Magnesium in PDB 4riy: Crystal Structure of An Egfr/HER3 Kinase Domain Heterodimer Containing the Cancer-Associated HER3-E909G Mutation
Enzymatic activity of Crystal Structure of An Egfr/HER3 Kinase Domain Heterodimer Containing the Cancer-Associated HER3-E909G Mutation
All present enzymatic activity of Crystal Structure of An Egfr/HER3 Kinase Domain Heterodimer Containing the Cancer-Associated HER3-E909G Mutation:
2.7.10.1;
Protein crystallography data
The structure of Crystal Structure of An Egfr/HER3 Kinase Domain Heterodimer Containing the Cancer-Associated HER3-E909G Mutation, PDB code: 4riy
was solved by
P.Littlefield,
L.Liu,
N.Jura,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
56.20 /
2.98
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
65.334,
155.140,
87.297,
90.00,
110.93,
90.00
|
R / Rfree (%)
|
21.6 /
26.7
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of An Egfr/HER3 Kinase Domain Heterodimer Containing the Cancer-Associated HER3-E909G Mutation
(pdb code 4riy). 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 An Egfr/HER3 Kinase Domain Heterodimer Containing the Cancer-Associated HER3-E909G Mutation, PDB code: 4riy:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 4riy
Go back to
Magnesium Binding Sites List in 4riy
Magnesium binding site 1 out
of 4 in the Crystal Structure of An Egfr/HER3 Kinase Domain Heterodimer Containing the Cancer-Associated HER3-E909G Mutation
 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 An Egfr/HER3 Kinase Domain Heterodimer Containing the Cancer-Associated HER3-E909G Mutation within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1102
b:23.3
occ:1.00
|
OD2
|
A:ASP833
|
2.0
|
47.2
|
1.0
|
OD1
|
A:ASN820
|
2.3
|
40.6
|
1.0
|
O3A
|
A:ANP1101
|
2.4
|
89.5
|
1.0
|
O2A
|
A:ANP1101
|
2.7
|
39.5
|
1.0
|
O3G
|
A:ANP1101
|
2.8
|
62.6
|
1.0
|
CG
|
A:ASP833
|
3.0
|
43.6
|
1.0
|
N3B
|
A:ANP1101
|
3.0
|
59.8
|
1.0
|
PA
|
A:ANP1101
|
3.2
|
41.8
|
1.0
|
PB
|
A:ANP1101
|
3.3
|
25.9
|
1.0
|
PG
|
A:ANP1101
|
3.3
|
42.6
|
1.0
|
CG
|
A:ASN820
|
3.5
|
41.6
|
1.0
|
OD1
|
A:ASP833
|
3.6
|
51.4
|
1.0
|
O1G
|
A:ANP1101
|
3.7
|
49.4
|
1.0
|
NZ
|
A:LYS723
|
3.9
|
43.5
|
1.0
|
CB
|
A:ASP833
|
4.0
|
32.7
|
1.0
|
ND2
|
A:ASN820
|
4.1
|
49.0
|
1.0
|
O5'
|
A:ANP1101
|
4.2
|
55.0
|
1.0
|
O1B
|
A:ANP1101
|
4.2
|
32.6
|
1.0
|
O1A
|
A:ANP1101
|
4.3
|
47.6
|
1.0
|
O2B
|
A:ANP1101
|
4.5
|
76.2
|
1.0
|
CB
|
A:ASN820
|
4.6
|
37.1
|
1.0
|
O2G
|
A:ANP1101
|
4.8
|
27.5
|
1.0
|
CA
|
A:ASN820
|
4.9
|
31.8
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 4riy
Go back to
Magnesium Binding Sites List in 4riy
Magnesium binding site 2 out
of 4 in the Crystal Structure of An Egfr/HER3 Kinase Domain Heterodimer Containing the Cancer-Associated HER3-E909G Mutation
 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 An Egfr/HER3 Kinase Domain Heterodimer Containing the Cancer-Associated HER3-E909G Mutation within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1002
b:60.9
occ:1.00
|
OD1
|
B:ASN818
|
2.8
|
37.7
|
1.0
|
O2B
|
B:ADP1001
|
2.9
|
0.4
|
1.0
|
O1B
|
B:ADP1001
|
3.2
|
0.9
|
1.0
|
O2A
|
B:ADP1001
|
3.3
|
0.0
|
1.0
|
PB
|
B:ADP1001
|
3.5
|
0.2
|
1.0
|
CG
|
B:ASN818
|
3.8
|
37.1
|
1.0
|
O3A
|
B:ADP1001
|
4.1
|
0.4
|
1.0
|
ND2
|
B:ASN818
|
4.1
|
36.9
|
1.0
|
OD2
|
B:ASP831
|
4.2
|
90.1
|
1.0
|
PA
|
B:ADP1001
