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Sodium in PDB 4cnn: High Resolution Structure of Salmonella Typhi Type I Dehydroquinase

Enzymatic activity of High Resolution Structure of Salmonella Typhi Type I Dehydroquinase

All present enzymatic activity of High Resolution Structure of Salmonella Typhi Type I Dehydroquinase:
4.2.1.10;

Protein crystallography data

The structure of High Resolution Structure of Salmonella Typhi Type I Dehydroquinase, PDB code: 4cnn 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) 51.20 / 1.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 60.273, 44.422, 84.711, 90.00, 95.19, 90.00
R / Rfree (%) 13.134 / 14.872

Other elements in 4cnn:

The structure of High Resolution Structure of Salmonella Typhi Type I Dehydroquinase also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the High Resolution Structure of Salmonella Typhi Type I Dehydroquinase (pdb code 4cnn). 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 Resolution Structure of Salmonella Typhi Type I Dehydroquinase, PDB code: 4cnn:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 4cnn

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Sodium binding site 1 out of 6 in the High Resolution Structure of Salmonella Typhi Type I Dehydroquinase


Mono view


Stereo pair view

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

b:9.9
occ:1.00
 O A:HOH2248 3.1 17.7 1.0
O A:HOH2435 3.1 19.9 1.0
N A:LYS85 3.5 7.5 0.5
N A:ALA84 3.5 10.1 1.0
CA A:THR91 3.6 7.2 1.0
N A:ILE92 3.6 7.0 1.0
CB A:SER83 3.8 10.3 1.0
CB A:THR91 3.8 7.6 1.0
O A:ILE92 3.9 8.3 1.0
CB A:ALA84 3.9 10.4 1.0
CG2 A:THR91 4.0 7.8 1.0
CB A:LYS85 4.0 8.7 0.5
C A:THR91 4.1 6.9 1.0
CA A:ALA84 4.1 9.1 1.0
N A:LYS85 4.2 12.0 0.5
C A:SER83 4.2 8.4 1.0
CA A:SER83 4.3 9.1 1.0
C A:ALA84 4.3 7.7 0.5
O A:HOH2128 4.3 24.9 1.0
CA A:LYS85 4.3 8.0 0.5
O A:GLN90 4.4 7.8 1.0
CG2 A:ILE92 4.5 7.2 1.0
OG A:SER83 4.5 10.2 1.0
CG A:LYS85 4.7 14.3 0.5
O A:HOH2249 4.7 23.7 1.0
N A:THR91 4.7 7.0 1.0
CA A:ILE92 4.7 7.0 1.0
C A:ALA84 4.7 10.8 0.5
C A:ILE92 4.7 7.2 1.0
O A:HOH2345 4.9 33.7 1.0
C A:GLN90 5.0 6.7 1.0

Sodium binding site 2 out of 6 in 4cnn

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Sodium binding site 2 out of 6 in the High Resolution Structure of Salmonella Typhi Type I Dehydroquinase


Mono view


Stereo pair view

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

b:16.6
occ:1.00
 NE2 A:HIS134 2.7 8.3 1.0
O A:HOH2436 2.7 14.4 1.0
CE1 A:HIS134 3.6 7.9 1.0
OH A:TYR130 3.6 8.8 1.0
CD2 A:HIS134 3.7 7.9 1.0
CB A:ASP106 3.9 6.3 1.0
O A:HOH2263 4.2 21.5 1.0
OD2 A:ASP106 4.3 8.2 1.0
CZ A:TYR130 4.4 7.5 1.0
CG A:ASP106 4.5 6.5 1.0
CE1 A:TYR130 4.8 7.6 1.0
ND1 A:HIS134 4.8 7.8 1.0
CG A:HIS134 4.8 7.5 1.0

Sodium binding site 3 out of 6 in 4cnn

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Sodium binding site 3 out of 6 in the High Resolution Structure of Salmonella Typhi Type I Dehydroquinase


Mono view


Stereo pair view

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

b:10.0
occ:1.00
 O A:ASP114 2.7 8.8 1.0
OD1 A:ASN101 2.8 5.0 0.5
N A:PHE81 2.9 5.1 1.0
ND2 A:ASN101 3.0 8.2 0.5
ND2 A:ASN101 3.1 6.1 0.5
CG A:ASN101 3.3 5.7 0.5
O A:HOH2230 3.4 7.5 1.0
CB A:PHE81 3.7 5.8 1.0
O A:PHE79 3.7 5.2 1.0
CA A:PHE81 3.7 5.6 1.0
C A:THR80 3.8 5.0 1.0
CA A:THR80 3.8 5.0 1.0
O A:PHE81 3.8 5.8 1.0
CE1 A:TYR97 3.8 5.9 1.0
C A:ASP114 3.9 5.8 1.0
CG A:ASN101 4.0 8.4 0.5
CD1 A:PHE79 4.0 5.8 1.0
CG1 A:ILE113 4.0 8.4 0.5
OH A:TYR97 4.2 6.5 1.0
C A:PHE81 4.2 5.7 1.0
OD1 A:ASN101 4.2 10.6 0.5
CE1 A:PHE79 4.2 6.2 1.0
CZ A:TYR97 4.3 5.8 1.0
C A:PHE79 4.3 4.7 1.0
N A:THR80 4.4 5.0 1.0
N A:ASP114 4.4 5.2 1.0
CB A:ASP114 4.5 6.6 1.0
CA A:ASP114 4.5 5.5 1.0
CD1 A:ILE113 4.5 8.8 0.5
CD1 A:TYR97 4.7 6.5 1.0
CB A:ASN101 4.8 6.8 0.5
O A:THR80 4.9 5.4 1.0
N A:LEU115 5.0 5.0 1.0

Sodium binding site 4 out of 6 in 4cnn

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Sodium binding site 4 out of 6 in the High Resolution Structure of Salmonella Typhi Type I Dehydroquinase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of High Resolution Structure of Salmonella Typhi Type I Dehydroquinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1254

b:14.6
occ:1.00
 O B:HOH2170 2.7 20.4 1.0
O B:HOH2148 2.8 23.6 1.0
N B:ILE92 3.2 10.4 1.0
N B:ALA84 3.4 12.6 1.0
O B:ILE92 3.4 10.4 1.0
O B:GLN90 3.5 15.9 1.0
CA B:THR91 3.6 11.4 1.0
CB B:SER83 3.7 11.4 1.0
CA B:SER83 3.7 10.4 1.0
C B:THR91 3.9 10.9 1.0
CE1 B:PHE81 4.0 10.5 1.0
CG1 B:ILE92 4.1 10.7 1.0
C B:SER83 4.1 11.0 1.0
CB B:ALA84 4.1 14.1 1.0
CA B:ILE92 4.2 10.5 1.0
C B:ILE92 4.2 9.9 1.0
O B:HOH2070 4.3 27.8 1.0
CA B:ALA84 4.3 13.1 1.0
C B:GLN90 4.4 12.2 1.0
CG2 B:THR91 4.5 12.4 1.0
N B:THR91 4.5 12.1 1.0
CB B:THR91 4.5 11.6 1.0
O B:HOH2169 4.6 23.2 1.0
O B:HOH2146 4.6 15.5 1.0
CZ B:PHE81 4.7 11.4 1.0
CB B:ILE92 4.7 10.5 1.0
OG B:SER83 4.8 12.2 1.0
N B:LYS85 4.9 12.8 1.0
OG1 B:THR91 4.9 13.8 1.0
CD1 B:PHE81 5.0 9.1 1.0

Sodium binding site 5 out of 6 in 4cnn

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Sodium binding site 5 out of 6 in the High Resolution Structure of Salmonella Typhi Type I Dehydroquinase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of High Resolution Structure of Salmonella Typhi Type I Dehydroquinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1255

b:13.8
occ:1.00
 O B:HOH2318 2.6 11.8 1.0
OH B:TYR130 2.7 8.3 1.0
CE1 B:HIS134 3.3 11.6 1.0
NE2 B:HIS134 3.4 11.1 1.0
CZ B:TYR130 3.7 7.6 1.0
CB B:ASP106 3.8 7.2 1.0
OD2 B:ASP106 3.9 8.2 1.0
O B:HOH2213 3.9 19.6 1.0
CE1 B:TYR130 4.1 9.0 1.0
CG B:ASP106 4.2 7.4 1.0
ND1 B:HIS134 4.4 10.8 1.0
CD2 B:HIS134 4.6 9.6 1.0
O B:HOH2184 4.6 11.8 1.0
CE2 B:TYR130 4.8 8.0 1.0

Sodium binding site 6 out of 6 in 4cnn

Go back to Sodium Binding Sites List in 4cnn
Sodium binding site 6 out of 6 in the High Resolution Structure of Salmonella Typhi Type I Dehydroquinase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of High Resolution Structure of Salmonella Typhi Type I Dehydroquinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1256

b:12.8
occ:1.00
 O B:ASP114 2.7 13.3 1.0
OD1 B:ASN101 2.8 9.2 1.0
N B:PHE81 2.9 7.5 1.0
ND2 B:ASN101 3.1 10.2 1.0
CG B:ASN101 3.3 8.6 1.0
O B:HOH2145 3.4 10.5 1.0
O B:PHE81 3.7 8.1 1.0
CA B:PHE81 3.7 7.8 1.0
CB B:PHE81 3.7 8.0 1.0
O B:PHE79 3.8 7.2 1.0
CA B:THR80 3.8 7.0 1.0
C B:THR80 3.8 7.1 1.0
C B:ASP114 3.9 8.9 1.0
CE1 B:TYR97 3.9 9.0 1.0
C B:PHE81 4.1 7.7 1.0
CD1 B:PHE79 4.1 7.3 1.0
OH B:TYR97 4.3 9.6 1.0
CE1 B:PHE79 4.3 8.1 1.0
N B:ASP114 4.4 7.3 1.0
C B:PHE79 4.4 6.8 1.0
CZ B:TYR97 4.4 8.8 1.0
N B:THR80 4.4 6.6 1.0
CA B:ASP114 4.5 8.2 1.0
CB B:ASP114 4.5 9.9 1.0
CD1 B:TYR97 4.8 8.8 1.0
CB B:ASN101 4.8 8.3 1.0
N B:LEU115 4.9 7.8 1.0
O B:THR80 5.0 7.8 1.0
CB B:THR80 5.0 7.3 1.0

Reference:

M.Maneiro, A.Peon, E.Lence, J.M.Otero, A.Llamas-Saiz, M.J.Vanraaij, 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 14:45:47 2024

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