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Sodium in PDB 4tvt: New Ligand For Thaumatin Discovered Using Acoustic High Throughput Screening

Protein crystallography data

The structure of New Ligand For Thaumatin Discovered Using Acoustic High Throughput Screening, PDB code: 4tvt was solved by E.Teplitsky, K.Joshi, D.L.Ericson, A.Scalia, J.D.Mullen, R.M.Sweet, A.S.Soares, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 53.95 / 1.20
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 57.837, 57.837, 149.584, 90.00, 90.00, 90.00
R / Rfree (%) 14.5 / 16.3

Sodium Binding Sites:

The binding sites of Sodium atom in the New Ligand For Thaumatin Discovered Using Acoustic High Throughput Screening (pdb code 4tvt). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the New Ligand For Thaumatin Discovered Using Acoustic High Throughput Screening, PDB code: 4tvt:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 4tvt

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Sodium binding site 1 out of 8 in the New Ligand For Thaumatin Discovered Using Acoustic High Throughput Screening


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of New Ligand For Thaumatin Discovered Using Acoustic High Throughput Screening within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na307

b:35.4
occ:1.00
 NA A:NA308 2.8 34.7 1.0
O A:HOH511 2.9 47.5 1.0
O A:GLY96 3.2 16.3 1.0
N A:GLY195 3.3 13.5 1.0
NZ A:LYS97 3.5 45.7 1.0
CA A:PRO194 3.7 12.5 1.0
CB A:PRO194 3.8 14.4 1.0
C A:PRO194 3.9 13.1 1.0
O A:HOH819 3.9 59.6 1.0
CE A:LYS97 4.3 40.1 1.0
CA A:GLY195 4.3 12.3 1.0
CD A:LYS97 4.3 24.1 1.0
C A:GLY96 4.4 15.8 1.0
O A:GLY195 4.6 12.9 1.0
O A:HOH753 4.8 46.7 1.0
CG A:PRO194 4.9 14.6 1.0
C A:GLY195 5.0 11.9 1.0

Sodium binding site 2 out of 8 in 4tvt

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Sodium binding site 2 out of 8 in the New Ligand For Thaumatin Discovered Using Acoustic High Throughput Screening


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of New Ligand For Thaumatin Discovered Using Acoustic High Throughput Screening within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na308

b:34.7
occ:1.00
 NA A:NA307 2.8 35.4 1.0
O A:GLY195 2.8 12.9 1.0
O A:HOH753 3.2 46.7 1.0
N A:GLY195 3.6 13.5 1.0
C A:GLY195 3.7 11.9 1.0
O A:HOH535 3.8 42.0 1.0
CA A:GLY195 3.8 12.3 1.0
C A:PRO194 4.2 13.1 1.0
CB A:PRO194 4.3 14.4 1.0
O A:HOH719 4.3 36.1 1.0
O A:HOH446 4.6 22.0 1.0
O1 A:ASC304 4.6 21.5 0.6
CA A:PRO194 4.6 12.5 1.0
O A:GLY96 4.6 16.3 1.0
C1 A:ASC304 4.8 16.4 0.6
N A:SER196 4.8 11.2 1.0
O A:HOH511 4.9 47.5 1.0
O A:PRO194 5.0 12.3 1.0

Sodium binding site 3 out of 8 in 4tvt

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Sodium binding site 3 out of 8 in the New Ligand For Thaumatin Discovered Using Acoustic High Throughput Screening


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of New Ligand For Thaumatin Discovered Using Acoustic High Throughput Screening within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na309

