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Magnesium in PDB 6p8q: Egfr in Complex with A Dihydrodibenzodiazepinone Allosteric Inhibitor.

Enzymatic activity of Egfr in Complex with A Dihydrodibenzodiazepinone Allosteric Inhibitor.

All present enzymatic activity of Egfr in Complex with A Dihydrodibenzodiazepinone Allosteric Inhibitor.:
2.7.10.1;

Protein crystallography data

The structure of Egfr in Complex with A Dihydrodibenzodiazepinone Allosteric Inhibitor., PDB code: 6p8q was solved by C.H.Yun, D.E.Heppner, M.J.Eck, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.44 / 1.90
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 57.151, 72.874, 79.927, 100.16, 103.16, 95.61
R / Rfree (%) 16.8 / 19.5

Other elements in 6p8q:

The structure of Egfr in Complex with A Dihydrodibenzodiazepinone Allosteric Inhibitor. also contains other interesting chemical elements:

Fluorine (F) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Egfr in Complex with A Dihydrodibenzodiazepinone Allosteric Inhibitor. (pdb code 6p8q). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Egfr in Complex with A Dihydrodibenzodiazepinone Allosteric Inhibitor., PDB code: 6p8q:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 6p8q

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Magnesium binding site 1 out of 5 in the Egfr in Complex with A Dihydrodibenzodiazepinone Allosteric Inhibitor.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Egfr in Complex with A Dihydrodibenzodiazepinone Allosteric Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2003

b:28.5
occ:1.00
 NZ A:LYS745 3.0 23.6 1.0
O1A A:ANP2001 3.1 20.2 1.0
O A:HOH2232 3.1 33.1 1.0
N A:PHE723 3.2 26.5 1.0
N A:GLY724 3.5 26.5 1.0
N A:ALA722 3.6 31.5 1.0
O1G A:ANP2001 3.6 21.9 1.0
CE A:LYS745 3.6 23.6 1.0
CA A:PHE723 3.8 30.2 1.0
CA A:GLY721 3.8 23.8 1.0
C A:GLY721 3.8 27.6 1.0
CB A:PHE723 3.9 29.8 1.0
C A:PHE723 4.0 28.8 1.0
O2A A:ANP2001 4.1 26.8 1.0
CD2 A:LEU858 4.1 28.0 1.0
PA A:ANP2001 4.1 26.8 1.0
C A:ALA722 4.2 30.4 1.0
N A:GLY721 4.2 27.2 1.0
O A:GLY724 4.3 25.8 1.0
CD2 A:PHE723 4.4 31.3 1.0
CA A:GLY724 4.4 28.2 1.0
CD A:LYS745 4.4 22.2 1.0
CA A:ALA722 4.4 31.3 1.0
O A:HOH2101 4.4 28.5 1.0
O3A A:ANP2001 4.4 24.5 1.0
O A:GLY721 4.4 21.6 1.0
CG A:PHE723 4.6 37.0 1.0
C A:GLY724 4.6 22.6 1.0
O2G A:ANP2001 4.7 22.1 0.8
PG A:ANP2001 4.8 21.5 0.6
CB A:ALA722 4.8 32.1 1.0

Magnesium binding site 2 out of 5 in 6p8q

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Magnesium binding site 2 out of 5 in the Egfr in Complex with A Dihydrodibenzodiazepinone Allosteric Inhibitor.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Egfr in Complex with A Dihydrodibenzodiazepinone Allosteric Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2004

b:16.2
occ:0.56
 O1B A:ANP2001 1.9 21.1 0.8
O2A A:ANP2001 2.0 26.8 1.0
O2G A:ANP2001 2.0 22.1 0.8
OD1 A:ASN842 2.2 15.4 1.0
O A:HOH2181 2.2 32.7 1.0
OD2 A:ASP855 2.3 26.4 1.0
PB A:ANP2001 2.9 21.7 0.5
PA A:ANP2001 3.0 26.8 1.0
O3A A:ANP2001 3.2 24.5 1.0
CG A:ASN842 3.3 16.4 1.0
PG A:ANP2001 3.3 21.5 0.6
CG A:ASP855 3.5 25.5 1.0
O5' A:ANP2001 3.6 24.9 1.0
N3B A:ANP2001 3.6 23.7 0.5
O A:HOH2101 3.7 28.5 1.0
ND2 A:ASN842 3.8 10.2 1.0
O A:HOH2232 3.9 33.1 1.0
O A:HOH2122 3.9 28.1 1.0
O A:HOH2184 4.0 28.3 1.0
O A:ARG841 4.1 14.0 1.0
O2B A:ANP2001 4.2 22.1 0.7
O1G A:ANP2001 4.3 21.9 1.0
O1A A:ANP2001 4.3 20.2 1.0
O3G A:ANP2001 4.3 18.5 0.9
OD1 A:ASP855 4.3 29.6 1.0
CB A:ASP855 4.4 15.0 1.0
CB A:ASN842 4.5 14.5 1.0
CA A:ASN842 4.7 13.6 1.0
C A:ARG841 4.7 17.4 1.0
O A:HOH2197 4.8 20.0 1.0
CG A:ARG841 4.9 12.9 1.0
C5' A:ANP2001 4.9 24.1 1.0
N A:ASN842 5.0 14.1 1.0

Magnesium binding site 3 out of 5 in 6p8q

Go back to Magnesium Binding Sites List in 6p8q
Magnesium binding site 3 out of 5 in the Egfr in Complex with A Dihydrodibenzodiazepinone Allosteric Inhibitor.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Egfr in Complex with A Dihydrodibenzodiazepinone Allosteric Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2003

b:18.0
occ:1.00
 O2P B:AMP2001 2.9 17.3 1.0
NZ B:LYS745 3.0 17.9 1.0
N B:PHE723 3.3 23.2 1.0
N B:GLY724 3.4 18.9 1.0
O B:HOH2312 3.5 31.4 1.0
CA B:GLY721 3.6 22.4 1.0
N B:ALA722 3.7 24.5 1.0
C B:GLY721 3.7 24.7 1.0
CE B:LYS745 3.7 14.8 1.0
CB B:PHE723 3.8 23.4 1.0
CA B:PHE723 3.8 20.6 1.0
C B:PHE723 3.9 23.6 1.0
CD2 B:LEU858 4.0 26.1 1.0
P B:AMP2001 4.0 20.3 1.0
O B:GLY724 4.0 23.6 1.0
O1P B:AMP2001 4.2 21.7 1.0
N B:GLY721 4.2 25.8 1.0
O3P B:AMP2001 4.2 24.2 1.0
CD B:LYS745 4.2 16.5 1.0
CA B:GLY724 4.3 23.8 1.0
CD2 B:PHE723 4.3 26.6 1.0
O B:GLY721 4.3 18.1 1.0
C B:ALA722 4.4 28.9 1.0
CA B:ALA722 4.5 23.7 1.0
CG B:PHE723 4.5 26.1 1.0
C B:GLY724 4.5 21.7 1.0
O B:HOH2164 4.7 41.1 1.0
O B:PHE723 4.9 25.2 1.0
O B:HOH2105 4.9 29.8 1.0
OD2 B:ASP855 4.9 23.9 1.0

