Magnesium in PDB 4j9v: Crystal Structure of the Trka Gating Ring Bound to Atp-Gamma-S

The structure of Crystal Structure of the Trka Gating Ring Bound to Atp-Gamma-S, PDB code: 4j9v was solved by H.Huang, E.J.Levin, X.Jin, Y.Cao, M.Zhou, New York Consortium On Membraneprotein Structure (Nycomps), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.17 / 3.05
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	109.324, 109.324, 337.656, 90.00, 90.00, 120.00
R / Rfree (%)	21.1 / 27.2

The binding sites of Magnesium atom in the Crystal Structure of the Trka Gating Ring Bound to Atp-Gamma-S (pdb code 4j9v). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the Trka Gating Ring Bound to Atp-Gamma-S, PDB code: 4j9v:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the Trka Gating Ring Bound to Atp-Gamma-S


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 Trka Gating Ring Bound to Atp-Gamma-S within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:70.9 occ:1.00 O B:ALA116 2.0 67.0 1.0 O A:ALA116 2.5 63.7 1.0 OE1 A:GLN84 2.7 81.0 1.0 OE1 B:GLN84 2.8 67.6 1.0 C B:ALA116 3.1 64.7 1.0 C A:ALA116 3.6 61.4 1.0 CD A:GLN84 3.6 75.7 1.0 CD B:GLN84 3.7 66.2 1.0 NE2 B:GLN84 3.8 63.1 1.0 CA B:ALA116 3.9 65.1 1.0 NE2 A:GLN84 4.0 76.3 1.0 CA A:ALA116 4.2 63.7 1.0 N B:ILE117 4.2 58.7 1.0 O B:GLY115 4.4 91.9 1.0 CD B:PRO118 4.6 60.2 1.0 CA B:ILE117 4.6 54.0 1.0 N A:ILE117 4.7 59.4 1.0 CB B:ALA116 4.8 55.5 1.0 O A:GLY115 4.8 74.4 1.0 CG B:PRO118 4.9 58.4 1.0 CG A:GLN84 4.9 67.4 1.0 CB A:ALA116 5.0 65.1 1.0 N B:ALA116 5.0 79.0 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Trka Gating Ring Bound to Atp-Gamma-S


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 Trka Gating Ring Bound to Atp-Gamma-S within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg505 b:65.5 occ:1.00 OD1 B:ASP424 3.3 1.0 1.0 N B:ASP424 4.0 95.3 1.0 NH1 B:ARG175 4.0 0.4 1.0 ND1 B:HIS423 4.0 0.7 1.0 CG B:ASP424 4.0 0.5 1.0 CA B:HIS423 4.3 87.4 1.0 CB B:HIS423 4.5 93.0 1.0 CB B:ASP424 4.5 0.4 1.0 CZ B:ARG175 4.7 0.1 1.0 C B:HIS423 4.7 89.7 1.0 NH1 B:ARG184 4.7 71.6 1.0 CG B:HIS423 4.7 97.2 1.0 OD2 B:ASP424 4.8 0.0 1.0 CA B:ASP424 4.9 0.8 1.0

Y.Cao, Y.Pan, H.Huang, X.Jin, E.J.Levin, B.Kloss, M.Zhou. Gating of the Trkh Ion Channel By Its Associated Rck Protein Trka. Nature V. 496 317 2013.
ISSN: ISSN 0028-0836
PubMed: 23598339
DOI: 10.1038/NATURE12056