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Magnesium in PDB 6lkm: Crystal Structure of Ribonucleotide Reductase R1 Subunit, RRM1 in Complex with 5-Chloro-N-((1S,2R)-2-(6-Fluoro-2,3-Dimethylphenyl)-1- (5-Oxo-4,5-Dihydro-1,3,4-Oxadiazol-2-Yl)Propyl)-4-Methyl-3,4-Dihydro- 2H-Benzo[B][1,4]Oxazine-8-Sulfonamide

Enzymatic activity of Crystal Structure of Ribonucleotide Reductase R1 Subunit, RRM1 in Complex with 5-Chloro-N-((1S,2R)-2-(6-Fluoro-2,3-Dimethylphenyl)-1- (5-Oxo-4,5-Dihydro-1,3,4-Oxadiazol-2-Yl)Propyl)-4-Methyl-3,4-Dihydro- 2H-Benzo[B][1,4]Oxazine-8-Sulfonamide

All present enzymatic activity of Crystal Structure of Ribonucleotide Reductase R1 Subunit, RRM1 in Complex with 5-Chloro-N-((1S,2R)-2-(6-Fluoro-2,3-Dimethylphenyl)-1- (5-Oxo-4,5-Dihydro-1,3,4-Oxadiazol-2-Yl)Propyl)-4-Methyl-3,4-Dihydro- 2H-Benzo[B][1,4]Oxazine-8-Sulfonamide:
1.17.4.1;

Protein crystallography data

The structure of Crystal Structure of Ribonucleotide Reductase R1 Subunit, RRM1 in Complex with 5-Chloro-N-((1S,2R)-2-(6-Fluoro-2,3-Dimethylphenyl)-1- (5-Oxo-4,5-Dihydro-1,3,4-Oxadiazol-2-Yl)Propyl)-4-Methyl-3,4-Dihydro- 2H-Benzo[B][1,4]Oxazine-8-Sulfonamide, PDB code: 6lkm was solved by S.Miyahara, K.T.Chong, T.Suzuki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 110.62 / 2.55
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 227.830, 66.920, 110.000, 90.00, 103.82, 90.00
R / Rfree (%) 21 / 27.7

Other elements in 6lkm:

The structure of Crystal Structure of Ribonucleotide Reductase R1 Subunit, RRM1 in Complex with 5-Chloro-N-((1S,2R)-2-(6-Fluoro-2,3-Dimethylphenyl)-1- (5-Oxo-4,5-Dihydro-1,3,4-Oxadiazol-2-Yl)Propyl)-4-Methyl-3,4-Dihydro- 2H-Benzo[B][1,4]Oxazine-8-Sulfonamide also contains other interesting chemical elements:

Fluorine (F) 2 atoms
Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Ribonucleotide Reductase R1 Subunit, RRM1 in Complex with 5-Chloro-N-((1S,2R)-2-(6-Fluoro-2,3-Dimethylphenyl)-1- (5-Oxo-4,5-Dihydro-1,3,4-Oxadiazol-2-Yl)Propyl)-4-Methyl-3,4-Dihydro- 2H-Benzo[B][1,4]Oxazine-8-Sulfonamide (pdb code 6lkm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Ribonucleotide Reductase R1 Subunit, RRM1 in Complex with 5-Chloro-N-((1S,2R)-2-(6-Fluoro-2,3-Dimethylphenyl)-1- (5-Oxo-4,5-Dihydro-1,3,4-Oxadiazol-2-Yl)Propyl)-4-Methyl-3,4-Dihydro- 2H-Benzo[B][1,4]Oxazine-8-Sulfonamide, PDB code: 6lkm:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6lkm

