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Magnesium in PDB 6l7l: Crystal Structure of Ribonucleotide Reductase R1 Subunit, RRM1 in Complex with 5-Chloro-2-(N-((1S,2R)-2-(2,3-Dihydro-1H-Inden-4-Yl)-1- (5-Oxo-4,5-Dihydro-1,3,4-Oxadiazol-2-Yl)Propyl)Sulfamoyl)Benzamide

Enzymatic activity of Crystal Structure of Ribonucleotide Reductase R1 Subunit, RRM1 in Complex with 5-Chloro-2-(N-((1S,2R)-2-(2,3-Dihydro-1H-Inden-4-Yl)-1- (5-Oxo-4,5-Dihydro-1,3,4-Oxadiazol-2-Yl)Propyl)Sulfamoyl)Benzamide

All present enzymatic activity of Crystal Structure of Ribonucleotide Reductase R1 Subunit, RRM1 in Complex with 5-Chloro-2-(N-((1S,2R)-2-(2,3-Dihydro-1H-Inden-4-Yl)-1- (5-Oxo-4,5-Dihydro-1,3,4-Oxadiazol-2-Yl)Propyl)Sulfamoyl)Benzamide:
1.17.4.1;

Protein crystallography data

The structure of Crystal Structure of Ribonucleotide Reductase R1 Subunit, RRM1 in Complex with 5-Chloro-2-(N-((1S,2R)-2-(2,3-Dihydro-1H-Inden-4-Yl)-1- (5-Oxo-4,5-Dihydro-1,3,4-Oxadiazol-2-Yl)Propyl)Sulfamoyl)Benzamide, PDB code: 6l7l 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) 76.49 / 2.17
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 70.900, 130.430, 76.610, 90.00, 93.15, 90.00
R / Rfree (%) 19.1 / 24.7

Other elements in 6l7l:

The structure of Crystal Structure of Ribonucleotide Reductase R1 Subunit, RRM1 in Complex with 5-Chloro-2-(N-((1S,2R)-2-(2,3-Dihydro-1H-Inden-4-Yl)-1- (5-Oxo-4,5-Dihydro-1,3,4-Oxadiazol-2-Yl)Propyl)Sulfamoyl)Benzamide also contains other interesting chemical elements:

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-2-(N-((1S,2R)-2-(2,3-Dihydro-1H-Inden-4-Yl)-1- (5-Oxo-4,5-Dihydro-1,3,4-Oxadiazol-2-Yl)Propyl)Sulfamoyl)Benzamide (pdb code 6l7l). 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-2-(N-((1S,2R)-2-(2,3-Dihydro-1H-Inden-4-Yl)-1- (5-Oxo-4,5-Dihydro-1,3,4-Oxadiazol-2-Yl)Propyl)Sulfamoyl)Benzamide, PDB code: 6l7l:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6l7l

Go back to Magnesium Binding Sites List in 6l7l
Magnesium binding site 1 out of 2 in the Crystal Structure of Ribonucleotide Reductase R1 Subunit, RRM1 in Complex with 5-Chloro-2-(N-((1S,2R)-2-(2,3-Dihydro-1H-Inden-4-Yl)-1- (5-Oxo-4,5-Dihydro-1,3,4-Oxadiazol-2-Yl)Propyl)Sulfamoyl)Benzamide


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-2-(N-((1S,2R)-2-(2,3-Dihydro-1H-Inden-4-Yl)-1- (5-Oxo-4,5-Dihydro-1,3,4-Oxadiazol-2-Yl)Propyl)Sulfamoyl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg801

b:63.1
occ:1.00
 O3G A:TTP802 2.1 94.2 1.0
O2A A:TTP802 2.2 69.2 1.0
O2B A:TTP802 3.2 80.0 1.0
PG A:TTP802 3.4 89.9 1.0
O3B A:TTP802 3.6 97.0 1.0
PA A:TTP802 3.7 64.7 1.0
O A:ASP226 3.8 43.6 1.0
PB A:TTP802 3.8 94.6 1.0
CB A:SER227 4.0 34.4 1.0
O1G A:TTP802 4.1 93.4 1.0
O3A A:TTP802 4.2 77.5 1.0
NH2 A:ARG256 4.4 53.3 1.0
C5' A:TTP802 4.4 56.3 1.0
O5' A:TTP802 4.6 57.8 1.0
O2G A:TTP802 4.6 75.2 1.0
CA A:SER227 4.6 35.2 1.0
O1A A:TTP802 4.7 64.0 1.0
C A:ASP226 4.8 39.1 1.0

Magnesium binding site 2 out of 2 in 6l7l

Go back to Magnesium Binding Sites List in 6l7l
Magnesium binding site 2 out of 2 in the Crystal Structure of Ribonucleotide Reductase R1 Subunit, RRM1 in Complex with 5-Chloro-2-(N-((1S,2R)-2-(2,3-Dihydro-1H-Inden-4-Yl)-1- (5-Oxo-4,5-Dihydro-1,3,4-Oxadiazol-2-Yl)Propyl)Sulfamoyl)Benzamide


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-2-(N-((1S,2R)-2-(2,3-Dihydro-1H-Inden-4-Yl)-1- (5-Oxo-4,5-Dihydro-1,3,4-Oxadiazol-2-Yl)Propyl)Sulfamoyl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg801

b:59.1
occ:1.00
 O2B E:TTP802 2.0 91.2 1.0
O2A E:TTP802 2.5 61.3 1.0
O3G E:TTP802 2.9 81.7 1.0
PB E:TTP802 3.4 86.4 1.0
PA E:TTP802 3.8 66.0 1.0
PG E:TTP802 3.8 94.0 1.0
CB E:SER227 3.8 34.2 1.0
O1G E:TTP802 3.8 84.2 1.0
O3B E:TTP802 3.9 95.5 1.0
O3A E:TTP802 4.0 78.9 1.0
O1A E:TTP802 4.5 56.6 1.0
O1B E:TTP802 4.6 90.8 1.0
O E:ASP226 4.6 39.5 1.0
OG E:SER227 4.8 35.7 1.0
CA E:SER227 4.8 35.0 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 10:21:49 2024

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