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Sodium in PDB 4cnp: Structure of the Salmonella Typhi Type I Dehydroquinase Inhibited By A 3-Epiquinic Acid Derivative

Enzymatic activity of Structure of the Salmonella Typhi Type I Dehydroquinase Inhibited By A 3-Epiquinic Acid Derivative

All present enzymatic activity of Structure of the Salmonella Typhi Type I Dehydroquinase Inhibited By A 3-Epiquinic Acid Derivative:
4.2.1.10;

Protein crystallography data

The structure of Structure of the Salmonella Typhi Type I Dehydroquinase Inhibited By A 3-Epiquinic Acid Derivative, PDB code: 4cnp was solved by J.M.Otero, A.L.Llamas-Saiz, M.Maneiro, A.Peon, E.Lence, H.Lamb, A.R.Hawkins, C.Gonzalez-Bello, M.J.Van Raaij, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 51.17 / 1.15
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 60.216, 44.473, 84.702, 90.00, 95.20, 90.00
R / Rfree (%) 13.344 / 16.031

Other elements in 4cnp:

The structure of Structure of the Salmonella Typhi Type I Dehydroquinase Inhibited By A 3-Epiquinic Acid Derivative also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of the Salmonella Typhi Type I Dehydroquinase Inhibited By A 3-Epiquinic Acid Derivative (pdb code 4cnp). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the Structure of the Salmonella Typhi Type I Dehydroquinase Inhibited By A 3-Epiquinic Acid Derivative, PDB code: 4cnp:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 4cnp

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Sodium binding site 1 out of 7 in the Structure of the Salmonella Typhi Type I Dehydroquinase Inhibited By A 3-Epiquinic Acid Derivative


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the Salmonella Typhi Type I Dehydroquinase Inhibited By A 3-Epiquinic Acid Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1253

b:27.6
occ:1.00
 O A:HOH2111 2.4 31.7 1.0
O A:MET23 2.4 7.8 0.5
O A:HOH2077 2.5 28.8 1.0
O A:HOH2393 2.6 17.5 1.0
OE2 A:GLU33 3.0 10.5 0.5
C A:MET23 3.5 7.9 0.5
CD A:GLU33 3.6 10.6 0.5
O A:HOH2073 3.7 9.7 0.5
CD A:GLU33 3.8 10.7 0.5
OE2 A:GLU33 3.9 14.0 0.5
O A:MET23 3.9 8.5 0.5
OE1 A:GLU33 3.9 12.4 0.5
C A:MET23 4.0 7.8 0.5
CG A:GLU33 4.1 9.5 0.5
CG A:GLU33 4.1 9.5 0.5
CB A:MET23 4.1 8.9 1.0
N A:GLY24 4.2 7.7 0.5
CA A:MET23 4.3 8.1 0.5
N A:GLY24 4.4 7.0 0.5
CA A:GLY24 4.4 7.3 0.5
CA A:GLY24 4.4 7.0 0.5
OE1 A:GLU33 4.4 10.5 0.5
O A:HOH2081 4.5 8.6 1.0
CA A:MET23 4.5 8.0 0.5
O A:HOH2097 4.6 11.8 1.0
N A:MET23 4.8 7.2 0.5
N A:MET23 4.8 7.7 0.5
O A:HOH2076 4.9 27.2 1.0

Sodium binding site 2 out of 7 in 4cnp

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Sodium binding site 2 out of 7 in the Structure of the Salmonella Typhi Type I Dehydroquinase Inhibited By A 3-Epiquinic Acid Derivative


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the Salmonella Typhi Type I Dehydroquinase Inhibited By A 3-Epiquinic Acid Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1254

b:34.4
occ:1.00
 O A:HOH2243 2.2 24.5 1.0
O A:HOH2241 2.3 28.1 1.0
O A:HOH2271 2.6 27.8 1.0
O A:HOH2273 2.8 26.9 1.0
O A:ASN135 2.8 8.6 1.0
O A:HOH2242 3.5 14.5 1.0
C A:ASN135 3.8 7.0 1.0
ND2 A:ASN135 3.8 15.0 1.0
O A:HIS134 4.0 8.6 1.0
CB A:ASN135 4.1 9.7 1.0
CG A:ASN135 4.2 12.5 1.0
O A:HOH2239 4.2 23.4 1.0
O A:HOH2244 4.3 21.1 1.0
CG2 A:VAL136 4.3 6.5 1.0
O A:VAL110 4.3 7.8 1.0
CA A:ASN135 4.5 7.9 1.0
N A:VAL136 4.6 5.9 1.0
CA A:VAL136 4.8 5.5 1.0
OD1 A:ASP111 4.8 14.2 1.0
OD1 A:ASN135 5.0 14.3 1.0
CA A:ASP111 5.0 6.1 1.0