Go back to Magnesium Binding Sites List in 6lkm
Magnesium binding site 1 out of 2 in the Crystal Structure of Ribonucleotide Reductase R1 Subunit, RRM1 in Complex with 5-Chloro-N-((1S,2R)-2-(6-Fluoro-2,3-Dimethylphenyl)-1- (5-Oxo-4,5-Dihydro-1,3,4-Oxadiazol-2-Yl)Propyl)-4-Methyl-3,4-Dihydro- 2H-Benzo[B][1,4]Oxazine-8-Sulfonamide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Ribonucleotide Reductase R1 Subunit, RRM1 in Complex with 5-Chloro-N-((1S,2R)-2-(6-Fluoro-2,3-Dimethylphenyl)-1- (5-Oxo-4,5-Dihydro-1,3,4-Oxadiazol-2-Yl)Propyl)-4-Methyl-3,4-Dihydro- 2H-Benzo[B][1,4]Oxazine-8-Sulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg801

b:47.2
occ:1.00
 O2B A:TTP802 1.8 75.6 1.0
O2A A:TTP802 2.0 57.8 1.0
O3G A:TTP802 2.3 73.6 1.0
PB A:TTP802 3.0 85.9 1.0
PA A:TTP802 3.1 56.7 1.0
PG A:TTP802 3.3 80.6 1.0
O3A A:TTP802 3.5 70.1 1.0
O3B A:TTP802 3.5 79.1 1.0
CB A:SER227 3.8 42.6 1.0
O1A A:TTP802 3.9 55.3 1.0
O1G A:TTP802 3.9 82.7 1.0
NZ B:LYS243 4.3 47.2 1.0
O1B A:TTP802 4.3 86.8 1.0
O5' A:TTP802 4.4 55.8 1.0
O2G A:TTP802 4.7 66.7 1.0
C5' A:TTP802 4.7 50.5 1.0
CA A:SER227 4.7 44.7 1.0
O A:ASP226 4.7 51.2 1.0
OG A:SER227 4.9 41.8 1.0
NH2 A:ARG256 5.0 47.2 1.0

Magnesium binding site 2 out of 2 in 6lkm

Go back to Magnesium Binding Sites List in 6lkm
Magnesium binding site 2 out of 2 in the Crystal Structure of Ribonucleotide Reductase R1 Subunit, RRM1 in Complex with 5-Chloro-N-((1S,2R)-2-(6-Fluoro-2,3-Dimethylphenyl)-1- (5-Oxo-4,5-Dihydro-1,3,4-Oxadiazol-2-Yl)Propyl)-4-Methyl-3,4-Dihydro- 2H-Benzo[B][1,4]Oxazine-8-Sulfonamide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Ribonucleotide Reductase R1 Subunit, RRM1 in Complex with 5-Chloro-N-((1S,2R)-2-(6-Fluoro-2,3-Dimethylphenyl)-1- (5-Oxo-4,5-Dihydro-1,3,4-Oxadiazol-2-Yl)Propyl)-4-Methyl-3,4-Dihydro- 2H-Benzo[B][1,4]Oxazine-8-Sulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg801

b:39.5
occ:1.00
 O2B B:TTP802 1.9 56.8 1.0
O2A B:TTP802 2.1 37.9 1.0
O3G B:TTP802 2.5 55.4 1.0
O B:HOH904 2.5 29.9 1.0
PB B:TTP802 2.9 68.9 1.0
O3B B:TTP802 3.1 66.2 1.0
PG B:TTP802 3.3 56.8 1.0
PA B:TTP802 3.4 36.4 1.0
O3A B:TTP802 3.7 46.9 1.0
O1G B:TTP802 3.8 65.7 1.0
CB B:SER227 4.0 31.8 1.0
O1A B:TTP802 4.3 41.5 1.0
O1B B:TTP802 4.3 63.5 1.0
O B:ASP226 4.4 34.6 1.0
O5' B:TTP802 4.5 39.4 1.0
NZ A:LYS243 4.6 46.8 1.0
C5' B:TTP802 4.6 37.5 1.0
O2G B:TTP802 4.7 54.7 1.0
CA B:SER227 4.7 33.8 1.0
NH2 B:ARG256 4.8 34.5 1.0

Reference:

S.Miyahara, S.Hara, K.T.Chong, T.Suzuki, Y.Ogino, T.Hoshino, S.Tsukioka, W.Yano, M.Suzuki, Y.Otsu, T.Yonekura, S.Ito, M.Terasaka, T.Suzuki, A.Hashimoto. TAS1553, A Novel Small Molecule Ribonucleotide Reductase (Rnr) Subunit Interaction Inhibitor, Displays Remarkable Anti-Tumor Activity To Be Published.
Page generated: Tue Oct 1 10:28:05 2024

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