Magnesium in PDB 6duk: Egfr with An Allosteric Inhibitor

Enzymatic activity of Egfr with An Allosteric Inhibitor

All present enzymatic activity of Egfr with An Allosteric Inhibitor:
2.7.10.1;

Protein crystallography data

The structure of Egfr with An Allosteric Inhibitor, PDB code: 6duk was solved by E.Park, M.J.Eck, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 88.50 / 2.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 57.481, 94.711, 97.398, 70.38, 77.46, 79.14
R / Rfree (%) 19 / 22.3

Other elements in 6duk:

The structure of Egfr with An Allosteric Inhibitor also contains other interesting chemical elements:

Fluorine (F) 6 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 6 in 6duk

Go back to Magnesium Binding Sites List in 6duk
Magnesium binding site 1 out of 6 in the Egfr with An 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 with An Allosteric Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1101

b:24.3
occ:1.00
O A:HOH1217 2.0 20.4 1.0
OD1 A:ASN842 2.0 30.2 1.0
OD2 A:ASP855 2.0 29.2 1.0
O2B A:ANP1102 2.0 21.6 1.0
O2A A:ANP1102 2.1 21.8 1.0
CG A:ASN842 3.1 26.5 1.0
CG A:ASP855 3.1 24.3 1.0
PB A:ANP1102 3.2 25.4 1.0
PA A:ANP1102 3.2 23.6 1.0
O3A A:ANP1102 3.6 24.5 1.0
ND2 A:ASN842 3.6 20.2 1.0
O5' A:ANP1102 3.7 26.3 1.0
CB A:ASP855 3.8 20.9 1.0
NZ A:LYS745 3.9 24.8 1.0
O1G A:ANP1102 4.1 25.2 1.0
OD1 A:ASP855 4.1 29.5 1.0
O A:ARG841 4.2 23.1 1.0
O1B A:ANP1102 4.2 22.3 1.0
O A:HOH1244 4.2 23.0 1.0
CB A:ASN842 4.4 21.3 1.0
N3B A:ANP1102 4.4 23.0 1.0
O3G A:ANP1102 4.5 21.3 1.0
CG2 A:THR854 4.6 25.3 1.0
O1A A:ANP1102 4.6 26.7 1.0
O A:HOH1272 4.6 29.3 1.0
CA A:ASN842 4.6 21.0 1.0
PG A:ANP1102 4.7 31.8 1.0
C A:ARG841 4.9 21.9 1.0
C3' A:ANP1102 4.9 25.5 1.0

Magnesium binding site 2 out of 6 in 6duk

Go back to Magnesium Binding Sites List in 6duk
Magnesium binding site 2 out of 6 in the Egfr with An 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 with An Allosteric Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1101

b:39.8
occ:1.00
OD1 B:ASN842 2.0 35.4 1.0
OD2 B:ASP855 2.1 40.3 1.0
O2B B:ANP1102 2.1 42.2 1.0
O2A B:ANP1102 2.2 32.8 1.0
O2G B:ANP1102 2.6 47.2 1.0
CG B:ASN842 3.0 39.2 1.0
CG B:ASP855 3.2 38.9 1.0
PB B:ANP1102 3.4 40.9 1.0
ND2 B:ASN842 3.4 35.6 1.0
PA B:ANP1102 3.4 38.5 1.0
CB B:ASP855 3.6 39.8 1.0
O3A B:ANP1102 3.7 40.2 1.0
PG B:ANP1102 3.8 44.4 1.0
NZ B:LYS745 4.0 41.9 1.0
O5' B:ANP1102 4.1 40.1 1.0
N3B B:ANP1102 4.1 41.6 1.0
O B:HOH1242 4.2 37.1 1.0
OD1 B:ASP855 4.3 40.1 1.0
CB B:ASN842 4.3 35.2 1.0
O3G B:ANP1102 4.4 32.8 1.0
O B:ARG841 4.4 36.0 1.0
O1B B:ANP1102 4.5 39.1 1.0
CA B:ASN842 4.7 38.7 1.0
O1A B:ANP1102 4.7 38.0 1.0
CG2 B:THR854 4.7 30.5 1.0
O3' B:ANP1102 4.9 43.7 1.0

