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Sodium in PDB 8w3m: Crystal Structure of Enterovirus 68 3C Protease with AG7404 at 1.97 Angstroms

Enzymatic activity of Crystal Structure of Enterovirus 68 3C Protease with AG7404 at 1.97 Angstroms

All present enzymatic activity of Crystal Structure of Enterovirus 68 3C Protease with AG7404 at 1.97 Angstroms:
2.7.7.48; 3.4.22.28; 3.4.22.29; 3.6.1.15;

Protein crystallography data

The structure of Crystal Structure of Enterovirus 68 3C Protease with AG7404 at 1.97 Angstroms, PDB code: 8w3m was solved by V.N.Azzolino, A.M.Shaqra, C.A.Schiffer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.16 / 1.97
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 56.491, 56.491, 170.72, 90, 90, 120
R / Rfree (%) 20.6 / 23.9

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Enterovirus 68 3C Protease with AG7404 at 1.97 Angstroms (pdb code 8w3m). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 10 binding sites of Sodium where determined in the Crystal Structure of Enterovirus 68 3C Protease with AG7404 at 1.97 Angstroms, PDB code: 8w3m:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 10 in 8w3m

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Sodium binding site 1 out of 10 in the Crystal Structure of Enterovirus 68 3C Protease with AG7404 at 1.97 Angstroms


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 Enterovirus 68 3C Protease with AG7404 at 1.97 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:71.8
occ:1.00
 O A:HOH331 3.2 52.0 1.0
CD A:ARG19 3.8 50.1 1.0
CA A:GLY23 4.1 45.7 1.0
CG A:ARG19 4.5 46.0 1.0
O A:HOH361 4.5 48.0 1.0
C A:GLY23 4.8 46.9 1.0
O A:HOH307 4.9 55.5 1.0
O A:HOH403 4.9 59.5 1.0
N A:GLY23 5.0 46.2 1.0

Sodium binding site 2 out of 10 in 8w3m

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Sodium binding site 2 out of 10 in the Crystal Structure of Enterovirus 68 3C Protease with AG7404 at 1.97 Angstroms


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 Enterovirus 68 3C Protease with AG7404 at 1.97 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:69.0
occ:1.00
 SG A:CYS60 3.1 57.2 0.6
CB A:CYS60 4.1 49.1 0.6
CG2 A:ILE74 4.1 38.9 1.0
CB A:CYS60 4.1 48.8 0.4
OD2 A:ASP58 4.1 47.9 1.0
CB A:ILE74 4.4 41.3 1.0
CG A:ASP58 4.6 51.5 1.0
O A:ILE74 4.6 40.5 1.0
CB A:ASP58 4.8 46.2 1.0
N A:CYS60 4.9 42.5 1.0

Sodium binding site 3 out of 10 in 8w3m

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Sodium binding site 3 out of 10 in the Crystal Structure of Enterovirus 68 3C Protease with AG7404 at 1.97 Angstroms


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 Enterovirus 68 3C Protease with AG7404 at 1.97 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na204

b:77.7
occ:1.00
 NA A:NA205 2.7 72.2 1.0
OD2 A:ASP181 3.1 82.0 1.0
N A:ASP181 3.6 66.8 1.0
CG A:ASP181 3.8 79.8 1.0
CA A:THR180 3.8 59.9 1.0
CB A:THR180 4.0 57.9 1.0
CG2 A:THR180 4.1 49.0 1.0
C A:THR180 4.3 61.0 1.0
OD1 A:ASP181 4.3 75.2 1.0
NH1 A:ARG87 4.4 47.5 1.0
CB A:ASP181 4.5 76.5 1.0
CA A:ASP181 4.7 77.4 1.0
O A:PHE179 4.7 51.2 1.0
CZ A:ARG87 4.8 55.2 1.0
N A:THR180 5.0 51.5 1.0

Sodium binding site 4 out of 10 in 8w3m

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Sodium binding site 4 out of 10 in the Crystal Structure of Enterovirus 68 3C Protease with AG7404 at 1.97 Angstroms


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 Enterovirus 68 3C Protease with AG7404 at 1.97 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na205

b:72.2
occ:1.00
 NA A:NA204 2.7 77.7 1.0
O A:HOH385 3.2 54.0 1.0
NE2 A:HIS176 3.7 53.3 1.0
NE A:ARG87 3.8 44.3 1.0
CZ A:ARG87 3.9 55.2 1.0
CD A:ARG87 3.9 45.1 1.0
CE1 A:HIS176 4.0 47.9 1.0
NH1 A:ARG87 4.2 47.5 1.0
CB A:ARG87 4.3 43.4 1.0
NH2 A:ARG87 4.4 54.1 1.0
CG2 A:THR180 4.7 49.0 1.0
CD2 A:HIS176 4.7 47.8 1.0
CG A:ARG87 4.8 41.4 1.0
O A:PHE179 4.9 51.2 1.0
CA A:THR180 5.0 59.9 1.0