b:19.5
occ:1.00
 O A:LEU74 2.8 14.8 1.0
NH1 A:ARG53 3.0 12.5 1.0
N A:CYS71 3.0 12.0 1.0
OD1 A:ASP70 3.0 18.5 1.0
SG A:CYS71 3.4 14.0 1.0
CA A:ASP70 3.5 10.5 1.0
CG A:ASP70 3.6 14.7 1.0
N A:LEU74 3.6 14.3 1.0
C A:ASP70 3.7 12.0 1.0
C A:LEU74 3.8 14.3 1.0
SG A:CYS66 3.9 13.1 1.0
CD A:ARG53 4.0 10.4 1.0
CZ A:PHE58 4.0 16.7 1.0
CA A:CYS71 4.0 13.4 1.0
C A:GLY73 4.0 15.3 1.0
O A:CYS71 4.1 15.8 1.0
CB A:ASP70 4.1 11.8 1.0
CZ A:ARG53 4.1 11.2 1.0
N A:GLY73 4.2 13.7 1.0
CE1 A:PHE58 4.2 17.1 1.0
OD2 A:ASP70 4.2 19.9 1.0
C A:CYS71 4.2 14.4 1.0
CA A:GLY73 4.2 14.8 1.0
CB A:CYS71 4.2 13.1 1.0
CA A:LEU74 4.3 14.8 1.0
NE A:ARG53 4.5 9.5 1.0
SG A:CYS77 4.5 13.4 1.0
O A:GLY69 4.6 10.7 1.0
N A:ASP70 4.7 10.6 1.0
CB A:CYS66 4.7 12.1 1.0
O A:GLY73 4.8 18.3 1.0
N A:LEU75 4.8 14.1 1.0
O A:ASP70 4.9 11.8 1.0
N A:GLY72 4.9 15.4 1.0
N A:CYS66 5.0 12.1 1.0

Sodium binding site 4 out of 8 in 4tvt

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Sodium binding site 4 out of 8 in the New Ligand For Thaumatin Discovered Using Acoustic High Throughput Screening


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of New Ligand For Thaumatin Discovered Using Acoustic High Throughput Screening within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na310

b:23.8
occ:1.00
 O A:HOH503 2.7 29.1 1.0
O A:HOH493 2.9 16.5 1.0
O A:HOH492 3.5 14.2 1.0
O A:HOH541 3.9 34.1 1.0
CA A:PRO135 4.3 14.0 1.0
O A:GLN133 4.4 11.8 1.0
O A:CYS134 4.8 13.2 1.0
N A:PRO135 4.8 11.3 1.0
N A:ALA136 5.0 14.6 1.0
O A:HOH494 5.0 15.3 1.0
C A:CYS134 5.0 12.0 1.0

Sodium binding site 5 out of 8 in 4tvt

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Sodium binding site 5 out of 8 in the New Ligand For Thaumatin Discovered Using Acoustic High Throughput Screening


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of New Ligand For Thaumatin Discovered Using Acoustic High Throughput Screening within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na311

b:18.7
occ:1.00
 OG1 A:THR206 2.8 30.9 1.0
O A:HOH822 2.9 35.4 1.0
N A:THR206 3.1 13.2 1.0
O A:HOH654 3.3 38.2 1.0
C A:CYS204 3.4 9.4 1.0
N A:PRO205 3.4 9.2 1.0
CA A:CYS204 3.5 8.9 1.0
CD A:PRO205 3.5 9.3 1.0
CG A:PRO111 3.7 12.9 1.0
CB A:PRO111 3.7 10.9 1.0
CB A:THR206 3.7 21.6 1.0
CA A:THR206 3.8 16.9 1.0
CB A:ALA127 3.9 17.4 1.0
O A:CYS204 4.0 10.3 1.0
CG2 A:THR206 4.0 20.9 1.0
CG A:PRO205 4.0 10.6 1.0
O A:ALA127 4.1 19.4 1.0
C A:PRO205 4.1 13.3 1.0
CB A:CYS204 4.2 9.8 1.0
N A:ALA207 4.2 28.9 1.0
C A:THR206 4.2 27.1 1.0
CA A:PRO205 4.3 11.7 1.0
N A:CYS204 4.6 8.8 1.0
CA A:ALA127 4.6 13.8 1.0
O A:HOH784 4.6 68.9 1.0
C A:ALA127 4.8 14.9 1.0
O A:HOH722 4.8 55.2 1.0
CB A:PRO205 4.9 10.7 1.0

Sodium binding site 6 out of 8 in 4tvt

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Sodium binding site 6 out of 8 in the New Ligand For Thaumatin Discovered Using Acoustic High Throughput Screening


