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Sodium in PDB 2y71: Structure of Mycobacterium Tuberculosis Type II Dehydroquinase Complexed with (1R,4S,5R)-1,4,5-Trihydroxy-3-((5-Methylbenzo(B) Thiophen-2-Yl)Methoxy)Cyclohex-2-Enecarboxylate

Enzymatic activity of Structure of Mycobacterium Tuberculosis Type II Dehydroquinase Complexed with (1R,4S,5R)-1,4,5-Trihydroxy-3-((5-Methylbenzo(B) Thiophen-2-Yl)Methoxy)Cyclohex-2-Enecarboxylate

All present enzymatic activity of Structure of Mycobacterium Tuberculosis Type II Dehydroquinase Complexed with (1R,4S,5R)-1,4,5-Trihydroxy-3-((5-Methylbenzo(B) Thiophen-2-Yl)Methoxy)Cyclohex-2-Enecarboxylate:
4.2.1.10;

Protein crystallography data

The structure of Structure of Mycobacterium Tuberculosis Type II Dehydroquinase Complexed with (1R,4S,5R)-1,4,5-Trihydroxy-3-((5-Methylbenzo(B) Thiophen-2-Yl)Methoxy)Cyclohex-2-Enecarboxylate, PDB code: 2y71 was solved by J.M.Otero, A.L.Llamas-Saiz, G.C.Fox, L.Tizon, V.F.V.Prazeres, H.Lamb, A.R.Hawkins, J.A.Ainsa, L.Castedo, 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) 21.41 / 1.50
Space group F 2 3
Cell size a, b, c (Å), α, β, γ (°) 126.650, 126.650, 126.650, 90.00, 90.00, 90.00
R / Rfree (%) 12.5 / 16.1

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Mycobacterium Tuberculosis Type II Dehydroquinase Complexed with (1R,4S,5R)-1,4,5-Trihydroxy-3-((5-Methylbenzo(B) Thiophen-2-Yl)Methoxy)Cyclohex-2-Enecarboxylate (pdb code 2y71). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Mycobacterium Tuberculosis Type II Dehydroquinase Complexed with (1R,4S,5R)-1,4,5-Trihydroxy-3-((5-Methylbenzo(B) Thiophen-2-Yl)Methoxy)Cyclohex-2-Enecarboxylate, PDB code: 2y71:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 2y71

Go back to Sodium Binding Sites List in 2y71
Sodium binding site 1 out of 2 in the Structure of Mycobacterium Tuberculosis Type II Dehydroquinase Complexed with (1R,4S,5R)-1,4,5-Trihydroxy-3-((5-Methylbenzo(B) Thiophen-2-Yl)Methoxy)Cyclohex-2-Enecarboxylate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Mycobacterium Tuberculosis Type II Dehydroquinase Complexed with (1R,4S,5R)-1,4,5-Trihydroxy-3-((5-Methylbenzo(B) Thiophen-2-Yl)Methoxy)Cyclohex-2-Enecarboxylate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1145

b:37.2
occ:1.00
 OD1 A:ASN6 2.8 18.4 1.0
O A:HOH2044 3.0 65.6 1.0
OE1 A:GLU70 3.0 22.9 1.0
O A:HOH2072 3.1 30.3 1.0
CG A:ASN6 3.7 15.3 1.0
CD A:GLU70 3.9 21.5 1.0
CG2 A:ILE4 3.9 18.8 1.0
ND2 A:ASN6 4.0 17.3 1.0
OE2 A:GLU70 4.0 25.4 1.0
CG2 A:VAL48 4.0 17.2 1.0
NH1 A:ARG50 4.2 25.5 0.5
CB A:VAL48 4.3 15.5 1.0
O A:HOH2045 4.3 29.8 1.0
CG1 A:VAL48 4.4 18.6 1.0
NH2 A:ARG50 4.4 28.0 0.5
CZ A:ARG50 4.6 27.1 0.5

Sodium binding site 2 out of 2 in 2y71

Go back to Sodium Binding Sites List in 2y71
Sodium binding site 2 out of 2 in the Structure of Mycobacterium Tuberculosis Type II Dehydroquinase Complexed with (1R,4S,5R)-1,4,5-Trihydroxy-3-((5-Methylbenzo(B) Thiophen-2-Yl)Methoxy)Cyclohex-2-Enecarboxylate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Mycobacterium Tuberculosis Type II Dehydroquinase Complexed with (1R,4S,5R)-1,4,5-Trihydroxy-3-((5-Methylbenzo(B) Thiophen-2-Yl)Methoxy)Cyclohex-2-Enecarboxylate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1146

b:31.3
occ:1.00
 O A:LEU128 3.0 14.5 1.0
N A:GLN131 3.0 14.8 1.0
N A:ILE130 3.4 14.4 1.0
CB A:GLN131 3.4 16.6 1.0
CA A:GLY129 3.6 12.7 1.0
C A:GLY129 3.7 13.4 1.0
CA A:GLN131 3.8 15.4 1.0
C A:LEU128 3.9 12.9 1.0
C A:ILE130 4.0 14.7 1.0
CG1 A:ILE130 4.1 18.5 0.5
CA A:ILE130 4.2 16.1 1.0
N A:GLY129 4.2 12.8 1.0
O A:HOH2118 4.3 54.2 1.0
CG1 A:ILE130 4.3 19.1 0.5
CD1 A:ILE130 4.4 21.5 0.5
O A:GLY129 4.5 13.3 1.0
OE1 A:GLN131 4.6 22.7 1.0
CG A:GLN131 4.7 19.1 1.0
CB A:ILE130 4.8 17.2 0.5
CB A:ILE130 4.9 17.4 0.5
C A:GLN131 5.0 14.4 1.0

Reference:

L.Tizon, J.M.Otero, V.F.Prazeres, A.L.Llamas-Saiz, G.C.Fox, M.J.Van Raaij, H.Lamb, A.R.Hawkins, J.A.Ainsa, L.Castedo, C.Gonzalez-Bello. A Prodrug Approach For Improving Antituberculosis Activity of Potent Mycobacterium Tuberculosis Type II Dehydroquinase Inhibitors. J. Med. Chem. V. 54 6063 2011.
ISSN: ISSN 1520-4804
PubMed: 21780742
DOI: 10.1021/JM2006063
Page generated: Tue Dec 15 06:00:19 2020

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