Sodium binding site 5 out of 10 in 8w3m

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Sodium binding site 5 out of 10 in the Crystal Structure of Enterovirus 68 3C Protease with AG7404 at 1.97 Angstroms


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 Enterovirus 68 3C Protease with AG7404 at 1.97 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na206

b:67.0
occ:1.00
 O A:HOH421 3.3 62.5 1.0
NE A:ARG92 3.4 66.0 1.0
ND1 A:HIS176 3.6 49.7 1.0
CG A:HIS176 3.7 46.0 1.0
CE1 A:HIS176 3.9 47.9 1.0
NH2 A:ARG92 3.9 80.5 1.0
CD2 A:HIS176 4.1 47.8 1.0
NE2 A:HIS176 4.1 53.3 1.0
CZ A:ARG92 4.2 72.7 1.0
CB A:ARG92 4.2 42.7 1.0
CB A:HIS176 4.2 40.1 1.0
CG A:ARG92 4.3 55.2 1.0
CD A:ARG92 4.3 56.2 1.0
O A:HOH423 4.7 60.0 1.0
CA A:ARG92 4.9 44.0 1.0

Sodium binding site 6 out of 10 in 8w3m

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Sodium binding site 6 out of 10 in the Crystal Structure of Enterovirus 68 3C Protease with AG7404 at 1.97 Angstroms


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 Enterovirus 68 3C Protease with AG7404 at 1.97 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na207

b:75.6
occ:1.00
 H24 A:XNV201 3.2 57.6 1.0
H23 A:XNV201 3.3 57.0 1.0
CA A:GLY128 3.8 51.4 1.0
C24 A:XNV201 4.0 47.8 1.0
C23 A:XNV201 4.0 47.2 1.0
C A:GLY128 4.1 56.6 1.0
O A:GLY128 4.3 56.5 1.0
N A:GLY129 4.7 56.1 1.0
N A:GLY128 4.9 55.3 1.0

Sodium binding site 7 out of 10 in 8w3m

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Sodium binding site 7 out of 10 in the Crystal Structure of Enterovirus 68 3C Protease with AG7404 at 1.97 Angstroms


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 Enterovirus 68 3C Protease with AG7404 at 1.97 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na208

b:71.6
occ:1.00
 O A:HOH350 3.3 58.1 1.0
CD A:GLN168 4.0 56.1 1.0
NE2 A:GLN168 4.1 58.0 1.0
CG A:GLN168 4.2 51.0 1.0
CB A:ALA167 4.3 48.4 1.0
OE1 A:GLN168 4.3 53.7 1.0

Sodium binding site 8 out of 10 in 8w3m

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Sodium binding site 8 out of 10 in the Crystal Structure of Enterovirus 68 3C Protease with AG7404 at 1.97 Angstroms


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 Enterovirus 68 3C Protease with AG7404 at 1.97 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na209

b:82.0
occ:1.00
 OH A:TYR122 3.8 51.3 1.0
CZ A:TYR122 4.5 50.6 1.0
CE1 A:TYR122 4.8 46.9 1.0

Sodium binding site 9 out of 10 in 8w3m

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Sodium binding site 9 out of 10 in the Crystal Structure of Enterovirus 68 3C Protease with AG7404 at 1.97 Angstroms


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 Enterovirus 68 3C Protease with AG7404 at 1.97 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na210

b:74.8
occ:1.00
 O A:HOH451 2.6 63.2 1.0
O A:HOH434 3.1 57.4 1.0
O A:HOH412 3.6 59.6 1.0
O A:HOH437 3.8 47.4 1.0
CA A:GLY145 4.2 38.8 1.0
NZ A:LYS108 4.2 64.6 1.0
O A:ALA144 4.2 43.2 1.0
C A:ALA144 4.5 43.5 1.0
N A:GLY145 4.5 40.6 1.0
O A:HOH372 4.6 52.9 1.0
CD A:LYS108 4.6 56.7 1.0
CB A:ALA144 4.8 41.9 1.0
O A:HOH330 4.8 43.7 1.0

Sodium binding site 10 out of 10 in 8w3m

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Sodium binding site 10 out of 10 in the Crystal Structure of Enterovirus 68 3C Protease with AG7404 at 1.97 Angstroms


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 Enterovirus 68 3C Protease with AG7404 at 1.97 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na211

b:71.7
occ:1.00
 O A:HOH443 3.9 64.3 1.0
CB A:SER107 4.5 48.3 1.0
O A:SER107 4.7 43.4 1.0
C A:SER107 4.9 44.8 1.0

Reference:

V.N.Azzolino, A.M.Shaqra, A.Ali, N.K.Yilmaz, C.A.Schiffer. Structural Analysis of Inhibitor Binding to Enterovirus-D68 3C Protease Viruses 2025.
ISSN: ESSN 1999-4915
DOI: 10.3390/V17010075
Page generated: Sat Feb 8 23:46:36 2025

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