Magnesium in PDB 2hen: Crystal Structure of the EPHB2 Receptor Kinase Domain in Complex with Adp

All present enzymatic activity of Crystal Structure of the EPHB2 Receptor Kinase Domain in Complex with Adp:
2.7.10.1;

The structure of Crystal Structure of the EPHB2 Receptor Kinase Domain in Complex with Adp, PDB code: 2hen was solved by L.E.Wybenga-Groot, F.Sicheri, T.Pawson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.72 / 2.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.798, 98.304, 114.168, 90.00, 90.18, 90.00
R / Rfree (%)	20.5 / 26

The binding sites of Magnesium atom in the Crystal Structure of the EPHB2 Receptor Kinase Domain in Complex with Adp (pdb code 2hen). 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 EPHB2 Receptor Kinase Domain in Complex with Adp, PDB code: 2hen:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of the EPHB2 Receptor Kinase Domain in Complex with Adp


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 EPHB2 Receptor Kinase Domain in Complex with Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:56.1 occ:1.00 O2A A:ADP400 2.6 53.5 1.0 O A:HOH61 2.9 34.9 1.0 O1B A:ADP400 3.3 63.0 1.0 OD1 A:ASN759 3.5 24.4 1.0 O3B A:ADP400 3.5 62.7 1.0 PA A:ADP400 3.6 47.6 1.0 O3A A:ADP400 3.6 56.0 1.0 PB A:ADP400 3.7 62.0 1.0 O A:ARG758 4.1 27.3 1.0 O1A A:ADP400 4.3 49.7 1.0 CG A:ASN759 4.7 21.1 1.0 O A:HOH151 4.8 31.7 1.0 O5' A:ADP400 4.9 46.5 1.0 C A:ARG758 5.0 24.9 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of the EPHB2 Receptor Kinase Domain in Complex with Adp


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 EPHB2 Receptor Kinase Domain in Complex with Adp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg405 b:39.2 occ:1.00 OD1 B:ASN759 2.6 35.0 1.0 O2A B:ADP401 2.7 44.9 1.0 OD2 B:ASP772 2.7 37.6 1.0 O3B B:ADP401 2.8 54.1 1.0 NH2 B:ARG758 3.3 54.4 1.0 PA B:ADP401 3.6 45.6 1.0 CG B:ASP772 3.7 35.6 1.0 CG B:ASN759 3.8 31.4 1.0 PB B:ADP401 3.8 54.3 1.0 O1A B:ADP401 3.9 43.8 1.0 CZ B:ARG758 3.9 53.6 1.0 O3A B:ADP401 3.9 49.3 1.0 CB B:ASP772 4.0 32.7 1.0 O1B B:ADP401 4.1 53.0 1.0 O B:ARG758 4.3 27.4 1.0 NE B:ARG758 4.4 49.0 1.0 CA B:ASN759 4.4 25.8 1.0 O B:HOH62 4.5 33.8 1.0 CB B:ASN759 4.6 27.9 1.0 NH1 B:ARG758 4.7 55.8 1.0 ND2 B:ASN759 4.7 30.1 1.0 C B:ARG758 4.9 24.9 1.0 OD1 B:ASP772 4.9 37.4 1.0 N B:ASN759 5.0 25.3 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of the EPHB2 Receptor Kinase Domain in Complex with Adp


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 EPHB2 Receptor Kinase Domain in Complex with Adp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg406 b:49.5 occ:1.00 O2A C:ADP402 2.9 50.9 1.0 O3B C:ADP402 3.0 63.2 1.0 OD1 C:ASN759 3.0 21.9 1.0 PA C:ADP402 3.6 47.9 1.0 O1A C:ADP402 3.7 49.4 1.0 OD1 C:ASP772 3.7 42.1 1.0 CB C:ASP772 3.9 37.8 1.0 PB C:ADP402 4.0 62.8 1.0 CG C:ASP772 4.0 40.2 1.0 O3A C:ADP402 4.1 56.2 1.0 CG C:ASN759 4.2 17.8 1.0 O1B C:ADP402 4.2 62.6 1.0 O C:ARG758 4.5 22.7 1.0 CA C:ASP772 4.6 34.8 1.0 O C:HOH24 4.6 22.9 1.0 CA C:ASN759 4.7 17.2 1.0 CB C:ASN759 4.8 16.2 1.0 OD2 C:ASP772 5.0 43.2 1.0 N C:ASP772 5.0 32.1 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of the EPHB2 Receptor Kinase Domain in Complex with Adp


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 EPHB2 Receptor Kinase Domain in Complex with Adp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg407 b:47.0 occ:1.00 O2A D:ADP403 2.7 47.2 1.0 OD1 D:ASN759 2.7 35.8 1.0 O3B D:ADP403 2.7 57.0 1.0 OD2 D:ASP772 2.8 42.7 1.0 NH2 D:ARG758 3.3 57.7 1.0 PA D:ADP403 3.5 46.9 1.0 O1A D:ADP403 3.7 46.4 1.0 PB D:ADP403 3.7 55.8 1.0 CG D:ASP772 3.8 41.3 1.0 O3A D:ADP403 3.8 51.5 1.0 CG D:ASN759 3.9 32.8 1.0 CB D:ASP772 4.0 37.6 1.0 O1B D:ADP403 4.0 55.5 1.0 CZ D:ARG758 4.2 56.6 1.0 O D:ARG758 4.2 31.6 1.0 NE D:ARG758 4.3 53.4 1.0 O D:HOH221 4.5 29.4 1.0 CA D:ASN759 4.6 30.6 1.0 CB D:ASN759 4.8 31.7 1.0 ND2 D:ASN759 4.9 30.8 1.0 OD1 D:ASP772 4.9 43.3 1.0 O5' D:ADP403 5.0 44.4 1.0

S.Wiesner, L.E.Wybenga-Groot, N.Warner, H.Lin, T.Pawson, J.D.Forman-Kay, F.Sicheri. A Change in Conformational Dynamics Underlies the Activation of Eph Receptor Tyrosine Kinases Embo J. V. 25 4686 2006.
ISSN: ISSN 0261-4189
PubMed: 16977320
DOI: 10.1038/SJ.EMBOJ.7601315