Magnesium in PDB 9bak: Crystal Structure of Gdp-Bound Human K-Ras in A Covalent Complex with Aryl Sulfonyl Fluoride Compounds.
Enzymatic activity of Crystal Structure of Gdp-Bound Human K-Ras in A Covalent Complex with Aryl Sulfonyl Fluoride Compounds.
All present enzymatic activity of Crystal Structure of Gdp-Bound Human K-Ras in A Covalent Complex with Aryl Sulfonyl Fluoride Compounds.:
3.6.5.2;
Protein crystallography data
The structure of Crystal Structure of Gdp-Bound Human K-Ras in A Covalent Complex with Aryl Sulfonyl Fluoride Compounds., PDB code: 9bak
was solved by
A.D.Landgraf,
R.J.Brenner,
M.K.Ghozayel,
K.Bum-Erdene,
G.Gonzalez-Gutierrez,
S.Meroueh,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
52.34 /
1.67
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
35.867,
83.885,
104.689,
90,
90,
90
|
R / Rfree (%)
|
27 /
28.9
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of Gdp-Bound Human K-Ras in A Covalent Complex with Aryl Sulfonyl Fluoride Compounds.
(pdb code 9bak). 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 Gdp-Bound Human K-Ras in A Covalent Complex with Aryl Sulfonyl Fluoride Compounds., PDB code: 9bak:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 9bak
Go back to
Magnesium Binding Sites List in 9bak
Magnesium binding site 1 out
of 4 in the Crystal Structure of Gdp-Bound Human K-Ras in A Covalent Complex with Aryl Sulfonyl Fluoride Compounds.
 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 Gdp-Bound Human K-Ras in A Covalent Complex with Aryl Sulfonyl Fluoride Compounds. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg201
b:13.2
occ:1.00
|
O
|
A:HOH368
|
2.0
|
11.9
|
1.0
|
OG
|
A:SER17
|
2.0
|
11.1
|
1.0
|
O3B
|
A:GDP202
|
2.1
|
14.1
|
1.0
|
O
|
A:HOH310
|
2.1
|
9.2
|
1.0
|
O
|
A:HOH357
|
2.2
|
16.2
|
1.0
|
O
|
A:HOH324
|
2.2
|
15.2
|
1.0
|
HB2
|
A:SER17
|
3.1
|
13.6
|
1.0
|
CB
|
A:SER17
|
3.1
|
11.6
|
1.0
|
PB
|
A:GDP202
|
3.2
|
15.5
|
1.0
|
H
|
A:SER17
|
3.2
|
12.1
|
1.0
|
HA
|
A:PRO34
|
3.4
|
14.6
|
1.0
|
O2B
|
A:GDP202
|
3.4
|
14.8
|
1.0
|
HD2
|
A:TYR32
|
3.6
|
18.3
|
1.0
|
HB3
|
A:SER17
|
3.8
|
13.6
|
1.0
|
N
|
A:SER17
|
3.8
|
10.3
|
1.0
|
O1A
|
A:GDP202
|
3.9
|
20.2
|
1.0
|
OD2
|
A:ASP57
|
4.0
|
17.2
|
1.0
|
CA
|
A:SER17
|
4.0
|
11.3
|
1.0
|
OD1
|
A:ASP57
|
4.0
|
16.1
|
1.0
|
HB2
|
A:LYS16
|
4.0
|
10.1
|
1.0
|
O1B
|
A:GDP202
|
4.2
|
16.2
|
1.0
|
O3A
|
A:GDP202
|
4.3
|
14.7
|
1.0
|
CA
|
A:PRO34
|
4.3
|
12.4
|
1.0
|
HA
|
A:SER17
|
4.3
|
13.2
|
1.0
|
HE2
|
A:LYS16
|
4.3
|
8.9
|
1.0
|
O
|
A:ASP33
|
4.4
|
12.3
|
1.0
|
PA
|
A:GDP202
|
4.4
|
18.9
|
1.0
|
O
|
A:THR58
|
4.4
|
19.4
|
1.0
|
O
|
A:PRO34
|
4.4
|
12.9
|
1.0
|
CG
|
A:ASP57
|
4.4
|
16.4
|
1.0
|
O2A
|
A:GDP202
|
4.5
|
15.2
|
1.0
|
CD2
|
A:TYR32
|
4.5
|
15.5
|
1.0
|
HZ3
|
A:LYS16
|
4.7
|
8.6
|
1.0
|
O
|
A:ILE36
|
4.7
|
11.7
|
1.0
|
HE2
|
A:TYR32
|
4.7
|
18.1
|
1.0
|
C
|
A:PRO34
|
4.7
|
12.3
|
1.0
|
HZ1
|
A:LYS16
|
4.8
|
8.6
|
1.0
|
HB3
|
A:TYR32
|
4.8
|
19.6
|
1.0
|
O
|
A:TYR32
|
4.9
|
15.2
|
1.0
|
HB3
|
A:PRO34
|
4.9
|
13.8
|
1.0
|
O
|
A:HOH373
|
4.9
|
15.8
|
1.0
|
C
|
A:LYS16
|
4.9
|
10.0
|
1.0
|
CB
|
A:LYS16
|
5.0
|
8.6
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 9bak
Go back to
Magnesium Binding Sites List in 9bak
Magnesium binding site 2 out
of 4 in the Crystal Structure of Gdp-Bound Human K-Ras in A Covalent Complex with Aryl Sulfonyl Fluoride Compounds.
 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 Gdp-Bound Human K-Ras in A Covalent Complex with Aryl Sulfonyl Fluoride Compounds. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg201
b:15.5
occ:1.00
|
O
|
B:HOH313
|
2.0
|
15.8
|
1.0
|
O
|
B:HOH341
|
2.1
|
17.0
|
1.0
|
O
|
B:HOH343
|
2.1
|
19.0
|
1.0
|
O1B
|
B:GDP202
|
2.1
|
15.2
|
1.0
|
OG
|
B:SER17
|
2.2
|
15.2
|
1.0
|
O
|
B:HOH303
|
2.2
|
14.8
|
1.0
|
HB2
|
B:SER17
|
3.1
|
17.6
|
1.0
|
CB
|
B:SER17
|
3.2
|
14.9
|
1.0
|
PB
|
B:GDP202
|
3.3
|
15.4
|
1.0
|
H
|
B:SER17
|
3.3
|
16.3
|
1.0
|
HA
|
B:PRO34
|
3.3
|
20.3
|
1.0
|
HD1
|
B:TYR32
|
3.4
|
25.1
|
1.0
|
O3B
|
B:GDP202
|
3.5
|
18.8
|
1.0
|
OD2
|
B:ASP57
|
3.8
|
17.7
|
1.0
|
HB3
|
B:SER17
|
3.9
|
17.6
|
1.0
|
N
|
B:SER17
|
3.9
|
13.8
|
1.0
|
O2A
|
B:GDP202
|
4.0
|
21.2
|
1.0
|
HE1
|
B:TYR32
|
4.0
|
25.4
|
1.0
|
OD1
|
B:ASP57
|
4.1
|
17.5
|
1.0
|
CA
|
B:SER17
|
4.1
|
14.4
|
1.0
|
HB2
|
B:LYS16
|
4.2
|
18.2
|
1.0
|
CD1
|
B:TYR32
|
4.2
|
21.1
|
1.0
|
O
|
B:ASP33
|
4.2
|
19.4
|
1.0
|
O
|
B:PRO34
|
4.2
|
17.1
|
1.0
|
O2B
|
B:GDP202
|
4.2
|
15.6
|
1.0
|
CA
|
B:PRO34
|
4.3
|
17.2
|
1.0
|
O
|
B:THR58
|
4.3
|
21.6
|
1.0
|
CG
|
B:ASP57
|
4.4
|
17.5
|
1.0
|
O3A
|
B:GDP202
|
4.4
|
15.3
|
1.0
|
HA
|
B:SER17
|
4.4
|
17.0
|
1.0
|
CE1
|
B:TYR32
|
4.4
|
21.4
|
1.0
|
HZ3
|
B:LYS16
|
4.5
|
18.7
|
1.0
|
PA
|
B:GDP202
|
4.5
|
17.9
|
1.0
|
HE2
|
B:LYS16
|
4.5
|
17.9
|
1.0
|
C
|
B:PRO34
|
4.6
|
17.6
|
1.0
|
O
|
B:ILE36
|
4.6
|
17.5
|
1.0
|
O1A
|
B:GDP202
|
4.6
|
13.3
|
1.0
|
O
|
B:TYR32
|
4.8
|
21.7
|
1.0
|
O
|
B:HOH384
|
4.9
|
20.4
|
1.0
|
HB3
|
B:PRO34
|
4.9
|
20.3
|
1.0
|
C
|
B:ASP33
|
5.0
|
19.7
|
1.0
|
HA
|
B:ALA59
|
5.0
|
27.6
|
1.0
|
HB3
|
B:TYR32
|
5.0
|
24.9
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 9bak
Go back to
Magnesium Binding Sites List in 9bak
Magnesium binding site 3 out
of 4 in the Crystal Structure of Gdp-Bound Human K-Ras in A Covalent Complex with Aryl Sulfonyl Fluoride Compounds.
