Atomistry » Sodium » PDB 4c6s-4cnt » 4cnp
Atomistry »
  Sodium »
    PDB 4c6s-4cnt »
      4cnp »

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

Go back to Sodium Binding Sites List in 4cnp
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

Go back to Sodium Binding Sites List in 4cnp
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

Go back to Sodium Binding Sites List in 4cnp
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

Go back to Sodium Binding Sites List in 4cnp
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

Go back to Sodium Binding Sites List in 4cnp
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

Go back to Sodium Binding Sites List in 4cnp
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

Go back to Sodium Binding Sites List in 4cnp
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: Tue Dec 15 06:35:54 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy