Magnesium in PDB 5y3j: Crystal Structure of Horse TLR9 in Complex with Two Dnas (Cpg Dna and Tcgcac Dna)

The structure of Crystal Structure of Horse TLR9 in Complex with Two Dnas (Cpg Dna and Tcgcac Dna), PDB code: 5y3j was solved by U.Ohto, H.Ishida, T.Shimizu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.40 / 1.81
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	109.493, 125.199, 139.294, 90.00, 94.78, 90.00
R / Rfree (%)	17.8 / 20.6

The binding sites of Magnesium atom in the Crystal Structure of Horse TLR9 in Complex with Two Dnas (Cpg Dna and Tcgcac Dna) (pdb code 5y3j). 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 Horse TLR9 in Complex with Two Dnas (Cpg Dna and Tcgcac Dna), PDB code: 5y3j:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Horse TLR9 in Complex with Two Dnas (Cpg Dna and Tcgcac Dna)


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 Horse TLR9 in Complex with Two Dnas (Cpg Dna and Tcgcac Dna) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1011 b:18.8 occ:1.00 OG A:SER589 2.7 24.0 1.0 NH2 A:ARG590 3.2 17.6 1.0 O A:HOH1334 3.2 24.7 1.0 N A:GLY563 3.2 18.2 1.0 O A:HOH1721 3.2 37.7 1.0 CD A:ARG590 3.6 16.9 1.0 O A:HOH1263 3.7 32.7 1.0 CG A:ARG590 3.8 16.8 1.0 CA A:ARG562 4.0 21.3 1.0 CB A:ARG590 4.0 16.6 1.0 CA A:GLY563 4.1 17.7 1.0 CB A:SER589 4.1 20.2 1.0 C A:ARG562 4.1 19.7 1.0 CZ A:ARG590 4.1 17.4 1.0 O A:SER589 4.3 17.2 1.0 CE1 A:HIS588 4.3 22.3 1.0 NE A:ARG590 4.3 17.0 1.0 C A:SER589 4.4 17.5 1.0 O A:MET561 4.4 19.6 0.5 O A:MET561 4.5 18.4 0.5 N A:VAL564 4.5 15.7 1.0 NE2 A:HIS588 4.6 22.4 1.0 C A:GLY563 4.6 16.9 1.0 O A:VAL564 4.7 14.9 1.0 N A:ARG590 4.7 16.8 1.0 O A:HOH1618 4.7 29.5 1.0 CB A:ARG562 4.7 26.3 1.0 CA A:SER589 4.8 18.2 1.0 O A:HOH1423 5.0 17.5 1.0 CG A:ARG562 5.0 32.6 1.0 N A:ARG562 5.0 19.5 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Horse TLR9 in Complex with Two Dnas (Cpg Dna and Tcgcac Dna)


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 Horse TLR9 in Complex with Two Dnas (Cpg Dna and Tcgcac Dna) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1010 b:17.7 occ:1.00 OG B:SER589 2.7 23.4 1.0 O B:HOH1727 3.2 36.7 1.0 N B:GLY563 3.2 18.2 1.0 NH2 B:ARG590 3.2 17.9 1.0 O B:HOH1429 3.2 21.5 1.0 CD B:ARG590 3.6 16.4 1.0 O B:HOH1315 3.6 33.6 1.0 CG B:ARG590 3.7 16.1 1.0 CA B:ARG562 3.9 22.6 1.0 CA B:GLY563 4.0 17.5 1.0 CB B:ARG590 4.0 16.0 1.0 C B:ARG562 4.0 20.4 1.0 CB B:SER589 4.1 19.3 1.0 CZ B:ARG590 4.2 17.2 1.0 O B:SER589 4.3 16.0 1.0 NE B:ARG590 4.3 16.8 1.0 CE1 B:HIS588 4.4 22.2 1.0 C B:SER589 4.4 16.9 1.0 O B:MET561 4.4 20.7 1.0 N B:VAL564 4.5 15.7 1.0 C B:GLY563 4.6 16.7 1.0 O B:VAL564 4.7 14.8 1.0 N B:ARG590 4.7 16.4 1.0 O B:HOH1649 4.7 32.4 1.0 NE2 B:HIS588 4.7 22.4 1.0 CB B:ARG562 4.7 27.3 1.0 CA B:SER589 4.8 17.7 1.0 CG B:ARG562 4.9 33.6 1.0 N B:ARG562 5.0 20.9 1.0

U.Ohto, H.Ishida, T.Shibata, R.Sato, K.Miyake, T.Shimizu. Toll-Like Receptor 9 Contains Two Dna Binding Sites That Function Cooperatively to Promote Receptor Dimerization and Activation Immunity V. 48 649 2018.
ISSN: ISSN 1097-4180
PubMed: 29625894
DOI: 10.1016/J.IMMUNI.2018.03.013