Sodium binding site 3 out of 7 in 4cnp

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Sodium binding site 3 out of 7 in the Structure of the Salmonella Typhi Type I Dehydroquinase Inhibited By A 3-Epiquinic Acid Derivative


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of the Salmonella Typhi Type I Dehydroquinase Inhibited By A 3-Epiquinic Acid Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1255

b:18.8
occ:1.00
 O A:HOH2264 2.4 25.9 1.0
O A:HOH2394 2.7 16.9 1.0
NE2 A:HIS134 2.7 8.5 1.0
CE1 A:HIS134 3.6 8.3 1.0
OH A:TYR130 3.6 8.8 1.0
CD2 A:HIS134 3.8 8.2 1.0
CB A:ASP106 3.9 6.6 1.0
CZ A:TYR130 4.3 7.2 1.0
O A:HOH2235 4.3 21.7 1.0
OD2 A:ASP106 4.3 9.0 1.0
CG A:ASP106 4.5 6.9 1.0
O A:HOH2237 4.6 17.6 1.0
CE1 A:TYR130 4.7 7.6 1.0
ND1 A:HIS134 4.7 8.4 1.0
CG A:HIS134 4.9 7.6 1.0

Sodium binding site 4 out of 7 in 4cnp

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Sodium binding site 4 out of 7 in the Structure of the Salmonella Typhi Type I Dehydroquinase Inhibited By A 3-Epiquinic Acid Derivative


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of the Salmonella Typhi Type I Dehydroquinase Inhibited By A 3-Epiquinic Acid Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1256

b:11.0
occ:1.00
 OD1 A:ASN101 2.7 6.4 0.5
O A:ASP114 2.8 8.8 1.0
N A:PHE81 2.9 5.2 1.0
OD1 A:ASN101 2.9 7.0 0.5
ND2 A:ASN101 3.1 7.9 0.5
O A:HOH2201 3.3 8.8 1.0
CG A:ASN101 3.3 6.5 0.5
O A:PHE79 3.7 5.1 1.0
CB A:PHE81 3.7 6.2 1.0
CA A:PHE81 3.8 5.7 1.0
CA A:THR80 3.8 5.1 1.0
C A:THR80 3.8 5.1 1.0
CG A:ASN101 3.8 7.6 0.5
CE1 A:TYR97 3.9 6.3 1.0
O A:PHE81 3.9 6.3 1.0
C A:ASP114 3.9 5.9 1.0
CD1 A:PHE79 4.0 5.7 1.0
ND2 A:ASN101 4.1 8.7 0.5
CG1 A:ILE113 4.1 7.7 0.5
OH A:TYR97 4.2 6.9 1.0
CE1 A:PHE79 4.2 6.2 1.0
C A:PHE81 4.2 5.8 1.0
CZ A:TYR97 4.3 5.9 1.0
C A:PHE79 4.3 4.4 1.0
N A:THR80 4.4 5.0 1.0
N A:ASP114 4.4 5.5 1.0
CB A:ASP114 4.4 7.5 1.0
CA A:ASP114 4.5 5.8 1.0
CD1 A:ILE113 4.6 8.3 0.5
CD1 A:TYR97 4.7 6.8 1.0
CB A:ASN101 4.8 6.6 0.5
O A:THR80 5.0 5.6 1.0
N A:LEU115 5.0 5.0 1.0
OD1 A:ASP114 5.0 9.7 1.0
CB A:THR80 5.0 5.7 1.0

Sodium binding site 5 out of 7 in 4cnp

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Sodium binding site 5 out of 7 in the Structure of the Salmonella Typhi Type I Dehydroquinase Inhibited By A 3-Epiquinic Acid Derivative


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of the Salmonella Typhi Type I Dehydroquinase Inhibited By A 3-Epiquinic Acid Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1253

b:16.4
occ:1.00
 O B:HOH2274 2.6 14.6 1.0
OH B:TYR130 2.7 9.6 1.0
CE1 B:HIS134 3.3 13.0 1.0
NE2 B:HIS134 3.4 12.6 1.0
CZ B:TYR130 3.7 8.2 1.0
CB B:ASP106 3.7 8.1 1.0
OD2 B:ASP106 3.9 10.4 1.0
CE1 B:TYR130 4.0 9.6 1.0
CG B:ASP106 4.1 8.6 1.0
O B:HOH2179 4.1 24.3 1.0
ND1 B:HIS134 4.4 12.2 1.0
CD2 B:HIS134 4.6 10.7 1.0
O B:HOH2158 4.7 17.7 1.0
CE2 B:TYR130 4.8 8.4 1.0

