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Magnesium in PDB 5x2a: Crystal Structure of Egfr 696-1022 T790M/V948R in Complex with Sklb(3)

Enzymatic activity of Crystal Structure of Egfr 696-1022 T790M/V948R in Complex with Sklb(3)

All present enzymatic activity of Crystal Structure of Egfr 696-1022 T790M/V948R in Complex with Sklb(3):
2.7.10.1;

Protein crystallography data

The structure of Crystal Structure of Egfr 696-1022 T790M/V948R in Complex with Sklb(3), PDB code: 5x2a was solved by C.H.Yun, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.49 / 1.85
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 72.185, 103.973, 87.150, 90.00, 101.40, 90.00
R / Rfree (%) 17.4 / 21.9

Other elements in 5x2a:

The structure of Crystal Structure of Egfr 696-1022 T790M/V948R in Complex with Sklb(3) also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Egfr 696-1022 T790M/V948R in Complex with Sklb(3) (pdb code 5x2a). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Egfr 696-1022 T790M/V948R in Complex with Sklb(3), PDB code: 5x2a:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5x2a

Go back to Magnesium Binding Sites List in 5x2a
Magnesium binding site 1 out of 4 in the Crystal Structure of Egfr 696-1022 T790M/V948R in Complex with Sklb(3)


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 Egfr 696-1022 T790M/V948R in Complex with Sklb(3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1109

b:31.5
occ:0.45
 O2A A:ANP1108 2.3 39.8 0.5
O2B A:ANP1108 2.5 37.0 0.5
OD1 A:ASN842 2.7 26.7 1.0
O A:ARG841 3.3 18.5 1.0
CAA A:7XO1107 3.4 32.3 0.9
PA A:ANP1108 3.5 38.5 0.5
CG2 A:THR854 3.6 18.9 1.0
PB A:ANP1108 3.8 26.6 0.5
O A:HOH1247 3.8 31.0 1.0
CG A:ASN842 3.9 25.1 1.0
NAV A:7XO1107 3.9 30.9 0.9
CBD A:7XO1107 3.9 31.8 0.9
OD2 A:ASP855 3.9 41.2 1.0
CA A:ASN842 4.0 14.0 1.0
O5' A:ANP1108 4.0 30.9 0.5
O3A A:ANP1108 4.1 37.9 0.5
O3G A:ANP1108 4.1 34.7 0.5
CG A:ASP855 4.1 32.2 1.0
C A:ARG841 4.2 19.7 1.0
OD1 A:ASP855 4.3 35.2 1.0
C8 A:7XO1107 4.4 23.0 0.9
N9 A:7XO1107 4.5 21.7 0.9
CB A:ASN842 4.5 15.1 1.0
N A:ASN842 4.5 18.3 1.0
O1B A:ANP1108 4.6 35.7 0.5
CAH A:7XO1107 4.7 38.5 0.9
C5' A:ANP1108 4.7 29.6 0.5
CAW A:7XO1107 4.8 30.8 0.9
O1A A:ANP1108 4.8 39.4 0.5
CB A:ASP855 4.8 24.8 1.0
NZ A:LYS745 4.9 40.8 1.0
ND2 A:ASN842 4.9 20.1 1.0
N3B A:ANP1108 5.0 31.0 0.5
C A:ASN842 5.0 16.9 1.0

Magnesium binding site 2 out of 4 in 5x2a

Go back to Magnesium Binding Sites List in 5x2a
Magnesium binding site 2 out of 4 in the Crystal Structure of Egfr 696-1022 T790M/V948R in Complex with Sklb(3)


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 Egfr 696-1022 T790M/V948R in Complex with Sklb(3) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1107

b:33.0
occ:0.60
 O1A B:ANP1106 2.4 33.5 0.6
O1B B:ANP1106 2.5 38.9 0.6
OD1 B:ASN842 3.0 28.2 1.0
CG2 B:THR854 3.4 17.3 1.0
O B:ARG841 3.5 19.2 1.0
PA B:ANP1106 3.6 37.5 0.6
OD2 B:ASP855 3.7 44.0 1.0
PB B:ANP1106 3.9 35.0 0.6
O1G B:ANP1106 3.9 36.8 0.6
C8 B:ANP1106 3.9 24.8 1.0
CG B:ASP855 3.9 32.6 1.0
O5' B:ANP1106 4.0 29.8 0.6
OD1 B:ASP855 4.0 38.0 1.0
C2' B:ANP1106 4.1 34.9 1.0
O3A B:ANP1106 4.1 36.6 0.6
CA B:ASN842 4.2 13.6 1.0
CG B:ASN842 4.2 26.1 1.0
O B:HOH1332 4.3 35.4 1.0
C B:ARG841 4.5 18.2 1.0
O B:HOH1395 4.6 40.8 1.0
NZ B:LYS745 4.6 32.6 1.0
N9 B:ANP1106 4.7 27.0 1.0
CB B:ASN842 4.7 14.4 1.0
N7 B:ANP1106 4.7 27.4 1.0
O2B B:ANP1106 4.7 35.6 0.6
CD2 B:LEU844 4.7 20.8 1.0
N B:ASN842 4.8 16.3 1.0
C3' B:ANP1106 4.8 34.5 0.6
O2' B:ANP1106 4.8 41.2 1.0
C5' B:ANP1106 4.8 26.9 0.6
CB B:ASP855 4.9 18.0 1.0
CB B:THR854 4.9 17.2 1.0
O2A B:ANP1106 4.9 34.8 0.6
N3B B:ANP1106 4.9 32.7 0.6
C1' B:ANP1106 5.0 33.2 1.0

Magnesium binding site 3 out of 4 in 5x2a

Go back to Magnesium Binding Sites List in 5x2a
Magnesium binding site 3 out of 4 in the Crystal Structure of Egfr 696-1022 T790M/V948R in Complex with Sklb(3)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Egfr 696-1022 T790M/V948R in Complex with Sklb(3) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1101

b:54.6
occ:1.00
 O D:HOH1289 2.3 30.7 1.0
O1G D:ANP1102 2.4 35.3 0.7
O1A D:ANP1102 2.6 46.4 0.7
O2A D:ANP1102 2.8 40.1 0.7
MG D:MG1103 2.8 42.7 0.7
PA D:ANP1102 2.9 42.5 0.7
CE D:LYS745 2.9 44.3 1.0
O3A D:ANP1102 3.3 45.4 0.7
NZ D:LYS745 3.4 43.2 1.0
OD1 D:ASP855 3.6 49.5 1.0
PG D:ANP1102 3.8 30.3 0.7
O1B D:ANP1102 3.9 42.5 0.7
CD1 D:LEU858 4.0 36.4 1.0
CG D:ASP855 4.0 43.9 1.0
CD2 D:PHE723 4.0 43.9 1.0
CB D:PHE723 4.1 44.7 1.0
PB D:ANP1102 4.1 40.5 0.7
CD D:LYS745 4.2 33.9 1.0
OD2 D:ASP855 4.3 52.6 1.0
O5' D:ANP1102 4.4 40.0 1.0
N3B D:ANP1102 4.4 24.6 0.7
O2G D:ANP1102 4.5 36.5 0.7
N D:PHE723 4.5 37.2 1.0
CG D:PHE723 4.6 41.1 1.0
N D:GLY724 4.6 35.4 1.0
CA D:GLY721 4.7 40.1 1.0
CA D:PHE723 4.7 37.6 1.0
O D:GLY724 4.8 37.7 1.0
CB D:ASP855 4.9 37.2 1.0
O3G D:ANP1102 4.9 24.0 0.7
C D:PHE723 5.0 37.1 1.0
N D:GLY721 5.0 38.9 1.0
OD1 D:ASN842 5.0 40.1 1.0

Magnesium binding site 4 out of 4 in 5x2a

Go back to Magnesium Binding Sites List in 5x2a
Magnesium binding site 4 out of 4 in the Crystal Structure of Egfr 696-1022 T790M/V948R in Complex with Sklb(3)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Egfr 696-1022 T790M/V948R in Complex with Sklb(3) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1103

b:42.7
occ:0.70
 OD2 D:ASP855 2.2 52.6 1.0
CG D:ASP855 2.2 43.9 1.0
OD1 D:ASN842 2.4 40.1 1.0
O2A D:ANP1102 2.6 40.1 0.7
CB D:ASP855 2.8 37.2 1.0
OD1 D:ASP855 2.8 49.5 1.0
O1G D:ANP1102 2.8 35.3 0.7
MG D:MG1101 2.8 54.6 1.0
O1B D:ANP1102 3.0 42.5 0.7
CG D:ASN842 3.4 36.7 1.0
ND2 D:ASN842 3.7 29.2 1.0
PA D:ANP1102 3.8 42.5 0.7
O D:HOH1206 4.0 40.2 1.0
PG D:ANP1102 4.0 30.3 0.7
PB D:ANP1102 4.1 40.5 0.7
O3G D:ANP1102 4.2 24.0 0.7
CA D:ASP855 4.2 37.0 1.0
O3A D:ANP1102 4.2 45.4 0.7
OD2 D:ASP837 4.4 34.0 1.0
NZ D:LYS745 4.4 43.2 1.0
O1A D:ANP1102 4.4 46.4 0.7
CD1 D:LEU858 4.4 36.4 1.0
N3B D:ANP1102 4.6 24.6 0.7
CB D:ASN842 4.6 28.4 1.0
CE D:LYS745 4.6 44.3 1.0
O D:HOH1334 4.7 33.7 1.0
CG2 D:THR854 4.7 34.3 1.0
N D:ASP855 4.9 28.8 1.0
O D:THR854 4.9 27.1 1.0
O D:HOH1289 5.0 30.7 1.0
O5' D:ANP1102 5.0 40.0 1.0
O D:ASP855 5.0 42.1 1.0

Reference:

S.J.Zhu, P.Zhao, J.Yang, R.Ma, X.E.Yan, S.Y.Yang, J.W.Yang, C.H.Yun. Structural Insights Into Drug Development Strategy Targeting Egfr T790M/C797S. Oncotarget V. 9 13652 2018.
ISSN: ESSN 1949-2553
PubMed: 29568384
DOI: 10.18632/ONCOTARGET.24113
Page generated: Mon Sep 30 09:00:25 2024

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