Magnesium binding site 3 out of 6 in 6duk

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Magnesium binding site 3 out of 6 in the Egfr with An 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 with An Allosteric Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1101

b:40.4
occ:1.00
O2B C:ANP1102 1.8 41.9 1.0
O2A C:ANP1102 1.9 38.7 1.0
OD2 C:ASP855 2.0 37.4 1.0
OD1 C:ASN842 2.3 40.2 1.0
PA C:ANP1102 3.1 36.5 1.0
PB C:ANP1102 3.1 40.5 1.0
CG C:ASP855 3.2 34.1 1.0
CG C:ASN842 3.4 37.2 1.0
O3A C:ANP1102 3.5 37.7 1.0
O1G C:ANP1102 3.6 48.0 1.0
O5' C:ANP1102 3.7 37.8 1.0
ND2 C:ASN842 3.9 33.8 1.0
NZ C:LYS745 4.0 37.1 1.0
CB C:ASP855 4.0 31.2 1.0
O3G C:ANP1102 4.1 35.2 1.0
OD1 C:ASP855 4.1 34.6 1.0
N3B C:ANP1102 4.1 44.1 1.0
O1B C:ANP1102 4.2 40.6 1.0
PG C:ANP1102 4.2 43.2 1.0
O C:HOH1218 4.2 31.4 1.0
O C:ARG841 4.3 34.3 1.0
O1A C:ANP1102 4.4 34.4 1.0
O C:HOH1255 4.5 37.8 1.0
CB C:ASN842 4.7 27.9 1.0
C3' C:ANP1102 4.7 38.4 1.0
CA C:ASN842 4.8 34.4 1.0
C8 C:ANP1102 4.9 34.6 1.0
CG2 C:THR854 4.9 32.1 1.0
C5' C:ANP1102 4.9 35.8 1.0
C C:ARG841 5.0 39.1 1.0
O3' C:ANP1102 5.0 40.5 1.0

Magnesium binding site 4 out of 6 in 6duk

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Magnesium binding site 4 out of 6 in the Egfr with An 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 with An Allosteric Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1101

b:26.9
occ:1.00
O2B D:ANP1102 1.9 28.4 1.0
OD2 D:ASP855 2.0 30.8 1.0
ND2 D:ASN842 2.0 25.0 1.0
O2A D:ANP1102 2.3 23.3 1.0
CG D:ASP855 3.0 27.5 1.0
CG D:ASN842 3.1 27.3 1.0
PB D:ANP1102 3.3 24.4 1.0
PA D:ANP1102 3.4 29.2 1.0
OD1 D:ASN842 3.5 29.2 1.0
CB D:ASP855 3.5 24.3 1.0
O3A D:ANP1102 3.7 30.9 1.0
O2G D:ANP1102 3.7 30.8 1.0
NZ D:LYS745 4.0 24.5 1.0
OD1 D:ASP855 4.1 28.5 1.0
O5' D:ANP1102 4.1 27.6 1.0
O1B D:ANP1102 4.2 22.7 1.0
O D:ARG841 4.3 31.7 1.0
O D:HOH1255 4.3 25.6 1.0
O3G D:ANP1102 4.4 28.7 1.0
CB D:ASN842 4.4 23.5 1.0
N3B D:ANP1102 4.4 25.0 1.0
PG D:ANP1102 4.5 30.2 1.0
CA D:ASN842 4.6 24.5 1.0
O1A D:ANP1102 4.7 27.7 1.0
CG2 D:THR854 4.7 19.8 1.0
C D:ARG841 4.9 28.4 1.0

