Magnesium in PDB 6gom: Kras-169 Q61H Gppnhp + Ppin-1
Protein crystallography data
The structure of Kras-169 Q61H Gppnhp + Ppin-1, PDB code: 6gom
was solved by
A.Cruz-Migoni,
P.Canning,
C.E.Quevedo,
S.B.Carr,
S.E.V.Phillips,
T.H.Rabbitts,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
66.13 /
1.63
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
64.180,
119.840,
158.600,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18.6 /
20.7
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Kras-169 Q61H Gppnhp + Ppin-1
(pdb code 6gom). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the
Kras-169 Q61H Gppnhp + Ppin-1, PDB code: 6gom:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
Magnesium binding site 1 out
of 6 in 6gom
Go back to
Magnesium Binding Sites List in 6gom
Magnesium binding site 1 out
of 6 in the Kras-169 Q61H Gppnhp + Ppin-1
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Kras-169 Q61H Gppnhp + Ppin-1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg202
b:16.1
occ:1.00
|
O2G
|
A:GNP201
|
2.0
|
18.7
|
1.0
|
O
|
A:HOH336
|
2.0
|
15.2
|
1.0
|
O2B
|
A:GNP201
|
2.1
|
15.5
|
1.0
|
OG
|
A:SER17
|
2.1
|
16.1
|
1.0
|
OG1
|
A:THR35
|
2.1
|
16.9
|
1.0
|
O
|
A:HOH341
|
2.1
|
15.7
|
1.0
|
CB
|
A:THR35
|
3.2
|
19.8
|
1.0
|
CB
|
A:SER17
|
3.2
|
15.4
|
1.0
|
PB
|
A:GNP201
|
3.2
|
16.7
|
1.0
|
PG
|
A:GNP201
|
3.2
|
17.5
|
1.0
|
N3B
|
A:GNP201
|
3.5
|
15.8
|
1.0
|
N
|
A:THR35
|
3.9
|
16.5
|
1.0
|
N
|
A:SER17
|
3.9
|
14.7
|
1.0
|
OD2
|
A:ASP57
|
4.1
|
22.1
|
1.0
|
O3G
|
A:GNP201
|
4.1
|
19.4
|
1.0
|
CA
|
A:SER17
|
4.1
|
14.8
|
1.0
|
CA
|
A:THR35
|
4.1
|
19.0
|
1.0
|
O1A
|
A:GNP201
|
4.1
|
18.3
|
1.0
|
CG2
|
A:THR35
|
4.2
|
19.3
|
1.0
|
OD1
|
A:ASP57
|
4.3
|
20.5
|
1.0
|
O
|
A:HOH306
|
4.3
|
40.4
|
1.0
|
O1B
|
A:GNP201
|
4.3
|
16.7
|
1.0
|
O3A
|
A:GNP201
|
4.3
|
16.6
|
1.0
|
O1G
|
A:GNP201
|
4.4
|
19.1
|
1.0
|
O
|
A:HOH347
|
4.5
|
32.6
|
1.0
|
O
|
A:THR58
|
4.5
|
19.3
|
1.0
|
O
|
A:ASP33
|
4.5
|
21.2
|
1.0
|
CG
|
A:ASP57
|
4.6
|
20.1
|
1.0
|
PA
|
A:GNP201
|
4.6
|
16.6
|
1.0
|
O2A
|
A:GNP201
|
4.7
|
16.3
|
1.0
|
CB
|
A:LYS16
|
4.8
|
15.1
|
1.0
|
C
|
A:PRO34
|
4.8
|
22.4
|
1.0
|
C
|
A:LYS16
|
5.0
|
15.9
|
1.0
|
CE
|
A:LYS16
|
5.0
|
15.7
|
1.0
|
|
Magnesium binding site 2 out
of 6 in 6gom
Go back to
