Magnesium in PDB 5uc6: Structural Insights Into Il-1 Alpha Recognition By A Naphthyl-Modified Aptamer That Mimics Il-1RI Domain III

The structure of Structural Insights Into Il-1 Alpha Recognition By A Naphthyl-Modified Aptamer That Mimics Il-1RI Domain III, PDB code: 5uc6 was solved by X.Ren, A.Pyle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	64.77 / 2.10
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	74.790, 74.790, 86.360, 90.00, 90.00, 120.00
R / Rfree (%)	17.8 / 21.9

The structure of Structural Insights Into Il-1 Alpha Recognition By A Naphthyl-Modified Aptamer That Mimics Il-1RI Domain III also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Magnesium atom in the Structural Insights Into Il-1 Alpha Recognition By A Naphthyl-Modified Aptamer That Mimics Il-1RI Domain III (pdb code 5uc6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structural Insights Into Il-1 Alpha Recognition By A Naphthyl-Modified Aptamer That Mimics Il-1RI Domain III, PDB code: 5uc6:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structural Insights Into Il-1 Alpha Recognition By A Naphthyl-Modified Aptamer That Mimics Il-1RI Domain III


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structural Insights Into Il-1 Alpha Recognition By A Naphthyl-Modified Aptamer That Mimics Il-1RI Domain III within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:36.4 occ:1.00 ND2 A:ASN13 2.6 31.2 1.0 O A:LYS11 2.9 26.6 1.0 NZ A:LYS60 3.0 36.9 1.0 N A:SER62 3.1 28.1 1.0 C A:SER61 3.2 27.3 1.0 O A:LYS60 3.4 24.9 1.0 O A:SER61 3.4 25.7 1.0 CA A:SER62 3.6 33.0 1.0 CG A:LYS60 3.6 28.1 1.0 C A:LYS11 3.6 30.1 1.0 N A:ASN13 3.7 25.4 1.0 CG A:ASN13 3.7 33.1 1.0 CA A:SER61 3.8 22.9 1.0 C A:LYS60 3.9 26.6 1.0 CB A:SER62 3.9 26.9 1.0 CA A:TYR12 4.0 28.3 1.0 CE A:LYS60 4.0 27.2 1.0 CB A:ASN13 4.0 26.6 1.0 C A:TYR12 4.0 26.8 1.0 N A:SER61 4.1 27.2 1.0 N A:TYR12 4.1 27.8 1.0 CD A:LYS60 4.1 27.9 1.0 CA A:ASN13 4.5 29.9 1.0 CB A:LYS11 4.5 35.5 1.0 OG A:SER62 4.6 29.7 1.0 CB A:LYS60 4.7 27.4 1.0 CA A:LYS11 4.7 26.3 1.0 OD1 A:ASN13 4.8 39.9 1.0 CA A:LYS60 4.9 25.8 1.0 O A:TYR12 4.9 29.4 1.0 O A:HOH324 4.9 27.7 1.0

Magnesium binding site 2 out of 4 in the Structural Insights Into Il-1 Alpha Recognition By A Naphthyl-Modified Aptamer That Mimics Il-1RI Domain III


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structural Insights Into Il-1 Alpha Recognition By A Naphthyl-Modified Aptamer That Mimics Il-1RI Domain III within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:36.5 occ:1.00 O A:THR150 2.6 35.1 1.0 N A:PHE122 2.9 27.0 1.0 O A:ILE132 3.0 32.1 1.0 CA A:TYR121 3.4 28.4 1.0 C A:TYR121 3.6 29.7 1.0 CE2 A:PHE152 3.6 30.9 1.0 C A:THR150 3.6 38.3 1.0 O A:PHE122 3.7 27.5 1.0 CD2 A:PHE152 3.8 29.1 1.0 CB A:PHE131 3.8 27.9 1.0 CA A:PHE122 3.9 27.1 1.0 N A:ILE132 3.9 26.7 1.0 C A:ILE132 4.0 32.6 1.0 CB A:TYR121 4.0 35.0 1.0 CD2 A:PHE131 4.0 35.1 1.0 CA A:THR150 4.1 36.2 1.0 C A:PHE122 4.1 28.0 1.0 CB A:PHE122 4.1 22.6 1.0 CB A:THR150 4.2 34.9 1.0 O A:ASN120 4.2 30.0 1.0 CD2 A:PHE122 4.2 25.9 1.0 CB A:ILE132 4.2 24.0 1.0 CA A:ILE132 4.2 27.4 1.0 CG A:PHE131 4.4 37.5 1.0 CD2 A:TYR121 4.5 40.5 1.0 CA A:PHE131 4.5 25.5 1.0 C A:PHE131 4.5 28.3 1.0 N A:TYR121 4.5 28.5 1.0 CG A:PHE122 4.6 26.9 1.0 CG A:TYR121 4.6 35.2 1.0 N A:ASP151 4.8 38.2 1.0 C A:ASN120 4.8 32.7 1.0 O A:TYR121 4.8 27.0 1.0 CZ A:PHE152 4.9 32.7 1.0

Magnesium binding site 3 out of 4 in the Structural Insights Into Il-1 Alpha Recognition By A Naphthyl-Modified Aptamer That Mimics Il-1RI Domain III


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structural Insights Into Il-1 Alpha Recognition By A Naphthyl-Modified Aptamer That Mimics Il-1RI Domain III within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg204 b:45.5 occ:1.00 O A:VAL90 2.8 30.8 1.0 O A:VAL140 2.9 29.2 1.0 N A:LEU40 3.0 33.9 1.0 O A:LEU40 3.3 32.2 1.0 CB A:TYR39 3.3 36.1 1.0 CG2 A:VAL90 3.4 28.9 1.0 N A:VAL90 3.5 33.3 1.0 CA A:TYR39 3.5 35.8 1.0 CB A:PRO89 3.6 35.3 1.0 CB A:TRP139 3.7 40.8 1.0 C A:VAL90 3.7 30.6 1.0 C A:TYR39 3.8 35.3 1.0 N A:VAL140 3.8 39.9 1.0 CA A:LEU40 3.9 34.0 1.0 C A:VAL140 3.9 31.0 1.0 CD1 A:TYR39 4.0 38.2 1.0 C A:LEU40 4.0 31.6 1.0 C A:PRO89 4.0 35.8 1.0 CA A:PRO89 4.0 37.9 1.0 CG A:TYR39 4.0 45.0 1.0 CA A:VAL90 4.0 32.0 1.0 CB A:LEU40 4.1 29.1 1.0 CB A:VAL140 4.2 32.8 1.0 CA A:VAL140 4.2 28.2 1.0 CB A:VAL90 4.4 30.6 1.0 C A:TRP139 4.4 38.6 1.0 CG A:TRP139 4.5 48.7 1.0 CA A:TRP139 4.6 42.1 1.0 CG A:LEU40 4.7 29.2 1.0 O A:PRO89 4.9 33.0 1.0 N A:TYR39 4.9 37.4 1.0 CG A:PRO89 4.9 41.9 1.0 N A:LEU91 5.0 31.4 1.0 O A:TYR39 5.0 34.9 1.0

Magnesium binding site 4 out of 4 in the Structural Insights Into Il-1 Alpha Recognition By A Naphthyl-Modified Aptamer That Mimics Il-1RI Domain III


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structural Insights Into Il-1 Alpha Recognition By A Naphthyl-Modified Aptamer That Mimics Il-1RI Domain III within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg205 b:42.1 occ:1.00 OG A:SER124 2.6 28.5 1.0 O A:LEU110 2.8 26.6 1.0 O A:ASN108 2.9 30.8 1.0 C A:ASN108 3.3 29.7 1.0 CB A:SER124 3.3 23.8 1.0 CB A:ALA83 3.4 32.4 1.0 CA A:ASN108 3.4 34.6 1.0 CA A:SER124 3.4 29.2 1.0 O A:THR107 3.4 30.6 1.0 N A:VAL125 3.6 23.7 1.0 CE2 A:PHE111 3.8 26.8 1.0 CZ A:PHE111 3.8 26.3 1.0 C A:LEU110 3.8 28.5 1.0 N A:LEU110 3.9 23.5 1.0 C A:SER124 3.9 25.7 1.0 CD2 A:PHE111 4.1 26.4 1.0 N A:ALA126 4.1 29.4 1.0 CE1 A:PHE111 4.2 24.8 1.0 N A:LEU109 4.3 29.6 1.0 C A:THR107 4.3 33.1 1.0 N A:ASN108 4.3 32.0 1.0 CB A:ASN108 4.4 35.6 1.0 N A:ALA83 4.4 31.3 1.0 CA A:LEU110 4.5 23.5 1.0 CG A:PHE111 4.5 25.7 1.0 CD1 A:PHE111 4.5 22.4 1.0 C A:LEU109 4.5 28.7 1.0 CA A:ALA83 4.5 31.9 1.0 CB A:ALA126 4.5 31.9 1.0 N A:SER124 4.7 24.0 1.0 CA A:VAL125 4.7 23.8 1.0 CA A:LEU109 4.8 29.2 1.0 N A:PHE111 4.9 22.4 1.0 C A:VAL125 4.9 28.2 1.0 CA A:ALA126 5.0 34.9 1.0

X.Ren, A.D.Gelinas, I.Von Carlowitz, N.Janjic, A.M.Pyle. Structural Basis For Il-1 Alpha Recognition By A Modified Dna Aptamer That Specifically Inhibits Il-1 Alpha Signaling. Nat Commun V. 8 810 2017.
ISSN: ESSN 2041-1723
PubMed: 28993621
DOI: 10.1038/S41467-017-00864-2