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Sodium in PDB 6buv: Structure of Mycobacterium Tuberculosis Nadd in Complex with Inhibitor [(1~{R},2~{R},5~{S})-5-Methyl-2-Propan-2-Yl-Cyclohexyl] 2-[3-Methyl- 2-(Phenoxymethyl)Benzimidazol-1-Yl]Ethanoate

Enzymatic activity of Structure of Mycobacterium Tuberculosis Nadd in Complex with Inhibitor [(1~{R},2~{R},5~{S})-5-Methyl-2-Propan-2-Yl-Cyclohexyl] 2-[3-Methyl- 2-(Phenoxymethyl)Benzimidazol-1-Yl]Ethanoate

All present enzymatic activity of Structure of Mycobacterium Tuberculosis Nadd in Complex with Inhibitor [(1~{R},2~{R},5~{S})-5-Methyl-2-Propan-2-Yl-Cyclohexyl] 2-[3-Methyl- 2-(Phenoxymethyl)Benzimidazol-1-Yl]Ethanoate:
2.7.7.18;

Protein crystallography data

The structure of Structure of Mycobacterium Tuberculosis Nadd in Complex with Inhibitor [(1~{R},2~{R},5~{S})-5-Methyl-2-Propan-2-Yl-Cyclohexyl] 2-[3-Methyl- 2-(Phenoxymethyl)Benzimidazol-1-Yl]Ethanoate, PDB code: 6buv was solved by I.A.Rodionova, R.W.Reed, L.Sorci, A.L.Osterman, K.V.Korotkov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 52.10 / 1.86
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 163.730, 163.730, 153.650, 90.00, 90.00, 120.00
R / Rfree (%) 17.1 / 19.2

Other elements in 6buv:

The structure of Structure of Mycobacterium Tuberculosis Nadd in Complex with Inhibitor [(1~{R},2~{R},5~{S})-5-Methyl-2-Propan-2-Yl-Cyclohexyl] 2-[3-Methyl- 2-(Phenoxymethyl)Benzimidazol-1-Yl]Ethanoate also contains other interesting chemical elements:

Chlorine (Cl) 5 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Mycobacterium Tuberculosis Nadd in Complex with Inhibitor [(1~{R},2~{R},5~{S})-5-Methyl-2-Propan-2-Yl-Cyclohexyl] 2-[3-Methyl- 2-(Phenoxymethyl)Benzimidazol-1-Yl]Ethanoate (pdb code 6buv). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Structure of Mycobacterium Tuberculosis Nadd in Complex with Inhibitor [(1~{R},2~{R},5~{S})-5-Methyl-2-Propan-2-Yl-Cyclohexyl] 2-[3-Methyl- 2-(Phenoxymethyl)Benzimidazol-1-Yl]Ethanoate, PDB code: 6buv:

Sodium binding site 1 out of 1 in 6buv

Go back to Sodium Binding Sites List in 6buv
Sodium binding site 1 out of 1 in the Structure of Mycobacterium Tuberculosis Nadd in Complex with Inhibitor [(1~{R},2~{R},5~{S})-5-Methyl-2-Propan-2-Yl-Cyclohexyl] 2-[3-Methyl- 2-(Phenoxymethyl)Benzimidazol-1-Yl]Ethanoate


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 Nadd in Complex with Inhibitor [(1~{R},2~{R},5~{S})-5-Methyl-2-Propan-2-Yl-Cyclohexyl] 2-[3-Methyl- 2-(Phenoxymethyl)Benzimidazol-1-Yl]Ethanoate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na301

b:37.4
occ:1.00
 OD1 A:ASP154 2.3 60.3 1.0
O A:LEU156 2.3 33.8 1.0
O A:HOH426 2.5 42.9 1.0
OG1 A:THR157 2.6 40.3 1.0
HA A:THR157 2.9 34.6 1.0
HA A:ASP154 3.1 50.5 1.0
C A:LEU156 3.3 38.9 1.0
HH22 A:ARG128 3.3 0.1 1.0
CG A:ASP154 3.5 61.0 1.0
HH21 A:ARG128 3.5 0.1 1.0
CA A:THR157 3.5 28.9 1.0
CB A:THR157 3.6 36.0 1.0
NH2 A:ARG128 3.7 89.2 1.0
N A:THR157 3.8 29.5 1.0
H A:LEU156 3.9 41.8 1.0
HG23 A:THR157 3.9 44.2 1.0
HD23 A:LEU151 3.9 51.9 1.0
CA A:ASP154 3.9 42.0 1.0
CB A:ASP154 4.2 50.3 1.0
CG2 A:THR157 4.2 36.9 1.0
HB2 A:ASP154 4.3 60.4 1.0
HB A:THR157 4.4 43.3 1.0
OD2 A:ASP154 4.4 61.5 1.0
C A:ASP154 4.5 42.2 1.0
HD22 A:LEU151 4.5 51.9 1.0
HG21 A:THR157 4.5 44.2 1.0
N A:LEU156 4.5 34.8 1.0
CA A:LEU156 4.5 34.9 1.0
CD2 A:LEU151 4.6 43.2 1.0
H A:THR157 4.6 35.4 1.0
O A:ASP154 4.7 45.7 1.0
HA A:LEU151 4.7 54.1 1.0
O A:HOH440 4.7 61.9 1.0
H A:LEU158 4.8 37.7 1.0
O A:LEU151 4.9 44.3 1.0
CZ A:ARG128 4.9 85.0 1.0
C A:THR157 4.9 32.9 1.0
HA A:LEU156 4.9 41.9 1.0
HD21 A:LEU151 4.9 51.9 1.0
H A:ASP154 5.0 50.4 1.0

Reference:

A.L.Osterman, I.Rodionova, X.Li, E.Sergienko, C.T.Ma, A.Catanzaro, M.E.Pettigrove, R.W.Reed, R.Gupta, K.H.Rohde, K.V.Korotkov, L.Sorci. Novel Antimycobacterial Compounds Suppress Nad Biogenesis By Targeting A Unique Pocket of Namn Adenylyltransferase. Acs Chem.Biol. V. 14 949 2019.
ISSN: ESSN 1554-8937
PubMed: 30969758
DOI: 10.1021/ACSCHEMBIO.9B00124
Page generated: Tue Dec 15 11:59:49 2020

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