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of New Ligand For Thaumatin Discovered Using Acoustic High Throughput Screening within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na312

b:23.1
occ:1.00
 O A:HOH688 2.9 33.6 1.0
O A:HOH803 3.0 24.5 0.5
N A:GLU42 3.2 12.5 1.0
N A:ASP25 3.7 12.9 1.0
CA A:VAL41 3.8 12.1 1.0
CD2 A:LEU24 3.8 14.7 1.0
CA A:LEU24 3.8 12.8 1.0
O A:ASN40 3.9 14.7 1.0
CB A:GLU42 3.9 15.3 1.0
C A:VAL41 4.0 12.0 1.0
CB A:LEU24 4.1 12.6 1.0
O A:HOH667 4.2 40.2 1.0
CA A:GLU42 4.2 12.7 1.0
C A:LEU24 4.3 12.3 1.0
O A:HOH463 4.4 35.2 1.0
CG1 A:VAL41 4.5 13.5 1.0
CG A:LEU24 4.6 12.5 1.0
CB A:VAL41 4.6 11.3 1.0
C A:ASN40 4.6 12.3 1.0
O A:HOH640 4.6 32.9 1.0
O A:ALA23 4.7 16.1 1.0
OG1 A:THR45 4.7 12.9 1.0
N A:VAL41 4.7 10.8 1.0
O A:HOH703 4.8 30.9 1.0
CA A:ASP25 4.8 12.4 1.0
O A:HOH802 4.9 22.6 0.5

Sodium binding site 7 out of 8 in 4tvt

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Sodium binding site 7 out of 8 in the New Ligand For Thaumatin Discovered Using Acoustic High Throughput Screening


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of New Ligand For Thaumatin Discovered Using Acoustic High Throughput Screening within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na313

b:14.7
occ:1.00
 O A:THR86 2.7 9.4 1.0
O A:HOH743 2.8 19.9 0.5
ND2 A:ASN109 2.8 6.6 1.0
N A:ALA52 2.9 7.9 1.0
N A:THR86 3.6 8.3 1.0
O A:ALA52 3.6 9.3 1.0
CB A:TRP51 3.6 8.4 1.0
CA A:TRP51 3.6 7.9 1.0
CB A:ALA52 3.7 9.3 1.0
CA A:ALA52 3.7 7.8 1.0
C A:THR86 3.7 9.0 1.0
CB A:THR86 3.7 8.4 1.0
C A:TRP51 3.7 8.0 1.0
CE A:MET112 3.7 11.4 0.5
CG A:ASN109 3.8 8.9 1.0
CA A:THR86 3.9 8.9 1.0
OD1 A:ASN109 4.0 11.7 1.0
C A:ALA52 4.1 8.8 1.0
OG1 A:THR86 4.1 8.7 1.0
CE A:MET112 4.3 8.6 0.5
C A:THR85 4.4 8.3 1.0
CB A:VAL110 4.4 10.6 1.0
CE1 A:PHE203 4.4 10.2 1.0
O A:VAL110 4.5 9.8 1.0
N A:VAL110 4.6 8.8 1.0
CA A:THR85 4.6 8.8 1.0
CG A:TRP51 4.7 9.1 1.0
CD1 A:PHE203 4.8 10.6 1.0
CB A:THR85 4.9 9.7 1.0
N A:LEU87 4.9 8.2 1.0
CG2 A:VAL110 4.9 10.9 1.0
O A:TRP51 4.9 8.8 1.0
CG2 A:THR86 4.9 10.1 1.0
CD1 A:TRP51 5.0 8.8 1.0

Sodium binding site 8 out of 8 in 4tvt

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Sodium binding site 8 out of 8 in the New Ligand For Thaumatin Discovered Using Acoustic High Throughput Screening


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of New Ligand For Thaumatin Discovered Using Acoustic High Throughput Screening within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na314

b:20.2
occ:1.00
 O A:HOH551 3.0 15.3 0.5
CB A:PRO43 3.8 11.4 1.0
CG A:PRO43 3.8 13.2 1.0
OG A:SER196 4.1 12.6 1.0
O A:HOH446 4.2 22.0 1.0
OD1 A:ASN93 4.8 13.2 1.0

Reference:

E.Teplitsky, K.Joshi, D.L.Ericson, A.Scalia, J.D.Mullen, R.M.Sweet, A.S.Soares. High Throughput Screening Using Acoustic Droplet Ejection to Combine Protein Crystals and Chemical Libraries on Crystallization Plates at High Density Acta Crystallographica D 2014.
Page generated: Mon Oct 7 18:30:58 2024

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