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Fluorine 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 (Mg) 3 atoms
Iodine (I) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine 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 Fluorine atom.
In total 9 binding sites of Fluorine 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 Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in 3vvh

Go back to Fluorine Binding Sites List in 3vvh
Fluorine binding site 1 out of 9 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 Fluorine with other atoms in the F 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:F703

b:34.1
occ:1.00
 F24 A:4BM703 0.0 34.1 1.0
C06 A:4BM703 1.3 33.6 1.0
C05 A:4BM703 2.4 32.9 1.0
C01 A:4BM703 2.4 34.6 1.0
N07 A:4BM703 2.6 34.8 1.0
OD1 A:ASP208 3.1 30.4 1.0
CG2 A:ILE141 3.4 29.2 1.0
CD1 A:ILE141 3.6 28.3 1.0
C04 A:4BM703 3.6 33.4 1.0
O16 A:4BM703 3.6 41.2 1.0
CE A:MET143 3.6 32.9 1.0
C02 A:4BM703 3.7 32.1 1.0
CD A:LYS97 3.7 34.9 1.0
CB A:ILE141 3.9 28.1 1.0
NZ A:LYS97 3.9 33.8 1.0
C08 A:4BM703 4.0 38.4 1.0
CE A:LYS97 4.0 34.6 1.0
C03 A:4BM703 4.1 31.5 1.0
SD A:MET143 4.2 34.7 1.0
CG1 A:ILE141 4.3 28.5 1.0
CG A:ASP208 4.3 30.5 1.0
SG A:CYS207 4.5 33.5 0.3
C14 A:4BM703 4.5 45.0 1.0
CB A:LYS97 4.6 31.9 1.0
O A:HOH802 4.8 31.4 1.0
CG A:LYS97 4.8 33.5 1.0
C09 A:4BM703 4.8 40.3 1.0
CA A:ASP208 4.8 28.1 1.0
N A:ASP208 4.9 28.0 1.0
F25 A:4BM703 5.0 40.5 1.0
C13 A:4BM703 5.0 38.2 1.0

Fluorine binding site 2 out of 9 in 3vvh

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Fluorine binding site 2 out of 9 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 Fluorine with other atoms in the F 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
A:F703

b:40.5
occ:1.00
 F25 A:4BM703 0.0 40.5 1.0
C13 A:4BM703 1.3 38.2 1.0
C08 A:4BM703 2.4 38.4 1.0
C12 A:4BM703 2.5 40.7 1.0
F26 A:4BM703 2.8 43.9 1.0
C02 A:4BM703 2.8 32.1 1.0
N07 A:4BM703 2.8 34.8 1.0
C01 A:4BM703 3.0 34.6 1.0
CG2 A:VAL211 3.3 38.1 1.0
CD2 A:LEU115 3.3 35.6 1.0
O A:PHE209 3.5 30.7 1.0
C11 A:4BM703 3.7 40.4 1.0
C09 A:4BM703 3.8 40.3 1.0
C03 A:4BM703 3.9 31.5 1.0
CD2 A:LEU215 4.0 41.4 1.0
C10 A:4BM703 4.2 40.8 1.0
CD1 A:ILE141 4.3 28.3 1.0
C06 A:4BM703 4.3 33.6 1.0
CD1 A:LEU118 4.3 35.8 1.0
N A:VAL211 4.4 37.9 1.0
CB A:VAL211 4.7 40.7 1.0
C A:PHE209 4.7 31.9 1.0
N A:SER212 4.8 39.1 1.0
CG A:LEU115 4.8 34.9 1.0
C04 A:4BM703 4.9 33.4 1.0
F24 A:4BM703 5.0 34.1 1.0
C14 A:4BM703 5.0 45.0 1.0

Fluorine binding site 3 out of 9 in 3vvh

Go back to Fluorine Binding Sites List in 3vvh
Fluorine binding site 3 out of 9 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 Fluorine with other atoms in the F 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
A:F703

b:43.9
occ:1.00
 F26 A:4BM703 0.0 43.9 1.0
C12 A:4BM703 1.3 40.7 1.0
C13 A:4BM703 2.4 38.2 1.0
C11 A:4BM703 2.4 40.4 1.0
F25 A:4BM703 2.8 40.5 1.0
N A:SER212 3.0 39.1 1.0
N A:VAL211 3.3 37.9 1.0
O A:SER212 3.4 37.5 1.0
O A:PHE209 3.5 30.7 1.0
CA A:GLY210 3.6 34.2 1.0
C10 A:4BM703 3.7 40.8 1.0
CA A:SER212 3.7 38.3 1.0
CB A:SER212 3.7 36.6 1.0
C08 A:4BM703 3.7 38.4 1.0
C A:GLY210 3.7 36.5 1.0
CG2 A:VAL211 3.8 38.1 1.0
C A:SER212 3.9 37.6 1.0
CD2 A:LEU215 3.9 41.4 1.0
C A:VAL211 4.0 38.8 1.0
CA A:VAL211 4.1 38.7 1.0
C09 A:4BM703 4.2 40.3 1.0
CB A:LEU215 4.3 42.3 1.0
C A:PHE209 4.4 31.9 1.0
CG1 A:ILE216 4.5 50.5 1.0
N A:GLY210 4.5 33.0 1.0
CG A:LEU215 4.5 43.0 1.0
CD2 A:LEU115 4.6 35.6 1.0
CB A:VAL211 4.6 40.7 1.0
CD1 A:ILE216 4.7 49.3 1.0
O A:GLY210 4.7 35.6 1.0
OG A:SER212 4.7 37.1 1.0
N07 A:4BM703 4.8 34.8 1.0

Fluorine binding site 4 out of 9 in 3vvh

Go back to Fluorine Binding Sites List in 3vvh
Fluorine binding site 4 out of 9 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 Fluorine with other atoms in the F binding site number 4 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:F503

b:29.7
occ:1.00
 F24 B:4BM503 0.0 29.7 1.0
C06 B:4BM503 1.3 30.9 1.0
C01 B:4BM503 2.4 30.7 1.0
C05 B:4BM503 2.4 29.8 1.0
N07 B:4BM503 2.7 31.2 1.0
OD1 B:ASP208 3.2 30.3 1.0
CG2 B:ILE141 3.5 30.8 1.0
CD1 B:ILE141 3.6 29.8 1.0
CD B:LYS97 3.6 31.3 1.0
O16 B:4BM503 3.6 37.8 1.0
C04 B:4BM503 3.6 31.1 1.0
C02 B:4BM503 3.7 28.8 1.0
NZ B:LYS97 3.7 34.0 1.0
CB B:ILE141 3.9 29.8 1.0
C08 B:4BM503 4.0 32.6 1.0
CE B:LYS97 4.0 33.1 1.0
C03 B:4BM503 4.1 29.8 1.0
CE B:MET143 4.2 30.7 1.0
SD B:MET143 4.2 33.2 1.0
CG B:ASP208 4.3 29.8 1.0
CG1 B:ILE141 4.3 30.8 1.0
C14 B:4BM503 4.5 37.8 1.0
O B:HOH621 4.7 33.9 1.0
CG B:LYS97 4.7 29.4 1.0
SG B:CYS207 4.7 32.9 0.3
CB B:LYS97 4.7 27.9 1.0
CG B:MET143 4.8 31.1 1.0
C09 B:4BM503 4.8 35.3 1.0
CA B:ASP208 4.8 27.8 1.0
N B:ASP208 4.9 27.4 1.0

Fluorine binding site 5 out of 9 in 3vvh

Go back to Fluorine Binding Sites List in 3vvh
Fluorine binding site 5 out of 9 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 Fluorine with other atoms in the F binding site number 5 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:F503

b:35.1
occ:1.00
 F25 B:4BM503 0.0 35.1 1.0
C13 B:4BM503 1.3 32.9 1.0
C08 B:4BM503 2.4 32.6 1.0
C12 B:4BM503 2.4 34.1 1.0
F26 B:4BM503 2.8 37.9 1.0
C02 B:4BM503 2.8 28.8 1.0
N07 B:4BM503 2.8 31.2 1.0
C01 B:4BM503 3.0 30.7 1.0
CG2 B:VAL211 3.2 34.1 1.0
CD2 B:LEU115 3.3 31.7 1.0
O B:PHE209 3.3 27.8 1.0
C11 B:4BM503 3.7 34.5 1.0
C09 B:4BM503 3.8 35.3 1.0
C03 B:4BM503 3.9 29.8 1.0
C10 B:4BM503 4.2 34.6 1.0
CD2 B:LEU215 4.3 29.8 1.0
CD1 B:LEU118 4.3 31.2 1.0
C06 B:4BM503 4.3 30.9 1.0
N B:VAL211 4.3 29.6 1.0
CB B:VAL211 4.6 35.4 1.0
C B:PHE209 4.6 28.9 1.0
CD1 B:ILE141 4.8 29.8 1.0
CG B:LEU115 4.8 31.8 1.0
N B:SER212 4.8 32.5 1.0
CA B:VAL211 4.9 32.8 1.0
C04 B:4BM503 4.9 31.1 1.0

Fluorine binding site 6 out of 9 in 3vvh

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Fluorine binding site 6 out of 9 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 Fluorine with other atoms in the F binding site number 6 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:F503

b:37.9
occ:1.00
 F26 B:4BM503 0.0 37.9 1.0
C12 B:4BM503 1.3 34.1 1.0
C13 B:4BM503 2.4 32.9 1.0
C11 B:4BM503 2.4 34.5 1.0
F25 B:4BM503 2.8 35.1 1.0
N B:SER212 3.1 32.5 1.0
N B:VAL211 3.2 29.6 1.0
O B:PHE209 3.4 27.8 1.0
CA B:GLY210 3.5 30.5 1.0
C B:GLY210 3.6 31.4 1.0
O B:SER212 3.6 30.9 1.0
C10 B:4BM503 3.7 34.6 1.0
CB B:SER212 3.7 32.9 1.0
C08 B:4BM503 3.7 32.6 1.0
CG2 B:VAL211 3.8 34.1 1.0
CA B:SER212 3.8 32.0 1.0
C B:VAL211 4.0 32.7 1.0
CA B:VAL211 4.0 32.8 1.0
C B:SER212 4.1 31.4 1.0
CD2 B:LEU215 4.2 29.8 1.0
C09 B:4BM503 4.2 35.3 1.0
C B:PHE209 4.3 28.9 1.0
CB B:LEU215 4.3 28.3 1.0
N B:GLY210 4.4 29.5 1.0
CG1 B:ILE216 4.4 31.5 1.0
CB B:VAL211 4.6 35.4 1.0
CG B:LEU215 4.6 30.8 1.0
O B:GLY210 4.6 29.8 1.0
CD1 B:ILE216 4.7 34.5 1.0
CD2 B:LEU115 4.7 31.7 1.0
OG B:SER212 4.7 32.6 1.0
N07 B:4BM503 4.8 31.2 1.0
N B:ILE216 4.9 31.4 1.0

Fluorine binding site 7 out of 9 in 3vvh

Go back to Fluorine Binding Sites List in 3vvh
Fluorine binding site 7 out of 9 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 Fluorine with other atoms in the F binding site number 7 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:F503

b:32.4
occ:1.00
 F24 C:4BM503 0.0 32.4 1.0
C06 C:4BM503 1.3 32.2 1.0
C05 C:4BM503 2.4 30.6 1.0
C01 C:4BM503 2.4 31.7 1.0
N07 C:4BM503 2.7 33.9 1.0
OD1 C:ASP208 3.4 30.1 1.0
CG2 C:ILE141 3.4 30.6 1.0
O16 C:4BM503 3.6 39.2 1.0
CD1 C:ILE141 3.6 33.4 1.0
C04 C:4BM503 3.6 31.0 1.0
C02 C:4BM503 3.7 32.1 1.0
CE C:MET143 3.8 32.4 1.0
CD C:LYS97 3.9 30.3 1.0
CB C:ILE141 3.9 31.1 1.0
CE C:LYS97 4.0 31.1 1.0
C08 C:4BM503 4.0 33.3 1.0
NZ C:LYS97 4.1 31.6 1.0
C03 C:4BM503 4.1 31.0 1.0
SD C:MET143 4.2 34.0 1.0
CG1 C:ILE141 4.4 31.6 1.0
C14 C:4BM503 4.5 39.6 1.0
CG C:ASP208 4.5 32.0 1.0
SG C:CYS207 4.7 38.0 0.7
CB C:LYS97 4.8 31.4 1.0
O C:HOH635 4.8 39.3 1.0
C09 C:4BM503 4.8 36.1 1.0
CA C:ASP208 4.9 28.8 1.0
CG C:LYS97 4.9 31.5 1.0
N C:ASP208 5.0 28.8 1.0

Fluorine binding site 8 out of 9 in 3vvh

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Fluorine binding site 8 out of 9 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 Fluorine with other atoms in the F binding site number 8 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:F503

b:33.5
occ:1.00
 F25 C:4BM503 0.0 33.5 1.0
C13 C:4BM503 1.3 33.6 1.0
C08 C:4BM503 2.4 33.3 1.0
C12 C:4BM503 2.5 34.0 1.0
C02 C:4BM503 2.8 32.1 1.0
N07 C:4BM503 2.8 33.9 1.0
F26 C:4BM503 2.8 35.2 1.0
C01 C:4BM503 3.0 31.7 1.0
CG1 C:VAL211 3.3 36.2 1.0
CD2 C:LEU115 3.4 30.0 1.0
O C:PHE209 3.4 27.4 1.0
C11 C:4BM503 3.7 35.1 1.0
C09 C:4BM503 3.7 36.1 1.0
C03 C:4BM503 3.9 31.0 1.0
CD2 C:LEU215 4.0 28.4 1.0
C10 C:4BM503 4.2 34.9 1.0
C06 C:4BM503 4.3 32.2 1.0
N C:VAL211 4.4 31.6 1.0
CB C:VAL211 4.5 34.7 1.0
N C:SER212 4.6 34.0 1.0
C C:PHE209 4.7 29.0 1.0
CB C:SER212 4.8 33.0 1.0
CD1 C:LEU118 4.8 30.8 1.0
CA C:VAL211 4.9 33.4 1.0
CG C:LEU115 4.9 32.1 1.0
CD1 C:ILE141 4.9 33.4 1.0
C04 C:4BM503 4.9 31.0 1.0
C14 C:4BM503 5.0 39.6 1.0

Fluorine binding site 9 out of 9 in 3vvh

Go back to Fluorine Binding Sites List in 3vvh
Fluorine binding site 9 out of 9 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 Fluorine with other atoms in the F binding site number 9 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:F503

b:35.2
occ:1.00
 F26 C:4BM503 0.0 35.2 1.0
C12 C:4BM503 1.3 34.0 1.0
C11 C:4BM503 2.4 35.1 1.0
C13 C:4BM503 2.4 33.6 1.0
F25 C:4BM503 2.8 33.5 1.0
N C:SER212 3.0 34.0 1.0
N C:VAL211 3.4 31.6 1.0
O C:PHE209 3.4 27.4 1.0
O C:SER212 3.4 31.1 1.0
C10 C:4BM503 3.7 34.9 1.0
CA C:GLY210 3.7 30.1 1.0
CB C:SER212 3.7 33.0 1.0
CA C:SER212 3.7 33.7 1.0
C08 C:4BM503 3.7 33.3 1.0
C C:GLY210 3.8 31.6 1.0
C C:SER212 4.0 34.1 1.0
CG1 C:ILE216 4.0 30.4 1.0
C C:VAL211 4.1 34.6 1.0
CG1 C:VAL211 4.1 36.2 1.0
CB C:LEU215 4.2 29.9 1.0
CA C:VAL211 4.2 33.4 1.0
C09 C:4BM503 4.2 36.1 1.0
CD2 C:LEU215 4.2 28.4 1.0
C C:PHE209 4.3 29.0 1.0
N C:GLY210 4.5 30.2 1.0
CD1 C:ILE216 4.5 30.0 1.0
N C:ILE216 4.5 29.2 1.0
CG C:LEU215 4.6 30.6 1.0
O C:GLY210 4.6 30.3 1.0
OG C:SER212 4.7 31.6 1.0
CB C:VAL211 4.8 34.7 1.0
N07 C:4BM503 4.9 33.9 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: Wed Jul 31 23:25:01 2024

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