Magnesium Binding Sites List in 6gom
Magnesium binding site 2 out
of 6 in the Kras-169 Q61H Gppnhp + Ppin-1
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Kras-169 Q61H Gppnhp + Ppin-1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg202
b:20.7
occ:1.00
|
O2B
|
B:GNP201
|
2.0
|
16.1
|
1.0
|
O2G
|
B:GNP201
|
2.1
|
22.7
|
1.0
|
O
|
B:HOH309
|
2.1
|
20.1
|
1.0
|
OG
|
B:SER17
|
2.1
|
19.0
|
1.0
|
OG1
|
B:THR35
|
2.1
|
21.3
|
1.0
|
O
|
B:HOH340
|
2.2
|
21.9
|
1.0
|
CB
|
B:THR35
|
3.1
|
25.9
|
1.0
|
CB
|
B:SER17
|
3.2
|
16.9
|
1.0
|
PB
|
B:GNP201
|
3.2
|
17.4
|
1.0
|
PG
|
B:GNP201
|
3.3
|
22.1
|
1.0
|
N3B
|
B:GNP201
|
3.5
|
17.9
|
1.0
|
N
|
B:SER17
|
3.9
|
14.3
|
1.0
|
N
|
B:THR35
|
3.9
|
26.1
|
1.0
|
OD2
|
B:ASP57
|
4.0
|
28.5
|
1.0
|
CA
|
B:SER17
|
4.1
|
15.1
|
1.0
|
CG2
|
B:THR35
|
4.1
|
25.5
|
1.0
|
O3G
|
B:GNP201
|
4.1
|
23.8
|
1.0
|
CA
|
B:THR35
|
4.2
|
24.0
|
1.0
|
OD1
|
B:ASP57
|
4.2
|
27.6
|
1.0
|
O1A
|
B:GNP201
|
4.2
|
18.4
|
1.0
|
O3A
|
B:GNP201
|
4.3
|
17.9
|
1.0
|
O1B
|
B:GNP201
|
4.3
|
16.6
|
1.0
|
O
|
B:THR58
|
4.4
|
26.1
|
1.0
|
O1G
|
B:GNP201
|
4.4
|
23.3
|
1.0
|
CG
|
B:ASP57
|
4.5
|
27.3
|
1.0
|
O
|
B:ASP33
|
4.6
|
25.7
|
1.0
|
PA
|
B:GNP201
|
4.6
|
17.1
|
1.0
|
O2A
|
B:GNP201
|
4.6
|
17.5
|
1.0
|
CB
|
B:LYS16
|
4.8
|
14.4
|
1.0
|
C
|
B:LYS16
|
4.9
|
15.0
|
1.0
|
C
|
B:PRO34
|
4.9
|
25.6
|
1.0
|
|
Magnesium binding site 3 out
of 6 in 6gom
Go back to
Magnesium Binding Sites List in 6gom
Magnesium binding site 3 out
of 6 in the Kras-169 Q61H Gppnhp + Ppin-1
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Kras-169 Q61H Gppnhp + Ppin-1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg202
b:51.4
occ:1.00
|
O1B
|
C:GNP201
|
1.9
|
37.6
|
1.0
|
O1G
|
C:GNP201
|
2.0
|
50.0
|
1.0
|
OG
|
C:SER17
|
2.1
|
31.2
|
1.0
|
O
|
C:HOH301
|
2.2
|
39.5
|
1.0
|
O
|
C:HOH309
|
2.3
|
53.7
|
1.0
|
CB
|
C:SER17
|
3.1
|
30.3
|
1.0
|
PB
|
C:GNP201
|
3.1
|
34.0
|
1.0
|
PG
|
C:GNP201
|
3.3
|
55.8
|
1.0
|
N3B
|
C:GNP201
|
3.6
|
39.0
|
1.0
|
N
|
C:SER17
|
3.6
|
24.8
|
1.0
|
CA
|
C:SER17
|
3.9
|
27.6
|
1.0
|
OD2
|
C:ASP57
|
4.0
|
49.1
|
1.0
|
OD1
|
C:ASP57
|
4.0
|
49.1
|
1.0
|
O2G
|
C:GNP201
|
4.1
|
48.1
|
1.0
|
O2B
|
C:GNP201
|
4.2
|
31.7
|
1.0
|
O3A
|
C:GNP201
|
4.2
|
31.7
|
1.0
|
O2A
|
C:GNP201
|
4.2
|
31.4
|
1.0
|
O1A
|
C:GNP201
|
4.4
|
