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Magnesium in PDB 4hyp: Pyrrolopyrimidine Inhibitors of Dna Gyrase B and Topoisomerase IV, Part I: Structure Guided Discovery and Optimization of Dual Targeting Agents with Potent, Broad-Spectrum Enzymatic Activity.

Enzymatic activity of Pyrrolopyrimidine Inhibitors of Dna Gyrase B and Topoisomerase IV, Part I: Structure Guided Discovery and Optimization of Dual Targeting Agents with Potent, Broad-Spectrum Enzymatic Activity.

All present enzymatic activity of Pyrrolopyrimidine Inhibitors of Dna Gyrase B and Topoisomerase IV, Part I: Structure Guided Discovery and Optimization of Dual Targeting Agents with Potent, Broad-Spectrum Enzymatic Activity.:
5.99.1.3;

Protein crystallography data

The structure of Pyrrolopyrimidine Inhibitors of Dna Gyrase B and Topoisomerase IV, Part I: Structure Guided Discovery and Optimization of Dual Targeting Agents with Potent, Broad-Spectrum Enzymatic Activity., PDB code: 4hyp was solved by D.C.Bensen, C.J.Creighton, L.W.Tari, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.89 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 48.408, 101.312, 82.282, 90.00, 101.60, 90.00
R / Rfree (%) 19.5 / 29.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Pyrrolopyrimidine Inhibitors of Dna Gyrase B and Topoisomerase IV, Part I: Structure Guided Discovery and Optimization of Dual Targeting Agents with Potent, Broad-Spectrum Enzymatic Activity. (pdb code 4hyp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Pyrrolopyrimidine Inhibitors of Dna Gyrase B and Topoisomerase IV, Part I: Structure Guided Discovery and Optimization of Dual Targeting Agents with Potent, Broad-Spectrum Enzymatic Activity., PDB code: 4hyp:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4hyp

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Magnesium binding site 1 out of 4 in the Pyrrolopyrimidine Inhibitors of Dna Gyrase B and Topoisomerase IV, Part I: Structure Guided Discovery and Optimization of Dual Targeting Agents with Potent, Broad-Spectrum Enzymatic Activity.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pyrrolopyrimidine Inhibitors of Dna Gyrase B and Topoisomerase IV, Part I: Structure Guided Discovery and Optimization of Dual Targeting Agents with Potent, Broad-Spectrum Enzymatic Activity. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:25.9
occ:1.00
OE1 A:GLU42 2.3 25.8 1.0
O A:HOH465 2.4 19.8 1.0
O A:VAL122 2.6 21.9 1.0
OD2 A:ASP45 2.6 34.7 1.0
O A:LEU119 3.0 25.7 1.0
CD A:GLU42 3.4 25.9 1.0
O A:HOH466 3.6 22.6 1.0
N A:LEU119 3.6 26.4 1.0
CG A:ASP45 3.6 31.5 1.0
C A:GLY118 3.7 25.7 1.0
O A:HOH468 3.7 19.5 1.0
CA A:GLY118 3.7 24.1 1.0
OE2 A:GLU42 3.7 25.5 1.0
C A:VAL122 3.8 21.3 1.0
C A:LEU119 3.8 28.0 1.0
CB A:ASP45 4.0 27.4 1.0
N A:GLY118 4.3 25.4 1.0
N A:VAL122 4.3 22.7 1.0
O A:GLY118 4.3 26.2 1.0
CA A:LEU119 4.4 26.6 1.0
CA A:VAL122 4.4 21.6 1.0
CB A:VAL122 4.6 20.4 1.0
CG A:GLU42 4.7 25.5 1.0
OD1 A:ASP45 4.8 31.5 1.0
N A:HIS120 4.8 28.5 1.0
N A:GLY123 4.9 20.9 1.0

Magnesium binding site 2 out of 4 in 4hyp

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Magnesium binding site 2 out of 4 in the Pyrrolopyrimidine Inhibitors of Dna Gyrase B and Topoisomerase IV, Part I: Structure Guided Discovery and Optimization of Dual Targeting Agents with Potent, Broad-Spectrum Enzymatic Activity.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pyrrolopyrimidine Inhibitors of Dna Gyrase B and Topoisomerase IV, Part I: Structure Guided Discovery and Optimization of Dual Targeting Agents with Potent, Broad-Spectrum Enzymatic Activity. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:26.8
occ:1.00
OD2 B:ASP45 1.9 27.5 1.0
O B:VAL122 2.3 27.6 1.0
O B:HOH472 2.4 20.9 1.0
OE1 B:GLU42 2.4 29.0 1.0
O B:HOH473 2.5 13.2 1.0
CG B:ASP45 3.0 27.9 1.0
OD1 B:ASP45 3.3 31.4 1.0
C B:VAL122 3.5 27.1 1.0
CD B:GLU42 3.7 29.7 1.0
CA B:GLY123 4.1 25.2 1.0
O B:HOH478 4.1 15.0 1.0
CA B:GLU42 4.1 25.7 1.0
O B:HOH474 4.2 21.1 1.0
N B:GLY123 4.2 25.4 1.0
CB B:GLU42 4.3 25.5 1.0
CB B:ASP45 4.3 25.5 1.0
O B:GLU42 4.3 29.1 1.0
O B:LEU119 4.4 25.1 1.0
OD1 B:ASN46 4.4 24.3 1.0
C B:GLY123 4.5 24.6 1.0
C B:GLU42 4.5 26.2 1.0
OE2 B:GLU42 4.5 29.8 1.0
CG B:GLU42 4.6 26.3 1.0
CA B:VAL122 4.6 26.2 1.0
CA B:GLY118 4.7 28.7 1.0
CB B:VAL122 4.7 26.6 1.0
O B:GLY123 4.8 24.4 1.0
ND2 B:ASN46 4.9 23.0 1.0
CG1 B:VAL122 4.9 26.5 1.0
N B:VAL124 4.9 24.3 1.0
CG B:ASN46 5.0 24.1 1.0
N B:VAL122 5.0 27.0 1.0

