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Sodium in PDB 4cky: Structure of the Mycobacterium Tuberculosis Type II Dehydroquinase Inhibited By A 3-Dehydroquinic Acid Derivative

Enzymatic activity of Structure of the Mycobacterium Tuberculosis Type II Dehydroquinase Inhibited By A 3-Dehydroquinic Acid Derivative

All present enzymatic activity of Structure of the Mycobacterium Tuberculosis Type II Dehydroquinase Inhibited By A 3-Dehydroquinic Acid Derivative:
4.2.1.10;

Protein crystallography data

The structure of Structure of the Mycobacterium Tuberculosis Type II Dehydroquinase Inhibited By A 3-Dehydroquinic Acid Derivative, PDB code: 4cky was solved by J.M.Otero, A.L.Llamas-Saiz, M.Maneiro, A.Peon, A.Sedes, H.Lamb, A.R.Hawkins, C.Gonzalez-Bello, M.J.Vanraij, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.31 / 1.65
Space group F 2 3
Cell size a, b, c (Å), α, β, γ (°) 126.950, 126.950, 126.950, 90.00, 90.00, 90.00
R / Rfree (%) 10.258 / 14.434

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of the Mycobacterium Tuberculosis Type II Dehydroquinase Inhibited By A 3-Dehydroquinic Acid Derivative (pdb code 4cky). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Structure of the Mycobacterium Tuberculosis Type II Dehydroquinase Inhibited By A 3-Dehydroquinic Acid Derivative, PDB code: 4cky:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 4cky

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Sodium binding site 1 out of 3 in the Structure of the Mycobacterium Tuberculosis Type II Dehydroquinase Inhibited By A 3-Dehydroquinic 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 Mycobacterium Tuberculosis Type II Dehydroquinase Inhibited By A 3-Dehydroquinic Acid Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1144

b:29.7
occ:1.00
 O A:HOH2143 2.3 45.5 1.0
O A:HOH2052 2.5 40.1 1.0
OD1 A:ASN6 2.7 15.2 1.0
OE1 A:GLU70 2.9 19.5 1.0
O A:HOH2075 3.2 22.7 1.0
CG A:ASN6 3.7 14.3 1.0
CD A:GLU70 3.8 17.6 1.0
ND2 A:ASN6 3.9 14.5 1.0
OE2 A:GLU70 3.9 22.8 1.0
CG2 A:ILE4 4.0 18.5 1.0
CG2 A:VAL48 4.0 16.1 1.0
NH2 A:ARG50 4.1 30.8 1.0
CB A:VAL48 4.3 14.6 1.0
O A:HOH2004 4.3 24.4 1.0
CG1 A:VAL48 4.3 14.8 1.0
CZ A:ARG50 4.7 36.0 1.0
NH1 A:ARG50 4.7 47.2 1.0

Sodium binding site 2 out of 3 in 4cky

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Sodium binding site 2 out of 3 in the Structure of the Mycobacterium Tuberculosis Type II Dehydroquinase Inhibited By A 3-Dehydroquinic 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 Mycobacterium Tuberculosis Type II Dehydroquinase Inhibited By A 3-Dehydroquinic Acid Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1145

b:32.7
occ:1.00
 O A:LEU128 3.0 13.8 1.0
N A:GLN131 3.1 13.6 1.0
N A:ILE130 3.4 12.3 1.0
CG A:GLN131 3.4 22.5 0.5
CB A:GLN131 3.5 17.9 0.5
CB A:GLN131 3.6 14.1 0.5
O A:HOH2138 3.6 27.9 1.0
CA A:GLY129 3.7 12.8 1.0
C A:GLY129 3.7 11.4 1.0
CA A:GLN131 3.9 13.7 1.0
C A:LEU128 4.0 10.4 1.0
CG1 A:ILE130 4.0 25.8 1.0
C A:ILE130 4.1 12.6 1.0
CA A:ILE130 4.2 13.4 1.0
N A:GLY129 4.3 10.3 1.0
CD1 A:ILE130 4.6 42.5 1.0
O A:GLY129 4.6 12.2 1.0
OE1 A:GLN131 4.7 19.3 0.5
CB A:ILE130 4.7 19.0 1.0
CG A:GLN131 4.9 15.2 0.5
CD A:GLN131 4.9 24.6 0.5

Sodium binding site 3 out of 3 in 4cky

Go back to Sodium Binding Sites List in 4cky
Sodium binding site 3 out of 3 in the Structure of the Mycobacterium Tuberculosis Type II Dehydroquinase Inhibited By A 3-Dehydroquinic 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 Mycobacterium Tuberculosis Type II Dehydroquinase Inhibited By A 3-Dehydroquinic Acid Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1146

b:20.3
occ:1.00
 O A:HOH2128 3.0 45.3 1.0
O A:HOH2090 3.1 31.1 1.0
NE2 A:HIS114 3.2 24.7 1.0
NH1 A:ARG87 3.3 13.5 1.0
O A:HOH2042 3.7 48.5 1.0
CG A:PRO119 3.8 11.2 1.0
O A:SER115 4.0 11.3 1.0
CE1 A:HIS114 4.1 24.6 1.0
CD2 A:HIS114 4.2 21.2 1.0
CZ A:ARG87 4.3 12.3 1.0
CD1 A:TYR116 4.4 12.3 1.0
NH2 A:ARG87 4.4 16.6 1.0
CA A:TYR116 4.5 8.7 1.0
CD A:PRO119 4.5 11.0 1.0
CE1 A:TYR116 4.8 15.7 1.0
CB A:PRO119 4.8 11.7 1.0
C A:SER115 4.9 11.2 1.0
O A:TYR116 4.9 10.9 1.0

Reference:

M.Maneiro, J.M.Otero, A.Peon, A.Sedes, A.L.Llamas-Saiz, H.Lamb, A.R.Hawkins, M.J.Vanraaij, C.Gonzalez-Bello. Investigation of the Dehydratation Mechanism Catalyzed By the Type II Dehydroquinase To Be Published.
Page generated: Mon Oct 7 14:45:06 2024

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