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Sodium in PDB 4ciy: Crystal Structure of Mycobacterium Tuberculosis Type 2 Dehydroquinase in Complex with (1R,4R,5R)-1,4,5-Trihydroxy-3-((1R)-1-Hydroxy-2- Phenyl)Ethylcyclohex-2-En-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-((1R)-1-Hydroxy-2- Phenyl)Ethylcyclohex-2-En-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-((1R)-1-Hydroxy-2- Phenyl)Ethylcyclohex-2-En-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-((1R)-1-Hydroxy-2- Phenyl)Ethylcyclohex-2-En-1-Carboxylic Acid, PDB code: 4ciy 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) 38.08 / 2.10
Space group F 2 3
Cell size a, b, c (Å), α, β, γ (°) 126.205, 126.205, 126.205, 90.00, 90.00, 90.00
R / Rfree (%) 14.549 / 19.754

Other elements in 4ciy:

The structure of Crystal Structure of Mycobacterium Tuberculosis Type 2 Dehydroquinase in Complex with (1R,4R,5R)-1,4,5-Trihydroxy-3-((1R)-1-Hydroxy-2- Phenyl)Ethylcyclohex-2-En-1-Carboxylic Acid also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

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-((1R)-1-Hydroxy-2- Phenyl)Ethylcyclohex-2-En-1-Carboxylic Acid (pdb code 4ciy). 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-((1R)-1-Hydroxy-2- Phenyl)Ethylcyclohex-2-En-1-Carboxylic Acid, PDB code: 4ciy:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 4ciy

Go back to Sodium Binding Sites List in 4ciy
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-((1R)-1-Hydroxy-2- Phenyl)Ethylcyclohex-2-En-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-((1R)-1-Hydroxy-2- Phenyl)Ethylcyclohex-2-En-1-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1147

b:43.6
occ:1.00
 O A:HOH2057 2.1 42.1 1.0
O A:HOH2056 2.4 34.9 1.0
O A:LEU93 2.6 32.3 1.0
O A:HOH2085 2.7 48.4 1.0
O A:ALA91 3.0 28.8 1.0
O A:HOH2058 3.4 30.5 1.0
C A:ALA91 3.8 31.7 1.0
C A:LEU93 3.8 32.5 1.0
N A:LEU93 4.3 31.5 1.0
CA A:ALA91 4.3 28.3 1.0
O A:CYS90 4.4 23.9 1.0
CA A:LEU93 4.6 30.8 1.0
C A:GLU92 4.6 33.6 1.0
N A:GLU92 4.8 31.6 1.0
O A:ILE120 4.8 25.2 1.0
N A:SER94 4.8 35.4 1.0
CB A:LEU93 4.9 27.1 1.0
CA A:SER94 4.9 34.7 1.0

Sodium binding site 2 out of 3 in 4ciy

Go back to Sodium Binding Sites List in 4ciy
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-((1R)-1-Hydroxy-2- Phenyl)Ethylcyclohex-2-En-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-((1R)-1-Hydroxy-2- Phenyl)Ethylcyclohex-2-En-1-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1148

b:48.4
occ:1.00
 O A:HOH2092 2.7 42.5 1.0
OD1 A:ASN6 2.8 26.2 1.0
OE1 A:GLU70 2.8 34.5 1.0
O A:HOH2043 3.3 37.4 1.0
CD A:GLU70 3.6 34.0 1.0
CG A:ASN6 3.7 27.1 1.0
OE2 A:GLU70 3.7 39.4 1.0
ND2 A:ASN6 3.8 26.6 1.0
CG2 A:ILE4 3.8 32.3 1.0
CG2 A:VAL48 3.9 31.6 1.0
NH2 A:ARG50 4.0 27.1 0.5
CB A:VAL48 4.2 29.1 1.0
CG1 A:VAL48 4.3 32.1 1.0
O A:HOH2002 4.4 34.3 1.0
O A:HOH2042 4.4 41.0 1.0
CZ A:ARG50 4.9 33.7 0.5

Sodium binding site 3 out of 3 in 4ciy

Go back to Sodium Binding Sites List in 4ciy
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-((1R)-1-Hydroxy-2- Phenyl)Ethylcyclohex-2-En-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-((1R)-1-Hydroxy-2- Phenyl)Ethylcyclohex-2-En-1-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1149

b:45.9
occ:1.00
 O A:LEU128 3.0 27.7 1.0
N A:GLN131 3.1 26.6 1.0
O A:HOH2089 3.3 38.5 1.0
CB A:GLN131 3.3 34.3 1.0
N A:ILE130 3.5 26.6 1.0
CA A:GLY129 3.7 28.8 1.0
C A:GLY129 3.8 26.9 1.0
CA A:GLN131 3.8 28.8 1.0
C A:LEU128 3.9 27.1 1.0
CG1 A:ILE130 4.0 41.5 1.0
C A:ILE130 4.1 27.5 1.0
CA A:ILE130 4.2 30.6 1.0
N A:GLY129 4.3 26.4 1.0
OE1 A:GLN131 4.4 51.5 1.0
CG A:GLN131 4.6 41.4 1.0
O A:GLY129 4.6 27.3 1.0
CB A:ILE130 4.8 34.8 1.0
C A:GLN131 4.9 28.0 1.0
CD A:GLN131 5.0 43.7 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 14:44:42 2024

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