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Sodium in PDB 4ciw: Crystal Structure of Mycobacterium Tuberculosis Type 2 Dehydroquinase in Complex with (1R,4R,5R)-1,4,5-Trihydroxy-3- (2-Hydroxy)Ethylcyclohex-2-Ene-1-Carboxylic Acid

Enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Type 2 Dehydroquinase in Complex with (1R,4R,5R)-1,4,5-Trihydroxy-3- (2-Hydroxy)Ethylcyclohex-2-Ene-1-Carboxylic Acid

All present enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Type 2 Dehydroquinase in Complex with (1R,4R,5R)-1,4,5-Trihydroxy-3- (2-Hydroxy)Ethylcyclohex-2-Ene-1-Carboxylic Acid:
4.2.1.10;

Protein crystallography data

The structure of Crystal Structure of Mycobacterium Tuberculosis Type 2 Dehydroquinase in Complex with (1R,4R,5R)-1,4,5-Trihydroxy-3- (2-Hydroxy)Ethylcyclohex-2-Ene-1-Carboxylic Acid, PDB code: 4ciw was solved by J.M.Otero, A.L.Llamas-Saiz, H.Lamb, A.R.Hawkins, B.Blanco, A.Sedes, A.Peon, 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) 38.13 / 2.20
Space group F 2 3
Cell size a, b, c (Å), α, β, γ (°) 126.380, 126.380, 126.380, 90.00, 90.00, 90.00
R / Rfree (%) 14.177 / 19.227

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Mycobacterium Tuberculosis Type 2 Dehydroquinase in Complex with (1R,4R,5R)-1,4,5-Trihydroxy-3- (2-Hydroxy)Ethylcyclohex-2-Ene-1-Carboxylic Acid (pdb code 4ciw). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Mycobacterium Tuberculosis Type 2 Dehydroquinase in Complex with (1R,4R,5R)-1,4,5-Trihydroxy-3- (2-Hydroxy)Ethylcyclohex-2-Ene-1-Carboxylic Acid, PDB code: 4ciw:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 4ciw

Go back to Sodium Binding Sites List in 4ciw
Sodium binding site 1 out of 3 in the Crystal Structure of Mycobacterium Tuberculosis Type 2 Dehydroquinase in Complex with (1R,4R,5R)-1,4,5-Trihydroxy-3- (2-Hydroxy)Ethylcyclohex-2-Ene-1-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Mycobacterium Tuberculosis Type 2 Dehydroquinase in Complex with (1R,4R,5R)-1,4,5-Trihydroxy-3- (2-Hydroxy)Ethylcyclohex-2-Ene-1-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1145

b:45.2
occ:1.00
 O A:HOH2024 2.5 36.5 1.0
O A:HOH2080 2.7 43.2 1.0
OD1 A:ASN6 2.8 19.8 1.0
OE1 A:GLU70 2.8 24.1 1.0
O A:HOH2038 3.0 30.1 1.0
CD A:GLU70 3.6 24.0 1.0
CG A:ASN6 3.7 18.9 1.0
OE2 A:GLU70 3.8 25.8 1.0
CG2 A:ILE4 3.8 22.4 1.0
ND2 A:ASN6 3.9 18.2 1.0
CG2 A:VAL48 4.0 21.0 1.0
CB A:VAL48 4.3 20.7 1.0
NH2 A:ARG50 4.4 40.2 1.0
O A:HOH2002 4.4 30.9 1.0
CG1 A:VAL48 4.5 21.6 1.0

Sodium binding site 2 out of 3 in 4ciw

Go back to Sodium Binding Sites List in 4ciw
Sodium binding site 2 out of 3 in the Crystal Structure of Mycobacterium Tuberculosis Type 2 Dehydroquinase in Complex with (1R,4R,5R)-1,4,5-Trihydroxy-3- (2-Hydroxy)Ethylcyclohex-2-Ene-1-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Mycobacterium Tuberculosis Type 2 Dehydroquinase in Complex with (1R,4R,5R)-1,4,5-Trihydroxy-3- (2-Hydroxy)Ethylcyclohex-2-Ene-1-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1146

b:45.4
occ:1.00
 O A:LEU128 3.0 16.4 1.0
CG A:GLN131 3.2 21.4 0.5
N A:GLN131 3.5 19.3 1.0
N A:ILE130 3.6 19.9 1.0
CB A:GLN131 3.6 20.6 0.5
CA A:GLY129 3.8 18.4 1.0
CB A:GLN131 3.9 20.3 0.5
C A:GLY129 3.9 19.5 1.0
O A:HOH2012 3.9 35.5 1.0
C A:LEU128 4.0 16.9 1.0
CA A:GLN131 4.2 19.5 0.5
NE2 A:GLN131 4.2 23.0 0.5
CA A:GLN131 4.2 19.4 0.5
CG1 A:ILE130 4.2 26.1 1.0
CD A:GLN131 4.3 22.5 0.5
N A:GLY129 4.3 17.8 1.0
C A:ILE130 4.4 20.3 1.0
CA A:ILE130 4.4 21.4 1.0
CD1 A:ILE130 4.5 30.9 1.0
O A:GLY129 4.8 20.2 1.0
CG A:GLN131 4.9 22.2 0.5
CB A:ILE130 5.0 24.3 1.0

Sodium binding site 3 out of 3 in 4ciw

Go back to Sodium Binding Sites List in 4ciw
Sodium binding site 3 out of 3 in the Crystal Structure of Mycobacterium Tuberculosis Type 2 Dehydroquinase in Complex with (1R,4R,5R)-1,4,5-Trihydroxy-3- (2-Hydroxy)Ethylcyclohex-2-Ene-1-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Mycobacterium Tuberculosis Type 2 Dehydroquinase in Complex with (1R,4R,5R)-1,4,5-Trihydroxy-3- (2-Hydroxy)Ethylcyclohex-2-Ene-1-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1147

b:29.7
occ:1.00
 O A:HOH2051 3.1 35.0 1.0
NH1 A:ARG87 3.2 20.3 1.0
NE2 A:HIS114 3.5 35.5 1.0
CG A:PRO119 3.8 15.7 1.0
O A:SER115 4.2 17.4 1.0
CZ A:ARG87 4.3 20.2 1.0
CD1 A:TYR116 4.3 18.6 1.0
CE1 A:HIS114 4.4 33.7 1.0
CD2 A:HIS114 4.5 34.7 1.0
CD A:PRO119 4.5 16.3 1.0
CA A:TYR116 4.5 16.3 1.0
NH2 A:ARG87 4.7 20.5 1.0
CB A:PRO119 4.8 16.0 1.0
CE1 A:TYR116 4.8 20.1 1.0
O A:TYR116 4.9 16.5 1.0

Reference:

B.Blanco, A.Sedes, A.Peon, J.M.Otero, M.J.Van Raaij, P.Thompson, A.R.Hawkins, C.Gonzalez-Bello. Exploring the Water-Binding Pocket of the Type II Dehydroquinase Enzyme in the Structure-Based Design of Inhibitors. J.Med.Chem. V. 57 3494 2014.
ISSN: ISSN 0022-2623
PubMed: 24689821
DOI: 10.1021/JM500175Z
Page generated: Mon Oct 7 14:44:09 2024

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