Magnesium binding site 4 out of 5 in 6p8q

Go back to Magnesium Binding Sites List in 6p8q
Magnesium binding site 4 out of 5 in the Egfr in Complex with A Dihydrodibenzodiazepinone Allosteric Inhibitor.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Egfr in Complex with A Dihydrodibenzodiazepinone Allosteric Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2003

b:10.5
occ:1.00
 O2P C:AMP2001 3.0 18.2 1.0
NZ C:LYS745 3.0 12.9 1.0
O C:HOH2310 3.2 20.9 1.0
N C:PHE723 3.3 16.5 1.0
N C:GLY724 3.5 16.5 1.0
CA C:GLY721 3.6 16.2 1.0
C C:GLY721 3.7 18.8 1.0
N C:ALA722 3.7 16.7 1.0
CE C:LYS745 3.8 11.5 1.0
CB C:PHE723 3.9 15.1 1.0
CA C:PHE723 3.9 18.1 1.0
CD2 C:LEU858 3.9 21.8 1.0
P C:AMP2001 3.9 16.7 1.0
O C:GLY724 4.0 16.9 1.0
C C:PHE723 4.0 21.8 1.0
O1P C:AMP2001 4.1 15.5 1.0
N C:GLY721 4.2 18.0 1.0
O3P C:AMP2001 4.2 17.3 1.0
CD C:LYS745 4.2 13.8 1.0
O C:GLY721 4.3 18.5 1.0
CA C:GLY724 4.3 18.9 1.0
CD2 C:PHE723 4.3 18.4 1.0
C C:ALA722 4.4 18.5 1.0
O C:HOH2154 4.4 30.6 1.0
C C:GLY724 4.5 18.3 1.0
CG C:PHE723 4.6 17.5 1.0
CA C:ALA722 4.6 20.4 1.0
O C:HOH2117 4.6 20.8 1.0
OD2 C:ASP855 4.9 16.2 1.0
O C:PHE723 5.0 17.7 1.0

Magnesium binding site 5 out of 5 in 6p8q

Go back to Magnesium Binding Sites List in 6p8q
Magnesium binding site 5 out of 5 in the Egfr in Complex with A Dihydrodibenzodiazepinone Allosteric Inhibitor.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Egfr in Complex with A Dihydrodibenzodiazepinone Allosteric Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2003

b:22.5
occ:1.00
 O2P D:AMP2001 3.1 27.4 1.0
NZ D:LYS745 3.1 23.8 1.0
N D:GLY724 3.3 27.2 1.0
N D:PHE723 3.4 27.3 1.0
CA D:GLY721 3.6 28.7 1.0
O D:HOH2258 3.6 38.6 1.0
CE D:LYS745 3.7 16.0 1.0
C D:GLY721 3.8 30.4 1.0
N D:ALA722 3.8 28.6 1.0
CD1 D:LEU858 3.9 30.8 1.0
CA D:PHE723 3.9 28.1 1.0
C D:PHE723 4.0 27.4 1.0
CB D:PHE723 4.0 21.6 1.0
P D:AMP2001 4.0 30.1 1.0
O D:GLY724 4.0 25.4 1.0
N D:GLY721 4.1 32.9 1.0
CA D:GLY724 4.1 25.8 1.0
O1P D:AMP2001 4.1 26.3 1.0
O3P D:AMP2001 4.2 35.0 1.0
CD2 D:PHE723 4.2 29.2 1.0
CD D:LYS745 4.3 17.0 1.0
C D:GLY724 4.4 24.2 1.0
O D:GLY721 4.4 29.6 1.0
C D:ALA722 4.5 29.7 1.0
O D:HOH2257 4.5 36.4 1.0
CG D:PHE723 4.6 22.9 1.0
CA D:ALA722 4.7 28.8 1.0
O D:HOH2114 4.9 32.2 1.0

Reference:

D.J.H.De Clercq, D.E.Heppner, C.To, J.Jang, E.Park, C.H.Yun, M.Mushajiang, B.H.Shin, T.W.Gero, D.A.Scott, P.A.Janne, M.J.Eck, N.S.Gray. Discovery and Optimization of Dibenzodiazepinones As Allosteric Mutant-Selective Egfr Inhibitors. Acs Med.Chem.Lett. V. 10 1549 2019.
ISSN: ISSN 1948-5875
PubMed: 31749909
DOI: 10.1021/ACSMEDCHEMLETT.9B00381
Page generated: Tue Oct 1 13:58:53 2024

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