34.0
|
1.0
|
CG
|
C:ASP57
|
4.4
|
44.0
|
1.0
|
PA
|
C:GNP201
|
4.4
|
32.1
|
1.0
|
O3G
|
C:GNP201
|
4.5
|
51.4
|
1.0
|
CB
|
C:LYS16
|
4.5
|
29.9
|
1.0
|
O
|
C:THR58
|
4.6
|
50.8
|
1.0
|
O
|
C:ASP33
|
4.6
|
84.8
|
1.0
|
C
|
C:LYS16
|
4.6
|
29.2
|
1.0
|
CE
|
C:LYS16
|
4.9
|
35.7
|
1.0
|
CA
|
C:LYS16
|
5.0
|
29.2
|
1.0
|
NZ
|
C:LYS16
|
5.0
|
39.4
|
1.0
|
|
Magnesium binding site 4 out
of 6 in 6gom
Go back to
Magnesium Binding Sites List in 6gom
Magnesium binding site 4 out
of 6 in the Kras-169 Q61H Gppnhp + Ppin-1
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Kras-169 Q61H Gppnhp + Ppin-1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg202
b:72.0
occ:1.00
|
O2B
|
D:GNP201
|
1.7
|
30.6
|
1.0
|
O2G
|
D:GNP201
|
2.1
|
63.0
|
1.0
|
OG
|
D:SER17
|
2.2
|
33.0
|
1.0
|
O
|
D:HOH307
|
2.4
|
52.9
|
1.0
|
PB
|
D:GNP201
|
3.1
|
31.5
|
1.0
|
CB
|
D:SER17
|
3.1
|
31.0
|
1.0
|
PG
|
D:GNP201
|
3.2
|
59.7
|
1.0
|
N3B
|
D:GNP201
|
3.4
|
39.4
|
1.0
|
N
|
D:SER17
|
3.6
|
27.0
|
1.0
|
CA
|
D:SER17
|
3.9
|
25.8
|
1.0
|
O1A
|
D:GNP201
|
4.0
|
34.8
|
1.0
|
O3A
|
D:GNP201
|
4.1
|
30.7
|
1.0
|
O2A
|
D:GNP201
|
4.1
|
35.0
|
1.0
|
O1B
|
D:GNP201
|
4.1
|
28.7
|
1.0
|
O3G
|
D:GNP201
|
4.2
|
50.0
|
1.0
|
PA
|
D:GNP201
|
4.2
|
32.2
|
1.0
|
OD2
|
D:ASP57
|
4.2
|
53.1
|
1.0
|
OD1
|
D:ASP57
|
4.3
|
52.8
|
1.0
|
O1G
|
D:GNP201
|
4.3
|
58.4
|
1.0
|
CG
|
D:ASP57
|
4.7
|
46.3
|
1.0
|
CB
|
D:LYS16
|
4.7
|
25.5
|
1.0
|
C
|
D:LYS16
|
4.7
|
27.1
|
1.0
|
O
|
D:THR58
|
4.7
|
47.3
|
1.0
|
|
Magnesium binding site 5 out
of 6 in 6gom
Go back to
Magnesium Binding Sites List in 6gom
Magnesium binding site 5 out
of 6 in the Kras-169 Q61H Gppnhp + Ppin-1
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Kras-169 Q61H Gppnhp + Ppin-1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg202
b:44.0
occ:1.00
|
OG
|
E:SER17
|
2.0
|
30.1
|
1.0
|
O1B
|
E:GNP201
|
2.1
|
30.7
|
1.0
|
O1G
|
E:GNP201
|
2.1
|
46.7
|
1.0
|
O
|
E:HOH307
|
2.1
|
37.6
|
1.0
|
OG1
|
E:THR35
|
2.2
|
64.8
|
1.0
|
O
|
E:HOH318
|
2.4
|
40.3
|
1.0
|
CB
|
E:SER17
|
3.1
|
28.9
|
1.0
|
CB
|
E:THR35
|
3.2
|
73.5
|
1.0
|
PB
|
E:GNP201
|
3.4
|
30.5
|
1.0
|
PG
|
E:GNP201
|
3.4
|
46.2
|
1.0
|
N3B
|
E:GNP201
|
3.8
|
33.0
|
1.0
|
N
|
E:SER17
|
3.8
|
24.6
|
1.0
|
OD2
|
E:ASP57
|
3.9
|
45.0
|
1.0
|
N
|
E:THR35
|
4.0
|
69.7
|
1.0
|
CA
|
E:SER17
|
4.0
|
25.1
|
1.0
|
OD1
|
E:ASP57
|
4.1
|
42.9
|
1.0
|
CG2
|
E:THR35
|
4.2
|
72.3
|
1.0
|
CA
|
E:THR35
|
4.2
|
75.4
|
1.0
|
O2G
|
E:GNP201
|
4.3
|
42.9
|
1.0
|
O2A
|
E:GNP201
|
4.3
|
33.4
|
1.0
|
CG
|
E:ASP57
|
4.4
|
40.8
|
1.0
|
O3A
|
E:GNP201
|
4.4
|
28.2
|
1.0
|
O
|
E:THR58
|
4.5
|
39.5
|
1.0
|
O3G
|
E:GNP201
|
4.5
|
46.0
|
1.0
|
O2B
|
E:GNP201
|
4.5
|
30.3
|
1.0
|
O
|
E:ASP33
|
4.6
|
64.8
|
1.0
|
O1A
|
E:GNP201
|
4.7
|
32.0
|
1.0
|
PA
|
E:GNP201
|
4.7
|
30.2
|
1.0
|
CB
|
E:LYS16
|
4.8
|
27.7
|
1.0
|
C
|
E:LYS16
|
4.9
|
27.0
|
1.0
|
C
|
E:PRO34
|
5.0
|
69.6
|
1.0
|
|
Magnesium binding site 6 out
of 6 in 6gom
Go back to
Magnesium Binding Sites List in 6gom
Magnesium binding site 6 out
of 6 in the Kras-169 Q61H Gppnhp + Ppin-1
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Kras-169 Q61H Gppnhp + Ppin-1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg202
b:48.9
occ:1.00
|
O1B
|
F:GNP201
|
2.0
|
25.3
|
1.0
|
O
|
F:HOH302
|
2.0
|
37.7
|
1.0
|
O1G
|
F:GNP201
|
2.1
|
42.9
|
1.0
|
OG
|
F:SER17
|
2.2
|
26.0
|
1.0
|
O
|
F:HOH347
|
2.2
|
42.3
|
1.0
|
CB
|
F:SER17
|
3.3
|
23.6
|
1.0
|
PB
|
F:GNP201
|
3.3
|
24.6
|
1.0
|
PG
|
F:GNP201
|
3.4
|
41.7
|
1.0
|
N3B
|
F:GNP201
|
3.7
|
28.1
|
1.0
|
N
|
F:SER17
|
3.9
|
22.0
|
1.0
|
OD2
|
F:ASP57
|
3.9
|
31.5
|
0.5
|
OD1
|
F:ASP57
|
4.0
|
32.5
|
0.5
|
CA
|
F:SER17
|
4.1
|
21.1
|
1.0
|
O2G
|
F:GNP201
|
4.2
|
35.8
|
1.0
|
CG
|
F:ASP57
|
4.4
|
33.6
|
0.5
|
O2B
|
F:GNP201
|
4.4
|
23.3
|
1.0
|
O3A
|
F:GNP201
|
4.4
|
25.5
|
1.0
|
O2A
|
F:GNP201
|
4.4
|
27.3
|
1.0
|
O
|
F:THR58
|
4.4
|
44.1
|
1.0
|
O3G
|
F:GNP201
|
4.5
|
40.7
|
1.0
|
PA
|
F:GNP201
|
4.7
|
25.1
|
1.0
|
O1A
|
F:GNP201
|
4.7
|
24.7
|
1.0
|
CB
|
F:LYS16
|
4.7
|
20.5
|
1.0
|
O
|
F:ASP33
|
4.8
|
71.1
|
1.0
|
C
|
F:LYS16
|
4.9
|
22.4
|
1.0
|
|
Reference:
A.Cruz-Migoni,
P.Canning,
C.E.Quevedo,
C.J.R.Bataille,
N.Bery,
A.Miller,
A.J.Russell,
S.E.V.Phillips,
S.B.Carr,
T.H.Rabbitts.
Structure-Based Development of New Ras-Effector Inhibitors From A Combination of Active and Inactive Ras-Binding Compounds. Proc. Natl. Acad. Sci. V. 116 2545 2019U.S.A..
ISSN: ESSN 1091-6490
PubMed: 30683716
DOI: 10.1073/PNAS.1811360116
Page generated: Tue Oct 1 01:18:53 2024
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