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Iodine 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:

Fluorine (F) 9 atoms
Magnesium (Mg) 3 atoms

Iodine Binding Sites:

The binding sites of Iodine 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 Iodine atom.
In total 3 binding sites of Iodine 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 Iodine binding site number: 1; 2; 3;

Iodine binding site 1 out of 3 in 3vvh

Go back to Iodine Binding Sites List in 3vvh
Iodine 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 Iodine with other atoms in the I 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:I703

b:34.3
occ:1.00
I23 A:4BM703 0.0 34.3 1.0
C04 A:4BM703 2.1 33.4 1.0
C05 A:4BM703 3.0 32.9 1.0
C03 A:4BM703 3.1 31.5 1.0
O A:VAL127 3.2 27.2 1.0
CZ A:PHE209 4.0 31.5 1.0
C A:VAL127 4.1 27.1 1.0
SG A:CYS207 4.1 33.5 0.3
CE2 A:PHE209 4.1 29.8 1.0
CB A:VAL127 4.1 28.1 1.0
C06 A:4BM703 4.3 33.6 1.0
CD2 A:LEU118 4.4 36.0 1.0
C02 A:4BM703 4.4 32.1 1.0
O A:GLY128 4.5 31.4 1.0
CG1 A:VAL127 4.5 29.4 1.0
CA A:VAL127 4.6 27.7 1.0
CB A:PHE129 4.6 32.0 1.0
CB A:CYS207 4.7 28.6 0.7
CA A:CYS207 4.7 27.9 1.0
C A:GLY128 4.7 30.3 1.0
CB A:MET143 4.8 31.9 1.0
SD A:MET143 4.9 34.7 1.0
N A:VAL127 4.9 27.6 1.0
O A:LEU206 4.9 26.1 1.0
CB A:CYS207 4.9 30.1 0.3
C01 A:4BM703 4.9 34.6 1.0
N A:ASP208 4.9 28.0 1.0
N A:PHE129 5.0 31.2 1.0
CG2 A:ILE126 5.0 27.0 1.0
CE1 A:PHE209 5.0 29.8 1.0

Iodine binding site 2 out of 3 in 3vvh

Go back to Iodine Binding Sites List in 3vvh
Iodine 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 Iodine with other atoms in the I 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:I503

b:32.3
occ:1.00
I23 B:4BM503 0.0 32.3 1.0
C04 B:4BM503 2.1 31.1 1.0
C05 B:4BM503 3.0 29.8 1.0
C03 B:4BM503 3.1 29.8 1.0
O B:VAL127 3.2 25.5 1.0
SG B:CYS207 3.7 32.9 0.3
CE2 B:PHE209 4.0 27.9 1.0
CZ B:PHE209 4.1 26.7 1.0
C B:VAL127 4.1 27.0 1.0
CB B:VAL127 4.1 26.4 1.0
CG B:MET143 4.3 31.1 1.0
C06 B:4BM503 4.3 30.9 1.0
CG1 B:VAL127 4.4 27.6 1.0
C02 B:4BM503 4.4 28.8 1.0
CD2 B:LEU118 4.5 31.4 1.0
CB B:CYS207 4.6 26.8 0.7
CA B:CYS207 4.6 27.0 1.0
CA B:VAL127 4.6 25.8 1.0
CB B:PHE129 4.6 30.7 1.0
O B:GLY128 4.6 28.4 1.0
CB B:CYS207 4.8 28.9 0.3
SD B:MET143 4.8 33.2 1.0
C B:GLY128 4.8 29.2 1.0
N B:VAL127 4.8 25.4 1.0
N B:ASP208 4.9 27.4 1.0
O B:LEU206 4.9 27.6 1.0
CG2 B:ILE126 4.9 25.0 1.0
C01 B:4BM503 4.9 30.7 1.0
CD1 B:LEU118 4.9 31.2 1.0
CD2 B:PHE209 5.0 25.7 1.0

Iodine binding site 3 out of 3 in 3vvh

Go back to Iodine Binding Sites List in 3vvh
Iodine 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 Iodine with other atoms in the I 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:I503

b:34.8
occ:1.00
I23 C:4BM503 0.0 34.8 1.0
C04 C:4BM503 2.1 31.0 1.0
C05 C:4BM503 3.0 30.6 1.0
O C:VAL127 3.1 30.1 1.0
C03 C:4BM503 3.1 31.0 1.0
SG C:CYS207 3.9 38.0 0.7
C C:VAL127 3.9 32.3 1.0
CE2 C:PHE209 4.0 29.3 1.0
CB C:VAL127 4.1 31.6 1.0
CZ C:PHE209 4.1 28.5 1.0
CG1 C:VAL127 4.2 33.3 1.0
C06 C:4BM503 4.3 32.2 1.0
O C:GLY128 4.4 32.5 1.0
C02 C:4BM503 4.4 32.1 1.0
CD1 C:LEU118 4.4 30.8 1.0
CA C:VAL127 4.5 31.0 1.0
CD2 C:LEU118 4.5 30.0 1.0
C C:GLY128 4.6 33.2 1.0
CB C:PHE129 4.7 32.9 1.0
SD C:MET143 4.7 34.0 1.0
CA C:CYS207 4.7 28.1 1.0
CB C:MET143 4.7 31.4 1.0
CB C:CYS207 4.8 26.7 0.3
N C:GLY128 4.9 31.6 1.0
C01 C:4BM503 4.9 31.7 1.0
N C:PHE129 4.9 32.4 1.0
CB C:CYS207 4.9 31.3 0.7
N C:VAL127 4.9 31.7 1.0
N C:ASP208 4.9 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: Sun Dec 13 19:31:20 2020

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