Atomistry » Magnesium » PDB 6l57-6lkn » 6lkm
Atomistry »
  Magnesium »
    PDB 6l57-6lkn »
      6lkm »

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

Last articles

Sr in 1SFC
Sr in 1OQ7
Sr in 1U3E
Sr in 1VC0
Sr in 1F1T
Sr in 1J8G
Sr in 1NVY
Sr in 1TJM
Sr in 1NUV
Sr in 1M6G
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy