Magnesium in PDB 3vvh: X-Ray Structure of the Human Mitogen-Activated Protein Kinase Kinase 1 (MEK1) in Complex with An Inhibitor and Mgatp
Enzymatic activity of X-Ray Structure of the Human Mitogen-Activated Protein Kinase Kinase 1 (MEK1) in Complex with An Inhibitor and Mgatp
All present enzymatic activity of X-Ray Structure of the Human Mitogen-Activated Protein Kinase Kinase 1 (MEK1) in Complex with An Inhibitor and Mgatp:
2.7.12.2;
Protein crystallography data
The structure of X-Ray Structure of the Human Mitogen-Activated Protein Kinase Kinase 1 (MEK1) in Complex with An Inhibitor and Mgatp, PDB code: 3vvh
was solved by
N.Kudo,
R.Kato,
S.Wakatsuki,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
2.00
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
58.894,
129.090,
135.736,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19.8 /
22.5
|
Other elements in 3vvh:
The structure of X-Ray Structure of the Human Mitogen-Activated Protein Kinase Kinase 1 (MEK1) in Complex with An Inhibitor and Mgatp also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the X-Ray Structure of the Human Mitogen-Activated Protein Kinase Kinase 1 (MEK1) in Complex with An Inhibitor and Mgatp
(pdb code 3vvh). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the
X-Ray Structure of the Human Mitogen-Activated Protein Kinase Kinase 1 (MEK1) in Complex with An Inhibitor and Mgatp, PDB code: 3vvh:
Jump to Magnesium binding site number:
1;
2;
3;
Magnesium binding site 1 out
of 3 in 3vvh
Go back to
Magnesium Binding Sites List in 3vvh
Magnesium binding site 1 out
of 3 in the X-Ray Structure of the Human Mitogen-Activated Protein Kinase Kinase 1 (MEK1) in Complex with An Inhibitor and Mgatp
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of X-Ray Structure of the Human Mitogen-Activated Protein Kinase Kinase 1 (MEK1) in Complex with An Inhibitor and Mgatp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg701
b:26.3
occ:1.00
|
O1B
|
A:ATP702
|
2.0
|
32.0
|
1.0
|
O
|
A:HOH868
|
2.0
|
27.6
|
1.0
|
O2A
|
A:ATP702
|
2.0
|
30.8
|
1.0
|
OD2
|
A:ASP208
|
2.1
|
29.2
|
1.0
|
O
|
A:HOH809
|
2.1
|
30.0
|
1.0
|
OD1
|
A:ASN195
|
2.2
|
27.1
|
1.0
|
PB
|
A:ATP702
|
3.2
|
36.1
|
1.0
|
PA
|
A:ATP702
|
3.2
|
33.8
|
1.0
|
CG
|
A:ASP208
|
3.3
|
30.5
|
1.0
|
CG
|
A:ASN195
|
3.3
|
28.3
|
1.0
|
O3A
|
A:ATP702
|
3.5
|
35.8
|
1.0
|
ND2
|
A:ASN195
|
3.8
|
26.1
|
1.0
|
NZ
|
A:LYS97
|
3.9
|
33.8
|
1.0
|
O5'
|
A:ATP702
|
3.9
|
30.7
|
1.0
|
CB
|
A:ASP208
|
4.0
|
28.9
|
1.0
|
O
|
A:HOH802
|
4.0
|
31.4
|
1.0
|
O
|
A:SER194
|
4.1
|
28.1
|
1.0
|
C18
|
A:4BM703
|
4.1
|
62.3
|
1.0
|
O2G
|
A:ATP702
|
4.2
|
42.2
|
1.0
|
OD1
|
A:ASP208
|
4.2
|
30.4
|
1.0
|
OG
|
A:SER194
|
4.3
|
27.9
|
1.0
|
O2B
|
A:ATP702
|
4.3
|
35.6
|
1.0
|
O3B
|
A:ATP702
|
4.3
|
40.1
|
1.0
|
O1A
|
A:ATP702
|
4.5
|
33.3
|
1.0
|
CB
|
A:ASN195
|
4.5
|
26.9
|
1.0
|
C
|
A:SER194
|
4.6
|
28.8
|
1.0
|
CA
|
A:ASN195
|
4.7
|
27.0
|
1.0
|
O17
|
A:4BM703
|
4.8
|
62.9
|
1.0
|
SG
|
A:CYS207
|
4.8
|
27.5
|
0.7
|
N15
|
A:4BM703
|
4.8
|
51.5
|
1.0
|
PG
|
A:ATP702
|
4.9
|
39.6
|
1.0
|
N
|
A:ASN195
|
4.9
|
27.3
|
1.0
|
CE
|
A:LYS97
|
5.0
|
34.6
|
1.0
|
CB
|
A:SER194
|
5.0
|
27.6
|
1.0
|
|
Magnesium binding site 2 out
of 3 in 3vvh
Go back to
Magnesium Binding Sites List in 3vvh
Magnesium binding site 2 out
of 3 in the X-Ray Structure of the Human Mitogen-Activated Protein Kinase Kinase 1 (MEK1) in Complex with An Inhibitor and Mgatp
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of X-Ray Structure of the Human Mitogen-Activated Protein Kinase Kinase 1 (MEK1) in Complex with An Inhibitor and Mgatp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg501
b:25.5
occ:1.00
|
O2A
|
B:ATP502
|
2.0
|
31.9
|
1.0
|
OD2
|
B:ASP208
|
2.1
|
28.2
|
1.0
|
O1B
|
B:ATP502
|
2.1
|
30.6
|
1.0
|
O
|
B:HOH636
|
2.2
|
35.6
|
1.0
|
OD1
|
B:ASN195
|
2.2
|
28.4
|
1.0
|
O
|
B:HOH644
|
2.3
|
34.6
|
1.0
|
PA
|
B:ATP502
|
3.3
|
33.2
|
1.0
|
CG
|
B:ASP208
|
3.3
|
29.8
|
1.0
|
PB
|
B:ATP502
|
3.3
|
32.9
|
1.0
|
CG
|
B:ASN195
|
3.4
|
30.4
|
1.0
|
O3A
|
B:ATP502
|
3.6
|
33.4
|
1.0
|
O3B
|
B:ATP502
|
3.8
|
35.9
|
1.0
|
NZ
|
B:LYS97
|
3.9
|
34.0
|
1.0
|
O
|
B:SER194
|
3.9
|
29.7
|
1.0
|
ND2
|
B:ASN195
|
3.9
|
28.3
|
1.0
|
O
|
B:HOH621
|
4.0
|
33.9
|
1.0
|
CB
|
B:ASP208
|
4.0
|
28.7
|
1.0
|
O5'
|
B:ATP502
|
4.0
|
33.5
|
1.0
|
C18
|
B:4BM503
|
4.1
|
51.6
|
1.0
|
OD1
|
B:ASP208
|
4.2
|
30.3
|
1.0
|
OG
|
B:SER194
|
4.2
|
30.3
|
1.0
|
O2G
|
B:ATP502
|
4.4
|
35.9
|
1.0
|
C
|
B:SER194
|
4.5
|
30.2
|
1.0
|
O1A
|
B:ATP502
|
4.5
|
33.0
|
1.0
|
CB
|
B:ASN195
|
4.6
|
28.2
|
1.0
|
CA
|
B:ASN195
|
4.7
|
28.4
|
1.0
|
O2B
|
B:ATP502
|
4.7
|
34.2
|
1.0
|
N
|
B:ASN195
|
4.8
|
29.0
|
1.0
|
PG
|
B:ATP502
|
4.8
|
38.8
|
1.0
|
O17
|
B:4BM503
|
4.9
|
56.1
|
1.0
|
SG
|
B:CYS207
|
4.9
|
26.3
|
0.7
|
N15
|
B:4BM503
|
4.9
|
40.0
|
1.0
|
CB
|
B:SER194
|
4.9
|
30.0
|
1.0
|
CE
|
B:LYS97
|
4.9
|
33.1
|
1.0
|
|
Magnesium binding site 3 out
of 3 in 3vvh
Go back to
Magnesium Binding Sites List in 3vvh
Magnesium binding site 3 out
of 3 in the X-Ray Structure of the Human Mitogen-Activated Protein Kinase Kinase 1 (MEK1) in Complex with An Inhibitor and Mgatp
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of X-Ray Structure of the Human Mitogen-Activated Protein Kinase Kinase 1 (MEK1) in Complex with An Inhibitor and Mgatp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg501
b:27.9
occ:1.00
|
O1B
|
C:ATP502
|
2.0
|
36.3
|
1.0
|
OD2
|
C:ASP208
|
2.1
|
33.0
|
1.0
|
O2A
|
C:ATP502
|
2.1
|
34.7
|
1.0
|
O
|
C:HOH611
|
2.2
|
30.8
|
1.0
|
O
|
C:HOH603
|
2.2
|
31.5
|
1.0
|
OD1
|
C:ASN195
|
2.2
|
28.0
|
1.0
|
PB
|
C:ATP502
|
3.2
|
36.3
|
1.0
|
PA
|
C:ATP502
|
3.2
|
32.8
|
1.0
|
CG
|
C:ASP208
|
3.3
|
32.0
|
1.0
|
CG
|
C:ASN195
|
3.4
|
30.2
|
1.0
|
O3A
|
C:ATP502
|
3.5
|
34.4
|
1.0
|
O3B
|
C:ATP502
|
3.7
|
37.0
|
1.0
|
NZ
|
C:LYS97
|
3.8
|
31.6
|
1.0
|
O5'
|
C:ATP502
|
4.0
|
34.4
|
1.0
|
O
|
C:HOH635
|
4.0
|
39.3
|
1.0
|
ND2
|
C:ASN195
|
4.0
|
27.9
|
1.0
|
O
|
C:SER194
|
4.0
|
28.9
|
1.0
|
CB
|
C:ASP208
|
4.1
|
29.1
|
1.0
|
C18
|
C:4BM503
|
4.1
|
53.2
|
1.0
|
OD1
|
C:ASP208
|
4.2
|
30.1
|
1.0
|
OG
|
C:SER194
|
4.2
|
30.6
|
1.0
|
O2G
|
C:ATP502
|
4.3
|
36.2
|
1.0
|
O2B
|
C:ATP502
|
4.5
|
35.0
|
1.0
|
O1A
|
C:ATP502
|
4.5
|
35.2
|
1.0
|
C
|
C:SER194
|
4.6
|
29.0
|
1.0
|
CB
|
C:ASN195
|
4.6
|
28.3
|
1.0
|
CA
|
C:ASN195
|
4.7
|
28.3
|
1.0
|
PG
|
C:ATP502
|
4.8
|
38.6
|
1.0
|
N15
|
C:4BM503
|
4.8
|
43.5
|
1.0
|
N
|
C:ASN195
|
4.9
|
28.5
|
1.0
|
SG
|
C:CYS207
|
4.9
|
23.9
|
0.3
|
O17
|
C:4BM503
|
4.9
|
58.5
|
1.0
|
CE
|
C:LYS97
|
4.9
|
31.1
|
1.0
|
CB
|
C:SER194
|
5.0
|
28.8
|
1.0
|
|
Reference:
N.Kudo,
R.Kato,
S.Wakatsuki.
X-Ray Structure of the Human Mitogen-Activated Protein Kinase Kinase 1 (MEK1) in Complex with An Inhibitor and Mgatp To Be Published.
Page generated: Thu Aug 15 13:08:24 2024
|