Magnesium binding site 3 out of 4 in 4hyp

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Magnesium binding site 3 out of 4 in the Pyrrolopyrimidine Inhibitors of Dna Gyrase B and Topoisomerase IV, Part I: Structure Guided Discovery and Optimization of Dual Targeting Agents with Potent, Broad-Spectrum Enzymatic Activity.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Pyrrolopyrimidine Inhibitors of Dna Gyrase B and Topoisomerase IV, Part I: Structure Guided Discovery and Optimization of Dual Targeting Agents with Potent, Broad-Spectrum Enzymatic Activity. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:39.5
occ:1.00
OD2 C:ASP45 2.1 28.2 1.0
O C:VAL122 2.2 33.2 1.0
OE1 C:GLU42 2.4 29.5 1.0
O C:HOH477 2.5 28.2 1.0
CG C:ASP45 3.4 27.6 1.0
C C:VAL122 3.4 28.2 1.0
CD C:GLU42 3.6 28.6 1.0
O C:HOH483 3.6 17.3 1.0
O C:LEU119 3.6 26.1 1.0
CA C:GLY118 4.0 24.4 1.0
OE2 C:GLU42 4.0 28.1 1.0
OD1 C:ASP45 4.1 31.6 1.0
CA C:VAL122 4.2 27.8 1.0
C C:GLY118 4.2 24.7 1.0
N C:VAL122 4.3 26.6 1.0
CB C:VAL122 4.3 28.8 1.0
CB C:ASP45 4.4 26.0 1.0
N C:GLY123 4.4 26.8 1.0
N C:LEU119 4.5 26.2 1.0
CA C:GLY123 4.6 24.7 1.0
C C:LEU119 4.7 27.7 1.0
N C:GLY118 4.7 25.1 1.0
O C:HOH484 4.8 18.8 1.0
O C:GLY118 4.8 22.8 1.0
CG C:GLU42 4.9 27.0 1.0
OD1 C:ASN46 4.9 21.6 1.0
CG1 C:VAL122 4.9 28.9 1.0
CA C:GLU42 4.9 25.5 1.0

Magnesium binding site 4 out of 4 in 4hyp

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Magnesium binding site 4 out of 4 in the Pyrrolopyrimidine Inhibitors of Dna Gyrase B and Topoisomerase IV, Part I: Structure Guided Discovery and Optimization of Dual Targeting Agents with Potent, Broad-Spectrum Enzymatic Activity.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Pyrrolopyrimidine Inhibitors of Dna Gyrase B and Topoisomerase IV, Part I: Structure Guided Discovery and Optimization of Dual Targeting Agents with Potent, Broad-Spectrum Enzymatic Activity. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:27.9
occ:1.00
OD2 D:ASP45 1.8 31.7 1.0
OE1 D:GLU42 1.9 31.1 1.0
O D:VAL122 2.2 23.1 1.0
O D:HOH472 2.6 17.7 1.0
CG D:ASP45 3.1 27.9 1.0
CD D:GLU42 3.1 29.0 1.0
C D:VAL122 3.4 21.6 1.0
OE2 D:GLU42 3.8 28.1 1.0
OD1 D:ASP45 3.9 29.7 1.0
O D:LEU119 3.9 22.0 1.0
CB D:ASP45 4.0 26.6 1.0
CA D:GLU42 4.3 27.4 1.0
CG D:GLU42 4.3 27.9 1.0
CB D:GLU42 4.3 27.6 1.0
N D:GLY123 4.3 19.7 1.0
CA D:GLY118 4.3 22.8 1.0
CA D:GLY123 4.3 17.7 1.0
N D:LEU119 4.3 23.3 1.0
O D:HOH473 4.4 15.8 1.0
CA D:VAL122 4.4 21.9 1.0
O D:HOH481 4.5 24.6 1.0
C D:GLY118 4.6 22.9 1.0
N D:VAL122 4.6 21.5 1.0
O D:GLU42 4.6 30.3 1.0
CB D:VAL122 4.7 22.8 1.0
C D:LEU119 4.8 23.4 1.0
C D:GLU42 4.8 26.9 1.0
CG1 D:VAL122 4.9 21.7 1.0
OD1 D:ASN46 5.0 25.3 1.0
N D:GLY118 5.0 24.8 1.0

Reference:

L.W.Tari, M.Trzoss, D.C.Bensen, X.Li, Z.Chen, T.Lam, J.Zhang, C.J.Creighton, M.L.Cunningham, B.Kwan, M.Stidham, K.J.Shaw, F.C.Lightstone, S.E.Wong, T.B.Nguyen, J.Nix, J.Finn. Pyrrolopyrimidine Inhibitors of Dna Gyrase B (Gyrb) and Topoisomerase IV (Pare). Part I: Structure Guided Discovery and Optimization of Dual Targeting Agents with Potent, Broad-Spectrum Enzymatic Activity. Bioorg.Med.Chem.Lett. V. 23 1529 2013.
ISSN: ISSN 0960-894X
PubMed: 23352267
DOI: 10.1016/J.BMCL.2012.11.032
Page generated: Fri Aug 16 16:27:09 2024

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