|
4.3
|
0.1
|
1.0
|
OD2
|
B:ASP813
|
4.3
|
60.5
|
1.0
|
NE
|
B:ARG817
|
4.4
|
32.3
|
1.0
|
CG
|
B:ASP831
|
4.5
|
87.6
|
1.0
|
OD1
|
B:ASP831
|
4.5
|
89.9
|
1.0
|
C5'
|
B:ADP1001
|
4.8
|
82.1
|
1.0
|
CB
|
B:ARG817
|
4.8
|
32.8
|
1.0
|
O3B
|
B:ADP1001
|
5.0
|
0.4
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 4riy
Go back to
Magnesium Binding Sites List in 4riy
Magnesium binding site 3 out
of 4 in the Crystal Structure of An Egfr/HER3 Kinase Domain Heterodimer Containing the Cancer-Associated HER3-E909G Mutation
 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 An Egfr/HER3 Kinase Domain Heterodimer Containing the Cancer-Associated HER3-E909G Mutation within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1102
b:17.3
occ:1.00
|
OD2
|
C:ASP833
|
2.4
|
30.6
|
1.0
|
O2A
|
C:ANP1101
|
2.4
|
31.4
|
1.0
|
OD1
|
C:ASN820
|
2.5
|
29.8
|
1.0
|
O3A
|
C:ANP1101
|
2.5
|
67.2
|
1.0
|
N3B
|
C:ANP1101
|
2.5
|
38.1
|
1.0
|
PA
|
C:ANP1101
|
3.0
|
34.2
|
1.0
|
PB
|
C:ANP1101
|
3.0
|
17.3
|
1.0
|
O3G
|
C:ANP1101
|
3.1
|
26.9
|
1.0
|
CG
|
C:ASP833
|
3.3
|
37.9
|
1.0
|
PG
|
C:ANP1101
|
3.4
|
25.0
|
1.0
|
CG
|
C:ASN820
|
3.6
|
29.8
|
1.0
|
OD1
|
C:ASP833
|
3.8
|
54.2
|
1.0
|
NZ
|
C:LYS723
|
4.0
|
34.7
|
1.0
|
O1B
|
C:ANP1101
|
4.0
|
19.2
|
1.0
|
O1A
|
C:ANP1101
|
4.1
|
34.1
|
1.0
|
O5'
|
C:ANP1101
|
4.1
|
47.1
|
1.0
|
O2B
|
C:ANP1101
|
4.2
|
79.7
|
1.0
|
O1G
|
C:ANP1101
|
4.3
|
30.2
|
1.0
|
CB
|
C:ASP833
|
4.4
|
32.0
|
1.0
|
ND2
|
C:ASN820
|
4.4
|
31.8
|
1.0
|
O2G
|
C:ANP1101
|
4.6
|
26.4
|
1.0
|
CB
|
C:ASN820
|
4.7
|
25.8
|
1.0
|
C8
|
C:ANP1101
|
4.7
|
32.3
|
1.0
|
CA
|
C:ASN820
|
4.9
|
17.6
|
1.0
|
O
|
C:ARG819
|
4.9
|
30.8
|
1.0
|
C2'
|
C:ANP1101
|
5.0
|
26.2
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 4riy
Go back to
Magnesium Binding Sites List in 4riy
Magnesium binding site 4 out
of 4 in the Crystal Structure of An Egfr/HER3 Kinase Domain Heterodimer Containing the Cancer-Associated HER3-E909G Mutation
 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 An Egfr/HER3 Kinase Domain Heterodimer Containing the Cancer-Associated HER3-E909G Mutation within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg1002
b:59.3
occ:1.00
|
O2B
|
D:ADP1001
|
2.2
|
0.1
|
1.0
|
OD1
|
D:ASN818
|
2.4
|
48.2
|
1.0
|
O2A
|
D:ADP1001
|
2.7
|
0.6
|
1.0
|
CG
|
D:ASN818
|
3.5
|
44.6
|
1.0
|
PB
|
D:ADP1001
|
3.7
|
0.7
|
1.0
|
ND2
|
D:ASN818
|
3.9
|
45.8
|
1.0
|
PA
|
D:ADP1001
|
3.9
|
0.8
|
1.0
|
NE
|
D:ARG817
|
4.1
|
49.0
|
1.0
|
CB
|
D:ARG817
|
4.1
|
49.0
|
1.0
|
O5'
|
D:ADP1001
|
4.3
|
70.2
|
1.0
|
O3A
|
D:ADP1001
|
4.3
|
0.0
|
1.0
|
O3B
|
D:ADP1001
|
4.3
|
0.7
|
1.0
|
OD2
|
D:ASP831
|
4.5
|
90.7
|
1.0
|
C5'
|
D:ADP1001
|
4.6
|
69.5
|
1.0
|
C
|
D:ARG817
|
4.7
|
40.4
|
1.0
|
CD
|
D:ARG817
|
4.7
|
55.7
|
1.0
|
CB
|
D:ASN818
|
4.8
|
44.5
|
1.0
|
O1B
|
D:ADP1001
|
4.8
|
0.5
|
1.0
|
CG
|
D:ASP831
|
4.8
|
87.8
|
1.0
|
O
|
D:ARG817
|
4.8
|
33.7
|
1.0
|
OD2
|
D:ASP813
|
4.8
|
49.9
|
1.0
|
N
|
D:ASN818
|
4.8
|
40.7
|
1.0
|
CA
|
D:ASN818
|
4.9
|
43.9
|
1.0
|
|
Reference:
P.Littlefield,
L.Liu,
V.Mysore,
Y.Shan,
D.E.Shaw,
N.Jura.
Structural Analysis of the Egfr/HER3 Heterodimer Reveals the Molecular Basis For Activating HER3 Mutations. Sci.Signal. V. 7 RA114 2014.
ISSN: ESSN 1937-9145
PubMed: 25468994
DOI: 10.1126/SCISIGNAL.2005786
Page generated: Tue Aug 20 03:09:24 2024
|