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Magnesium in PDB 6l3r: Crystal Structure of Ribonucleotide Reductase R1 Subunit, RRM1 in Complex with 4-Bromo-N-((1S,2R)-2-(Naphthalen-1-Yl)-1-(5-Oxo-4,5- Dihydro-1,3,4-Oxadiazol-2-Yl)Propyl)Benzenesulfonamide

Enzymatic activity of Crystal Structure of Ribonucleotide Reductase R1 Subunit, RRM1 in Complex with 4-Bromo-N-((1S,2R)-2-(Naphthalen-1-Yl)-1-(5-Oxo-4,5- Dihydro-1,3,4-Oxadiazol-2-Yl)Propyl)Benzenesulfonamide

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

Protein crystallography data

The structure of Crystal Structure of Ribonucleotide Reductase R1 Subunit, RRM1 in Complex with 4-Bromo-N-((1S,2R)-2-(Naphthalen-1-Yl)-1-(5-Oxo-4,5- Dihydro-1,3,4-Oxadiazol-2-Yl)Propyl)Benzenesulfonamide, PDB code: 6l3r 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) 47.92 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 106.860, 108.400, 130.100, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 23.2

Other elements in 6l3r:

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

Bromine (Br) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Ribonucleotide Reductase R1 Subunit, RRM1 in Complex with 4-Bromo-N-((1S,2R)-2-(Naphthalen-1-Yl)-1-(5-Oxo-4,5- Dihydro-1,3,4-Oxadiazol-2-Yl)Propyl)Benzenesulfonamide (pdb code 6l3r). 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 4-Bromo-N-((1S,2R)-2-(Naphthalen-1-Yl)-1-(5-Oxo-4,5- Dihydro-1,3,4-Oxadiazol-2-Yl)Propyl)Benzenesulfonamide, PDB code: 6l3r:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6l3r

Go back to Magnesium Binding Sites List in 6l3r
Magnesium binding site 1 out of 2 in the Crystal Structure of Ribonucleotide Reductase R1 Subunit, RRM1 in Complex with 4-Bromo-N-((1S,2R)-2-(Naphthalen-1-Yl)-1-(5-Oxo-4,5- Dihydro-1,3,4-Oxadiazol-2-Yl)Propyl)Benzenesulfonamide


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 4-Bromo-N-((1S,2R)-2-(Naphthalen-1-Yl)-1-(5-Oxo-4,5- Dihydro-1,3,4-Oxadiazol-2-Yl)Propyl)Benzenesulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:34.0
occ:1.00
 O2B A:TTP801 2.1 26.8 1.0
O2A A:TTP801 2.2 31.3 1.0
O A:HOH928 2.3 23.0 1.0
O3G A:TTP801 2.3 29.6 1.0
PB A:TTP801 3.2 30.7 1.0
PG A:TTP801 3.4 30.6 1.0
PA A:TTP801 3.5 27.7 1.0
O1G A:TTP801 3.6 29.7 1.0
O3B A:TTP801 3.7 30.7 1.0
O3A A:TTP801 3.7 29.2 1.0
CB A:SER227 4.1 21.2 1.0
O A:ASP226 4.2 21.9 1.0
O1A A:TTP801 4.5 23.8 1.0
O1B A:TTP801 4.6 30.1 1.0
NH2 A:ARG256 4.6 28.2 1.0
C5' A:TTP801 4.7 24.7 1.0
O5' A:TTP801 4.7 24.1 1.0
CA A:SER227 4.8 23.2 1.0
O2G A:TTP801 4.8 28.9 1.0

Magnesium binding site 2 out of 2 in 6l3r

Go back to Magnesium Binding Sites List in 6l3r
Magnesium binding site 2 out of 2 in the Crystal Structure of Ribonucleotide Reductase R1 Subunit, RRM1 in Complex with 4-Bromo-N-((1S,2R)-2-(Naphthalen-1-Yl)-1-(5-Oxo-4,5- Dihydro-1,3,4-Oxadiazol-2-Yl)Propyl)Benzenesulfonamide


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

b:33.4
occ:1.00
 O3G E:TTP803 2.1 29.4 1.0
O2A E:TTP803 2.1 25.8 1.0
O2B E:TTP803 2.1 26.7 1.0
O E:HOH940 2.2 27.3 1.0
PB E:TTP803 3.2 34.9 1.0
PG E:TTP803 3.2 35.4 1.0
PA E:TTP803 3.5 24.7 1.0
O1G E:TTP803 3.5 35.6 1.0
O3B E:TTP803 3.6 35.8 1.0
O3A E:TTP803 3.8 25.4 1.0
O E:ASP226 4.3 20.5 1.0
CB E:SER227 4.4 23.1 1.0
C5' E:TTP803 4.5 25.0 1.0
NH2 E:ARG256 4.5 28.3 1.0
O5' E:TTP803 4.6 22.9 1.0
O1B E:TTP803 4.6 32.6 1.0
O2G E:TTP803 4.6 31.9 1.0
O1A E:TTP803 4.6 22.2 1.0
CA E:SER227 5.0 24.6 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 10:03:17 2024

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