Magnesium in PDB 4jry: Crystal Structure of SB47 Tcr-Hla B*3505-Lpep Complex

The structure of Crystal Structure of SB47 Tcr-Hla B*3505-Lpep Complex, PDB code: 4jry was solved by Y.C.Liu, J.Rossjohn, S.Gras, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	100.00 / 2.80
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	237.600, 237.600, 61.200, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 23.3

The structure of Crystal Structure of SB47 Tcr-Hla B*3505-Lpep Complex also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of SB47 Tcr-Hla B*3505-Lpep Complex (pdb code 4jry). 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 SB47 Tcr-Hla B*3505-Lpep Complex, PDB code: 4jry:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of SB47 Tcr-Hla B*3505-Lpep Complex


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 SB47 Tcr-Hla B*3505-Lpep Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg102 b:60.1 occ:1.00 OD1 B:ASN83 2.5 48.6 1.0 O B:LEU87 2.5 48.9 1.0 O B:HIS84 2.7 44.5 1.0 CG B:ASN83 3.2 53.3 1.0 ND2 B:ASN83 3.4 45.5 1.0 C B:LEU87 3.7 47.1 1.0 C B:HIS84 3.7 42.3 1.0 N B:HIS84 4.4 38.8 1.0 CA B:LEU87 4.4 39.3 1.0 CB B:LEU87 4.5 38.2 1.0 CA B:VAL85 4.5 35.7 1.0 N B:VAL85 4.5 36.3 1.0 O B:VAL85 4.5 45.0 1.0 C B:SER88 4.6 49.8 1.0 N B:LEU87 4.6 39.4 1.0 O B:SER88 4.6 51.0 1.0 CB B:ASN83 4.6 34.4 1.0 N B:SER88 4.7 44.0 1.0 C B:VAL85 4.7 43.5 1.0 CA B:HIS84 4.7 37.7 1.0 N B:GLN89 4.8 45.8 1.0 CA B:SER88 4.9 44.1 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of SB47 Tcr-Hla B*3505-Lpep Complex


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 SB47 Tcr-Hla B*3505-Lpep Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg103 b:53.3 occ:1.00 CA B:LYS58 3.8 40.9 1.0 O B:LYS58 3.8 48.4 1.0 CH2 B:TRP60 3.8 55.0 1.0 O B:SER57 3.9 42.1 1.0 CZ3 B:TRP60 3.9 54.3 1.0 CB A:MET98 4.1 45.1 1.0 CZ2 B:TRP60 4.1 55.2 1.0 SD A:MET98 4.1 57.0 1.0 C B:LYS58 4.2 47.7 1.0 CE3 B:TRP60 4.2 52.4 1.0 CE2 B:PHE56 4.4 47.8 1.0 CE2 B:TRP60 4.4 55.3 1.0 N B:LYS58 4.4 40.4 1.0 CD2 B:TRP60 4.4 50.8 1.0 C B:SER57 4.5 43.7 1.0 CG B:LYS58 4.5 55.5 0.5 CG A:MET98 4.6 50.5 1.0 CD2 B:PHE56 4.6 46.1 1.0 CE A:MET98 4.6 53.3 1.0 CB B:LYS58 4.7 42.3 1.0 OE1 A:GLN115 4.7 58.8 1.0

Y.C.Liu, J.J.Miles, M.A.Neller, E.Gostick, D.A.Price, A.W.Purcell, J.Mccluskey, S.R.Burrows, J.Rossjohn, S.Gras. Highly Divergent T-Cell Receptor Binding Modes Underlie Specific Recognition of A Bulged Viral Peptide Bound to A Human Leukocyte Antigen Class I Molecule. J.Biol.Chem. V. 288 15442 2013.
ISSN: ISSN 0021-9258
PubMed: 23569211
DOI: 10.1074/JBC.M112.447185