Sodium binding site 6 out of 7 in 4cnp

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Sodium binding site 6 out of 7 in the Structure of the Salmonella Typhi Type I Dehydroquinase Inhibited By A 3-Epiquinic Acid Derivative


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of the Salmonella Typhi Type I Dehydroquinase Inhibited By A 3-Epiquinic Acid Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1254

b:17.0
occ:1.00
 O B:HOH2149 2.7 23.1 1.0
O B:HOH2135 2.7 22.4 1.0
N B:ILE92 3.1 9.5 1.0
N B:ALA84 3.3 13.1 1.0
O B:ILE92 3.4 10.0 1.0
O B:GLN90 3.6 17.4 1.0
CA B:THR91 3.6 10.7 1.0
CB B:SER83 3.7 12.3 1.0
CA B:SER83 3.7 11.1 1.0
C B:THR91 3.8 9.7 1.0
CG1 B:ILE92 4.0 10.1 1.0
C B:SER83 4.0 11.5 1.0
CB B:ALA84 4.1 15.1 1.0
CE1 B:PHE81 4.1 10.0 1.0
CA B:ILE92 4.1 9.4 1.0
C B:ILE92 4.2 8.7 1.0
CA B:ALA84 4.3 13.7 1.0
CG2 B:THR91 4.3 12.5 1.0
O B:HOH2069 4.4 26.4 1.0
C B:GLN90 4.4 11.6 1.0
N B:THR91 4.4 10.2 1.0
CB B:THR91 4.5 11.8 1.0
O B:HOH2148 4.5 23.5 1.0
O B:HOH2132 4.6 16.5 1.0
CB B:ILE92 4.7 9.8 1.0
O B:HOH2147 4.7 30.4 1.0
OG B:SER83 4.8 13.6 1.0
CZ B:PHE81 4.8 10.4 1.0
N B:LYS85 4.8 13.0 1.0
OG1 B:THR91 4.8 14.0 1.0

Sodium binding site 7 out of 7 in 4cnp

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Sodium binding site 7 out of 7 in the Structure of the Salmonella Typhi Type I Dehydroquinase Inhibited By A 3-Epiquinic Acid Derivative


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Structure of the Salmonella Typhi Type I Dehydroquinase Inhibited By A 3-Epiquinic Acid Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1255

b:12.9
occ:1.00
 O B:ASP114 2.7 10.3 1.0
OD1 B:ASN101 2.8 9.9 1.0
N B:PHE81 2.9 6.9 1.0
ND2 B:ASN101 3.2 10.3 1.0
O B:HOH2131 3.3 10.8 1.0
CG B:ASN101 3.3 9.0 1.0
O B:PHE81 3.7 8.1 1.0
CA B:PHE81 3.7 7.0 1.0
CB B:PHE81 3.7 7.5 1.0
O B:PHE79 3.7 6.8 1.0
CA B:THR80 3.8 6.4 1.0
C B:THR80 3.8 6.6 1.0
C B:ASP114 3.8 7.6 1.0
CE1 B:TYR97 3.9 8.2 1.0
C B:PHE81 4.1 7.1 1.0
CD1 B:PHE79 4.2 6.7 1.0
CB B:ASP114 4.2 8.7 1.0
OH B:TYR97 4.2 8.8 1.0
N B:ASP114 4.3 7.0 1.0
CA B:ASP114 4.3 7.4 1.0
CZ B:TYR97 4.4 7.9 1.0
C B:PHE79 4.4 6.0 1.0
CE1 B:PHE79 4.4 7.5 1.0
N B:THR80 4.4 6.0 1.0
CD1 B:TYR97 4.8 8.1 1.0
CB B:ASN101 4.9 7.7 1.0
OD1 B:ASP114 4.9 10.1 1.0
N B:LEU115 4.9 7.3 1.0
O B:THR80 5.0 7.2 1.0
CB B:THR80 5.0 6.6 1.0

Reference:

M.Maneiro, A.Peon, E.Lence, J.M.Otero, A.L.Llamas-Saiz, M.J.Van Raaij, H.Lamb, A.R.Hawkins, C.Gonzalez-Bello. Mechanistic Insight Into the Reaction Catalyzed By Type I Dehydroquinase To Be Published.
Page generated: Mon Oct 7 14:45:48 2024

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