Magnesium in PDB 3gt8: Crystal Structure of the Inactive Egfr Kinase Domain in Complex with Amp-Pnp

All present enzymatic activity of Crystal Structure of the Inactive Egfr Kinase Domain in Complex with Amp-Pnp:
2.7.10.1;

The structure of Crystal Structure of the Inactive Egfr Kinase Domain in Complex with Amp-Pnp, PDB code: 3gt8 was solved by N.Jura, N.F.Endres, K.Engel, S.Deindl, R.Das, M.H.Lamers, D.E.Wemmer, X.Zhang, J.Kuriyan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.79 / 2.96
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.764, 72.411, 143.376, 90.00, 101.74, 90.00
R / Rfree (%)	21.6 / 27.5

The binding sites of Magnesium atom in the Crystal Structure of the Inactive Egfr Kinase Domain in Complex with Amp-Pnp (pdb code 3gt8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of the Inactive Egfr Kinase Domain in Complex with Amp-Pnp, PDB code: 3gt8:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of the Inactive Egfr Kinase Domain in Complex 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 Crystal Structure of the Inactive Egfr Kinase Domain in Complex with Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg12 b:77.2 occ:1.00 OD1 A:ASN818 1.9 40.2 1.0 OD2 A:ASP831 2.1 67.2 1.0 O3A A:ANP2 2.4 68.2 1.0 N3B A:ANP2 2.7 48.6 1.0 O A:HOH29 2.9 58.9 1.0 PB A:ANP2 3.1 53.8 1.0 CG A:ASN818 3.1 38.0 1.0 O2A A:ANP2 3.2 0.4 1.0 CG A:ASP831 3.3 65.7 1.0 PA A:ANP2 3.4 60.0 1.0 O A:ARG817 3.7 31.9 1.0 O1B A:ANP2 4.0 54.5 1.0 ND2 A:ASN818 4.0 38.9 1.0 PG A:ANP2 4.0 76.5 1.0 OD1 A:ASP831 4.0 67.6 1.0 O3G A:ANP2 4.0 19.9 1.0 CA A:ASN818 4.1 32.5 1.0 CB A:ASN818 4.1 33.8 1.0 O A:HOH35 4.2 51.8 1.0 O1A A:ANP2 4.3 59.1 1.0 OG1 A:THR830 4.3 76.6 1.0 CB A:ASP831 4.3 60.5 1.0 O2B A:ANP2 4.4 0.6 1.0 C A:ARG817 4.4 32.3 1.0 NZ A:LYS721 4.5 55.0 1.0 N A:ASN818 4.6 31.3 1.0 O2G A:ANP2 4.6 20.5 1.0 O5' A:ANP2 4.7 52.9 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of the Inactive Egfr Kinase Domain in Complex 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 Crystal Structure of the Inactive Egfr Kinase Domain in Complex with Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg11 b:35.5 occ:1.00 OD2 B:ASP831 2.1 58.5 1.0 OD1 B:ASN818 2.4 42.0 1.0 O1B B:ANP1 2.7 88.2 1.0 O2A B:ANP1 3.1 42.6 1.0 CG B:ASP831 3.2 56.6 1.0 N3B B:ANP1 3.3 25.6 1.0 PB B:ANP1 3.4 88.6 1.0 CG B:ASN818 3.5 38.4 1.0 O B:ARG817 3.7 39.9 1.0 CA B:ASN818 3.8 31.9 1.0 O5' B:ANP1 3.8 26.1 1.0 OD1 B:ASP831 3.9 56.8 1.0 PA B:ANP1 3.9 68.2 1.0 O3A B:ANP1 4.0 18.4 1.0 CB B:ASN818 4.2 33.2 1.0 CB