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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:

Bromine (Br) 26 atoms
Calcium (Ca) 1 atom

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

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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

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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

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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

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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

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