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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:

Fluorine (F) 9 atoms
Iodine (I) 3 atoms

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

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