 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 Gdp-Bound Human K-Ras in A Covalent Complex with Aryl Sulfonyl Fluoride Compounds. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg201
b:17.6
occ:1.00
|
O
|
C:HOH306
|
2.0
|
14.2
|
1.0
|
OG
|
C:SER17
|
2.1
|
15.4
|
1.0
|
O
|
C:HOH374
|
2.1
|
18.3
|
1.0
|
O
|
C:HOH322
|
2.1
|
21.8
|
1.0
|
O1B
|
C:GDP202
|
2.1
|
13.4
|
1.0
|
O
|
C:HOH351
|
2.2
|
23.9
|
1.0
|
HB2
|
C:SER17
|
3.1
|
17.6
|
1.0
|
CB
|
C:SER17
|
3.1
|
14.8
|
1.0
|
PB
|
C:GDP202
|
3.3
|
16.2
|
1.0
|
H
|
C:SER17
|
3.3
|
16.8
|
1.0
|
HA
|
C:PRO34
|
3.3
|
27.7
|
1.0
|
O3B
|
C:GDP202
|
3.5
|
16.9
|
1.0
|
HD2
|
C:TYR32
|
3.5
|
33.0
|
1.0
|
HB3
|
C:SER17
|
3.8
|
17.6
|
1.0
|
N
|
C:SER17
|
3.9
|
14.2
|
1.0
|
OD2
|
C:ASP57
|
3.9
|
19.5
|
1.0
|
O2A
|
C:GDP202
|
3.9
|
21.9
|
1.0
|
OD1
|
C:ASP57
|
4.0
|
18.6
|
1.0
|
HB2
|
C:LYS16
|
4.0
|
14.9
|
1.0
|
CA
|
C:SER17
|
4.1
|
14.2
|
1.0
|
CA
|
C:PRO34
|
4.3
|
23.3
|
1.0
|
O2B
|
C:GDP202
|
4.3
|
16.2
|
1.0
|
HE2
|
C:TYR32
|
4.3
|
32.5
|
1.0
|
HE2
|
C:LYS16
|
4.3
|
16.2
|
1.0
|
O
|
C:THR58
|
4.3
|
14.1
|
1.0
|
O
|
C:PRO34
|
4.3
|
22.2
|
1.0
|
O
|
C:ASP33
|
4.3
|
25.7
|
1.0
|
O3A
|
C:GDP202
|
4.3
|
12.5
|
1.0
|
CD2
|
C:TYR32
|
4.3
|
27.8
|
1.0
|
HA
|
C:SER17
|
4.4
|
16.8
|
1.0
|
CG
|
C:ASP57
|
4.4
|
18.9
|
1.0
|
PA
|
C:GDP202
|
4.4
|
16.2
|
1.0
|
O1A
|
C:GDP202
|
4.5
|
17.5
|
1.0
|
O
|
C:ILE36
|
4.6
|
21.1
|
1.0
|
C
|
C:PRO34
|
4.6
|
23.1
|
1.0
|
HZ1
|
C:LYS16
|
4.7
|
16.2
|
1.0
|
CE2
|
C:TYR32
|
4.7
|
27.3
|
1.0
|
HZ3
|
C:LYS16
|
4.7
|
16.2
|
1.0
|
O
|
C:HOH353
|
4.8
|
15.6
|
1.0
|
HB3
|
C:PRO34
|
4.8
|
28.1
|
1.0
|
O
|
C:TYR32
|
4.9
|
30.9
|
1.0
|
CB
|
C:LYS16
|
5.0
|
12.6
|
1.0
|
HB3
|
C:TYR32
|
5.0
|
35.1
|
1.0
|
C
|
C:LYS16
|
5.0
|
12.2
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 9bak
Go back to
Magnesium Binding Sites List in 9bak
Magnesium binding site 4 out
of 4 in the Crystal Structure of Gdp-Bound Human K-Ras in A Covalent Complex with Aryl Sulfonyl Fluoride Compounds.
 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 Gdp-Bound Human K-Ras in A Covalent Complex with Aryl Sulfonyl Fluoride Compounds. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg201
b:12.0
occ:1.00
|
O
|
D:HOH307
|
2.0
|
13.8
|
1.0
|
O
|
D:HOH361
|
2.0
|
20.1
|
1.0
|
O
|
D:HOH340
|
2.1
|
15.4
|
1.0
|
O1B
|
D:GDP202
|
2.1
|
14.0
|
1.0
|
O
|
D:HOH320
|
2.1
|
12.6
|
1.0
|
OG
|
D:SER17
|
2.1
|
14.6
|
1.0
|
HB2
|
D:SER17
|
3.2
|
17.7
|
1.0
|
CB
|
D:SER17
|
3.2
|
15.0
|
1.0
|
PB
|
D:GDP202
|
3.2
|
13.9
|
1.0
|
HA
|
D:PRO34
|
3.3
|
19.2
|
1.0
|
H
|
D:SER17
|
3.4
|
17.3
|
1.0
|
HD2
|
D:TYR32
|
3.4
|
25.2
|
1.0
|
O3B
|
D:GDP202
|
3.5
|
16.4
|
1.0
|
OD2
|
D:ASP57
|
3.9
|
16.7
|
1.0
|
HB3
|
D:SER17
|
3.9
|
17.7
|
1.0
|
HE2
|
D:TYR32
|
3.9
|
25.6
|
1.0
|
N
|
D:SER17
|
4.0
|
14.6
|
1.0
|
O2A
|
D:GDP202
|
4.0
|
18.8
|
1.0
|
OD1
|
D:ASP57
|
4.1
|
16.2
|
1.0
|
CA
|
D:SER17
|
4.2
|
15.0
|
1.0
|
O
|
D:PRO34
|
4.2
|
14.9
|
1.0
|
HB2
|
D:LYS16
|
4.2
|
12.8
|
1.0
|
CD2
|
D:TYR32
|
4.2
|
21.2
|
1.0
|
O2B
|
D:GDP202
|
4.2
|
14.5
|
1.0
|
CA
|
D:PRO34
|
4.2
|
16.2
|
1.0
|
O
|
D:ASP33
|
4.3
|
20.1
|
1.0
|
O
|
D:THR58
|
4.3
|
14.8
|
1.0
|
O3A
|
D:GDP202
|
4.4
|
17.3
|
1.0
|
CG
|
D:ASP57
|
4.4
|
16.9
|
1.0
|
CE2
|
D:TYR32
|
4.4
|
21.5
|
1.0
|
HZ3
|
D:LYS16
|
4.4
|
14.3
|
1.0
|
HA
|
D:SER17
|
4.4
|
17.7
|
1.0
|
HE2
|
D:LYS16
|
4.5
|
13.3
|
1.0
|
PA
|
D:GDP202
|
4.5
|
16.1
|
1.0
|
C
|
D:PRO34
|
4.5
|
15.8
|
1.0
|
O
|
D:ILE36
|
4.6
|
12.6
|
1.0
|
O1A
|
D:GDP202
|
4.6
|
14.3
|
1.0
|
HB3
|
D:PRO34
|
4.8
|
20.5
|
1.0
|
O
|
D:TYR32
|
4.9
|
23.1
|
1.0
|
O
|
D:HOH390
|
4.9
|
6.5
|
1.0
|
HZ1
|
D:LYS16
|
4.9
|
14.3
|
1.0
|
HA
|
D:ALA59
|
5.0
|
15.3
|
1.0
|
|
Reference:
A.Landgraf,
R.Brenner,
M.Ghozayel,
K.Bum-Erdene,
G.Gonzalez-Gutierrez,
S.Meroueh.
Small-Molecule Kras Inhibitors By Tyrosine Covalent Bond Formation. Chemmedchem 00624 2025.
ISSN: ESSN 1860-7187
PubMed: 40099978
DOI: 10.1002/CMDC.202400624
Page generated: Fri Aug 15 23:15:29 2025
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