B:ASP831 4.3 53.1 1.0 C B:ARG817 4.3 36.4 1.0 N B:ASN818 4.4 33.9 1.0 ND2 B:ASN818 4.4 41.8 1.0 OG1 B:THR830 4.6 48.9 1.0 PG B:ANP1 4.7 52.6 1.0 C B:ASN818 4.8 28.8 1.0 C8 B:ANP1 4.8 48.8 1.0 NZ B:LYS721 4.8 56.2 1.0 O3G B:ANP1 4.8 64.3 1.0 CB B:THR830 4.9 47.5 1.0 O2B B:ANP1 4.9 48.7 1.0 O B:ASN818 5.0 27.7 1.0 C3' B:ANP1 5.0 49.5 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of the Inactive Egfr Kinase Domain in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Inactive Egfr Kinase Domain in Complex with Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg13 b:47.0 occ:1.00 O1B C:ANP3 1.8 55.5 1.0 OD1 C:ASN818 2.3 56.4 1.0 O2A C:ANP3 2.3 76.3 1.0 OD2 C:ASP831 2.5 54.5 1.0 O C:HOH41 2.5 44.7 1.0 PB C:ANP3 3.2 54.9 1.0 CG C:ASP831 3.3 53.1 1.0 CG C:ASN818 3.4 49.0 1.0 O1G C:ANP3 3.4 46.9 1.0 O C:ARG817 3.7 36.9 1.0 PA C:ANP3 3.8 47.7 1.0 O2B C:ANP3 3.8 35.9 1.0 OD1 C:ASP831 3.8 53.1 1.0 O3A C:ANP3 4.0 57.9 1.0 CA C:ASN818 4.0 38.7 1.0 CB C:ASN818 4.1 41.5 1.0 C C:ARG817 4.2 36.5 1.0 PG C:ANP3 4.3 47.8 1.0 CB C:ASP831 4.4 50.9 1.0 N3B C:ANP3 4.4 59.0 1.0 N C:ASN818 4.4 37.7 1.0 ND2 C:ASN818 4.4 50.3 1.0 OG1 C:THR830 4.5 35.5 1.0 O1A C:ANP3 4.6 47.6 1.0 NZ C:LYS721 4.7 49.7 1.0 O3G C:ANP3 4.7 62.2 1.0 C3' C:ANP3 4.8 47.8 1.0 O5' C:ANP3 4.8 42.3 1.0 CB C:ARG817 4.9 30.3 1.0 C2' C:ANP3 5.0 46.3 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of the Inactive Egfr Kinase Domain in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Inactive Egfr Kinase Domain in Complex with Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg14 b:44.2 occ:1.00 O1B D:ANP4 1.7 80.3 1.0 OD1 D:ASN818 1.9 49.4 1.0 O2A D:ANP4 2.1 0.6 1.0 OD2 D:ASP831 2.7 59.3 1.0 CG D:ASN818 2.9 47.6 1.0 PB D:ANP4 2.9 79.5 1.0 CG D:ASP831 3.3 58.8 1.0 PA D:ANP4 3.5 48.8 1.0 O1G D:ANP4 3.5 46.3 1.0 O3A D:ANP4 3.6 40.9 1.0 N3B D:ANP4 3.7 56.1 1.0 OD1 D:ASP831 3.7 59.6 1.0 CB D:ASN818 3.8 45.5 1.0 ND2 D:ASN818 3.8 47.7 1.0 PG D:ANP4 3.8 46.9 1.0 O D:ARG817 3.9 46.6 1.0 O3G D:ANP4 3.9 71.5 1.0 CA D:ASN818 4.1 46.4 1.0 O2B D:ANP4 4.2 25.9 1.0 NZ D:LYS721 4.2 47.0 1.0 O5' D:ANP4 4.3 32.8 1.0 CB D:ASP831 4.4 56.8 1.0 C D:ARG817 4.4 46.4 1.0 N D:ASN818 4.4 46.7 1.0 O1A D:ANP4 4.5 47.8 1.0 C5' D:ANP4 4.8 30.8 1.0 C3' D:ANP4 5.0 57.4 1.0

N.Jura, N.F.Endres, K.Engel, S.Deindl, R.Das, M.H.Lamers, D.E.Wemmer, X.Zhang, J.Kuriyan. Mechanism For Activation of the Egf Receptor Catalytic Domain By the Juxtamembrane Segment. Cell(Cambridge,Mass.) V. 137 1293 2009.
ISSN: ISSN 0092-8674
PubMed: 19563760
DOI: 10.1016/J.CELL.2009.04.025