
|
A:THR157
|
4.4
|
12.1
|
1.0
|
OG1
|
A:THR157
|
4.8
|
9.9
|
1.0
|
N
|
A:THR157
|
5.0
|
10.3
|
1.0
|
|
Reference:
E.Teplitsky,
K.Joshi,
J.D.Mullen,
A.S.Soares.
High Throughput Screening Using Acoustic Droplet Ejection to Combine Protein Crystals and Chemical Libraries on Crystallization Plates at High Density To Be Published.
Page generated: Mon Oct 7 18:28:16 2024
|