Magnesium binding site 5 out of 6 in 6duk

Go back to Magnesium Binding Sites List in 6duk
Magnesium binding site 5 out of 6 in the Egfr with An 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 with An Allosteric Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1101

b:31.0
occ:1.00
O2B E:ANP1102 1.8 36.3 1.0
OD2 E:ASP855 2.1 32.0 1.0
OD1 E:ASN842 2.1 31.6 1.0
O2A E:ANP1102 2.1 30.4 1.0
CG E:ASN842 3.1 28.6 1.0
PB E:ANP1102 3.2 32.6 1.0
CG E:ASP855 3.2 32.1 1.0
O1G E:ANP1102 3.2 42.2 1.0
PA E:ANP1102 3.4 31.4 1.0
ND2 E:ASN842 3.5 24.1 1.0
O3A E:ANP1102 3.6 36.7 1.0
CB E:ASP855 3.7 28.0 1.0
NZ E:LYS745 4.0 33.8 1.0
PG E:ANP1102 4.1 39.5 1.0
O5' E:ANP1102 4.1 30.6 1.0
O3G E:ANP1102 4.1 28.9 1.0
N3B E:ANP1102 4.1 31.6 1.0
OD1 E:ASP855 4.2 31.9 1.0
O1B E:ANP1102 4.3 32.4 1.0
CB E:ASN842 4.5 26.1 1.0
O E:ARG841 4.6 29.0 1.0
O1A E:ANP1102 4.6 29.4 1.0
O E:HOH1217 4.7 28.5 1.0
CA E:ASN842 4.8 28.0 1.0
CG2 E:THR854 4.8 26.4 1.0

Magnesium binding site 6 out of 6 in 6duk

Go back to Magnesium Binding Sites List in 6duk
Magnesium binding site 6 out of 6 in the Egfr with An Allosteric Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Egfr with An Allosteric Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg1101

b:39.7
occ:1.00
OD2 F:ASP855 2.0 36.6 1.0
OD1 F:ASN842 2.0 34.0 1.0
O2B F:ANP1102 2.0 43.7 1.0
O2A F:ANP1102 2.1 43.0 1.0
CG F:ASN842 2.9 31.8 1.0
CG F:ASP855 3.1 35.2 1.0
O2G F:ANP1102 3.1 52.0 1.0
ND2 F:ASN842 3.2 33.7 1.0
PB F:ANP1102 3.3 40.0 1.0
PA F:ANP1102 3.4 39.9 1.0
CB F:ASP855 3.6 33.3 1.0
O3A F:ANP1102 3.6 40.2 1.0
NZ F:LYS745 3.9 33.0 1.0
PG F:ANP1102 4.0 44.9 1.0
O3G F:ANP1102 4.0 39.7 1.0
O5' F:ANP1102 4.1 31.3 1.0
OD1 F:ASP855 4.1 38.3 1.0
N3B F:ANP1102 4.2 44.6 1.0
CB F:ASN842 4.3 27.9 1.0
O F:HOH1235 4.3 28.2 1.0
O1B F:ANP1102 4.4 36.8 1.0
O1A F:ANP1102 4.5 33.7 1.0
O F:ARG841 4.7 29.7 1.0
CA F:ASN842 4.8 31.5 1.0
CG2 F:THR854 4.8 30.0 1.0

Reference:

C.To, J.Jang, T.Chen, E.Park, M.Mushajiang, D.J.H.De Clercq, M.Xu, S.Wang, M.D.Cameron, D.E.Heppner, B.H.Shin, T.W.Gero, A.Yang, S.E.Dahlberg, K.K.Wong, M.J.Eck, N.S.Gray, P.A.Janne. Single and Dual Targeting of Mutant Egfr with An Allosteric Inhibitor. Cancer Discov V. 9 926 2019.
ISSN: ESSN 2159-8290
PubMed: 31092401
DOI: 10.1158/2159-8290.CD-18-0903
Page generated: Mon Dec 14 22:37:11 2020

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