Magnesium in PDB 4kgq: Crystal Structure of A Human Light Loop Mutant in Complex with DCR3

The structure of Crystal Structure of A Human Light Loop Mutant in Complex with DCR3, PDB code: 4kgq was solved by W.Liu, C.Zhan, J.B.Bonanno, P.Sampathkumar, R.Toro, S.G.Nathenson, S.C.Almo, New York Structural Genomics Research Consortium (Nysgrc), Atoms-To-Animals: The Immune Function Network (Ifn), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.35 / 2.27
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	149.269, 149.269, 149.269, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 23.8

The binding sites of Magnesium atom in the Crystal Structure of A Human Light Loop Mutant in Complex with DCR3 (pdb code 4kgq). 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 A Human Light Loop Mutant in Complex with DCR3, PDB code: 4kgq:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of A Human Light Loop Mutant in Complex with DCR3


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 A Human Light Loop Mutant in Complex with DCR3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg301 b:47.1 occ:1.00 O C:ALA136 2.2 35.6 1.0 O C:SER161 2.3 42.9 1.0 O C:HOH401 2.5 40.4 1.0 O C:PRO133 2.5 38.4 1.0 OG C:SER159 2.5 36.0 1.0 O C:CYS132 2.8 42.1 1.0 C C:PRO133 3.2 47.5 1.0 C C:ALA136 3.5 31.7 1.0 CB C:SER159 3.5 40.2 1.0 C C:CYS132 3.5 42.6 1.0 C C:SER161 3.6 45.3 1.0 N C:PRO134 3.9 44.8 1.0 CB C:CYS132 4.0 48.9 1.0 CA C:PRO133 4.1 47.4 1.0 N C:PRO133 4.1 39.6 1.0 N C:ALA136 4.1 35.3 1.0 OE1 C:GLU166 4.1 42.6 1.0 CA C:PRO134 4.2 39.4 1.0 N C:SER163 4.2 50.2 1.0 CA C:CYS132 4.4 50.8 1.0 CA C:ALA136 4.4 34.5 1.0 CA C:GLY137 4.4 40.8 1.0 N C:GLY137 4.4 36.9 1.0 N C:SER162 4.5 51.4 1.0 N C:SER161 4.5 41.7 1.0 CA C:SER162 4.5 51.2 1.0 CA C:SER161 4.6 50.6 1.0 O C:GLU166 4.6 45.3 1.0 C C:PRO134 4.7 39.5 1.0 O C:SER163 4.7 45.9 1.0 N C:GLY135 4.7 32.5 1.0 CA C:SER159 4.8 33.0 1.0 O C:SER159 4.8 30.4 1.0 C C:SER162 4.8 52.6 1.0 C C:SER159 4.8 31.7 1.0 CB C:ALA136 5.0 40.7 1.0 CD C:GLU166 5.0 52.7 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of A Human Light Loop Mutant in Complex with DCR3


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 A Human Light Loop Mutant in Complex with DCR3 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg301 b:55.5 occ:1.00 O D:ALA136 2.3 51.8 1.0 OG D:SER159 2.4 49.0 1.0 O D:HOH402 2.5 56.1 1.0 O D:SER161 2.5 56.0 1.0 O D:PRO133 2.6 50.2 1.0 O D:CYS132 2.8 56.2 1.0 CB D:SER159 3.4 49.7 1.0 C D:PRO133 3.4 61.9 1.0 C D:ALA136 3.5 49.7 1.0 C D:CYS132 3.5 67.0 1.0 C D:SER161 3.8 66.4 1.0 CB D:CYS132 3.9 73.5 1.0 N D:PRO134 4.1 56.6 1.0 OE1 D:GLU166 4.1 53.6 1.0 N D:PRO133 4.2 65.3 1.0 CA D:PRO134 4.2 52.9 1.0 N D:ALA136 4.3 56.3 1.0 CA D:PRO133 4.3 61.6 1.0 CA D:CYS132 4.3 74.7 1.0 N D:GLY137 4.4 53.5 1.0 CA D:GLY137 4.4 56.5 1.0 CA D:ALA136 4.4 58.8 1.0 N D:SER163 4.4 66.2 1.0 N D:SER162 4.6 78.8 1.0 O D:GLU166 4.6 49.6 1.0 CA D:SER162 4.6 76.9 1.0 CA D:SER159 4.7 47.2 1.0 N D:SER161 4.7 59.9 1.0 O D:SER159 4.7 49.1 1.0 C D:SER159 4.7 48.8 1.0 O D:SER163 4.8 58.9 1.0 CG D:GLU166 4.8 75.9 1.0 CD D:GLU166 4.8 74.7 1.0 C D:PRO134 4.8 49.5 1.0 CA D:SER161 4.8 67.7 1.0 C D:SER162 5.0 73.4 1.0 N D:GLY135 5.0 48.5 1.0

W.Liu, C.Zhan, H.Cheng, P.R.Kumar, J.B.Bonanno, S.G.Nathenson, S.C.Almo. Mechanistic Basis For Functional Promiscuity in the Tnf and Tnf Receptor Superfamilies: Structure of the Light:DCR3 Assembly. Structure V. 22 1252 2014.
ISSN: ISSN 0969-2126
PubMed: 25087510
DOI: 10.1016/J.STR.2014.06.013