Atomistry » Magnesium » PDB 6p8q-6pgk » 6p8q
Atomistry »
  Magnesium »
    PDB 6p8q-6pgk »
      6p8q »

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

Go back to Magnesium Binding Sites List in 6p8q
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

Go back to Magnesium Binding Sites List in 6p8q
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: Wed Aug 13 13:40:27 2025

Last articles

Zn in 9T29
Zn in 9R0Z
Zn in 9QKY
Zn in 9R0T
Zn in 9Q9Z
Zn in 9QRN
Zn in 9QWS
Zn in 9QWU
Zn in 9QX1
Zn in 9QAV
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy