Magnesium in PDB 6opg: Phosphorylated ERK2 with Amp-Pnp

Enzymatic activity of Phosphorylated ERK2 with Amp-Pnp

All present enzymatic activity of Phosphorylated ERK2 with Amp-Pnp:
2.7.11.24;

Protein crystallography data

The structure of Phosphorylated ERK2 with Amp-Pnp, PDB code: 6opg was solved by G.P.Vigers, D.Smith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.89 / 2.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 41.850, 77.150, 152.160, 90.00, 90.00, 90.00
R / Rfree (%) 15.6 / 23.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Phosphorylated ERK2 with Amp-Pnp (pdb code 6opg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Phosphorylated ERK2 with Amp-Pnp, PDB code: 6opg:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6opg

Go back to Magnesium Binding Sites List in 6opg
Magnesium binding site 1 out of 2 in the Phosphorylated ERK2 with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Phosphorylated ERK2 with Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:39.6
occ:1.00
OD2 A:ASP165 2.3 46.6 1.0
O2B A:ANP401 2.4 48.1 1.0
O3G A:ANP401 2.4 51.0 1.0
OD1 A:ASP165 2.6 43.5 1.0
CG A:ASP165 2.8 39.9 1.0
O A:HOH512 3.6 41.2 1.0
PG A:ANP401 3.6 55.9 1.0
PB A:ANP401 3.7 57.8 1.0
O1G A:ANP401 3.8 52.6 1.0
N3B A:ANP401 4.1 56.4 1.0
OD2 A:ASP147 4.1 42.2 1.0
CA A:GLY167 4.1 40.9 1.0
CB A:ASP165 4.3 38.9 1.0
C A:GLY167 4.6 40.5 1.0
N A:GLY167 4.6 39.8 1.0
O1B A:ANP401 4.7 55.6 1.0
NZ A:LYS52 4.8 52.1 1.0
O3A A:ANP401 4.9 53.0 1.0
MG A:MG403 4.9 55.7 1.0
O2G A:ANP401 4.9 51.6 1.0
N A:LEU168 5.0 43.5 1.0

Magnesium binding site 2 out of 2 in 6opg

Go back to Magnesium Binding Sites List in 6opg
Magnesium binding site 2 out of 2 in the Phosphorylated ERK2 with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Phosphorylated ERK2 with Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:55.7
occ:1.00
O1G A:ANP401 1.6 52.6 1.0
OD1 A:ASN152 2.1 46.6 1.0
O2A A:ANP401 2.3 55.9 1.0
PG A:ANP401 3.0 55.9 1.0
CG A:ASN152 3.2 37.4 1.0
OD2 A:ASP165 3.4 46.6 1.0
OG A:SER151 3.5 41.2 1.0
N3B A:ANP401 3.6 56.4 1.0
CE A:LYS149 3.7 53.1 1.0
PA A:ANP401 3.7 49.8 1.0
ND2 A:ASN152 3.7 34.6 1.0
CG A:ASP165 3.8 39.9 1.0
NZ A:LYS149 3.8 57.8 1.0
O3G A:ANP401 3.8 51.0 1.0
O2G A:ANP401 3.8 51.6 1.0
CB A:ASP165 3.9 38.9 1.0
O3' A:ANP401 4.0 45.5 1.0
O3A A:ANP401 4.0 53.0 1.0
PB A:ANP401 4.2 57.8 1.0
O2B A:ANP401 4.3 48.1 1.0
C5' A:ANP401 4.4 47.5 1.0
CB A:ASN152 4.4 38.1 1.0
O A:SER151 4.5 48.3 1.0
O5' A:ANP401 4.5 45.1 1.0
N A:ASN152 4.5 41.3 1.0
C A:SER151 4.5 49.8 1.0
CA A:ASN152 4.6 40.0 1.0
OD1 A:ASP165 4.7 43.5 1.0
C3' A:ANP401 4.7 50.2 1.0
O1A A:ANP401 4.8 46.7 1.0
OD2 A:ASP147 4.8 42.2 1.0
CB A:SER151 4.8 42.8 1.0
MG A:MG402 4.9 39.6 1.0

Reference:

L.M.Pegram, J.C.Liddle, Y.Xiao, M.Hoh, J.Rudolph, D.B.Iverson, G.P.Vigers, D.Smith, H.Zhang, W.Wang, J.G.Moffat, N.G.Ahn. Activation Loop Dynamics Are Controlled By Conformation-Selective Inhibitors of ERK2. Proc.Natl.Acad.Sci.Usa V. 116 15463 2019.
ISSN: ESSN 1091-6490
PubMed: 31311868
DOI: 10.1073/PNAS.1906824116
Page generated: Mon Dec 14 23:44:14 2020

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