Magnesium in PDB 1yu4: Major Tropism Determinant U1 Variant

The structure of Major Tropism Determinant U1 Variant, PDB code: 1yu4 was solved by S.A.Mcmahon, J.L.Miller, J.A.Lawton, P.Ghosh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.40 / 1.87
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	86.684, 129.438, 312.649, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 21

The binding sites of Magnesium atom in the Major Tropism Determinant U1 Variant (pdb code 1yu4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Major Tropism Determinant U1 Variant, PDB code: 1yu4:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Major Tropism Determinant U1 Variant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Major Tropism Determinant U1 Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2001 b:2.0 occ:1.00 O A:PHE313 2.3 11.2 1.0 OE2 C:GLU312 2.3 10.8 1.0 O C:PHE313 2.3 12.5 1.0 O B:PHE313 2.3 11.3 1.0 OE2 A:GLU312 2.3 10.6 1.0 OE2 B:GLU312 2.3 9.2 1.0 CD C:GLU312 3.3 11.6 1.0 CD A:GLU312 3.3 10.8 1.0 CD B:GLU312 3.3 10.0 1.0 C C:PHE313 3.4 11.9 1.0 C A:PHE313 3.4 11.3 1.0 C B:PHE313 3.4 11.0 1.0 N B:PHE313 3.8 11.0 1.0 N C:PHE313 3.8 11.4 1.0 N A:PHE313 3.8 11.1 1.0 OE1 C:GLU312 3.9 10.8 1.0 OE1 A:GLU312 4.0 9.6 1.0 OE1 B:GLU312 4.0 10.2 1.0 CA B:PHE313 4.1 10.9 1.0 CA C:PHE313 4.1 11.6 1.0 CA A:PHE313 4.1 11.1 1.0 CG A:GLU312 4.2 11.0 1.0 CG C:GLU312 4.2 10.9 1.0 CG B:GLU312 4.2 10.1 1.0 CB B:PHE313 4.5 10.9 1.0 CB A:PHE313 4.5 11.6 1.0 N C:GLY314 4.5 12.2 1.0 N A:GLY314 4.5 11.3 1.0 N B:GLY314 4.5 10.7 1.0 CB C:PHE313 4.5 11.5 1.0 MG A:MG2002 4.6 13.5 1.0 CA A:GLY314 4.8 11.3 1.0 CA C:GLY314 4.8 12.3 1.0 CA B:GLY314 4.9 11.0 1.0 C C:GLU312 4.9 11.6 1.0 C B:GLU312 4.9 10.9 1.0 C A:GLU312 4.9 11.4 1.0

Magnesium binding site 2 out of 5 in the Major Tropism Determinant U1 Variant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Major Tropism Determinant U1 Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2002 b:13.5 occ:1.00 OE1 C:GLU312 2.1 10.8 1.0 O A:HOH2399 2.1 10.3 1.0 O C:HOH2009 2.1 7.9 1.0 OE1 B:GLU312 2.1 10.2 1.0 OE1 A:GLU312 2.2 9.6 1.0 O B:HOH2053 2.3 11.1 1.0 CD C:GLU312 3.2 11.6 1.0 CD A:GLU312 3.2 10.8 1.0 CD B:GLU312 3.2 10.0 1.0 OE2 A:GLU312 3.6 10.6 1.0 OE2 B:GLU312 3.6 9.2 1.0 OE2 C:GLU312 3.6 10.8 1.0 ND2 B:ASN254 4.0 13.4 1.0 ND2 C:ASN254 4.0 12.2 1.0 ND2 A:ASN254 4.0 13.0 1.0 O B:HOH2041 4.3 16.8 1.0 O A:HOH2070 4.3 17.1 1.0 O C:HOH2022 4.4 14.6 1.0 O A:ASN311 4.4 12.4 1.0 O C:ASN311 4.4 12.2 1.0 CG C:GLU312 4.5 10.9 1.0 O B:ASN311 4.5 11.2 1.0 CG B:GLU312 4.5 10.1 1.0 CG A:GLU312 4.5 11.0 1.0 MG A:MG2001 4.6 2.0 1.0 CB C:GLU312 4.7 11.4 1.0 CA C:GLU312 4.7 11.3 1.0 CB A:GLU312 4.8 11.5 1.0 CB B:GLU312 4.8 10.8 1.0 CA A:GLU312 4.8 11.7 1.0 CA B:GLU312 4.8 10.8 1.0

Magnesium binding site 3 out of 5 in the Major Tropism Determinant U1 Variant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Major Tropism Determinant U1 Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2004 b:20.5 occ:1.00 O A:HOH2060 2.0 16.3 1.0 O A:HOH2138 2.0 18.6 1.0 OD2 A:ASP214 2.0 16.6 1.0 O A:HOH2176 2.2 18.8 1.0 O A:HOH2007 2.2 13.6 1.0 O A:HOH2117 2.3 16.9 1.0 CG A:ASP214 3.1 16.4 1.0 OD1 A:ASP214 3.4 15.3 1.0 O A:HOH2101 3.8 22.4 1.0 OD1 A:ASP275 4.0 18.3 1.0 O A:HOH2163 4.0 31.5 1.0 O A:ILE212 4.1 16.0 1.0 O A:HOH2209 4.1 32.6 1.0 OD2 A:ASP275 4.1 20.8 1.0 O A:ALA367 4.4 13.2 1.0 CB A:ASP214 4.4 14.9 1.0 O A:VAL276 4.5 16.3 1.0 CB A:ALA217 4.5 18.2 1.0 O A:HOH2289 4.6 43.5 1.0 CG A:ASP275 4.6 18.2 1.0 CA A:PRO277 4.6 15.7 1.0

Magnesium binding site 4 out of 5 in the Major Tropism Determinant U1 Variant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Major Tropism Determinant U1 Variant within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2003 b:22.2 occ:1.00 O B:HOH2188 2.0 16.9 1.0 O B:HOH2026 2.1 14.2 1.0 O B:HOH2109 2.1 15.6 1.0 OD2 B:ASP214 2.2 15.5 1.0 O B:HOH2058 2.2 17.9 1.0 O B:HOH2060 2.2 18.6 1.0 CG B:ASP214 3.2 15.4 1.0 OD1 B:ASP214 3.5 14.6 1.0 O B:HOH2264 3.8 24.5 1.0 OD1 B:ASP275 4.0 21.2 1.0 O B:ILE212 4.1 13.8 1.0 OD2 B:ASP275 4.2 22.5 1.0 O B:HOH2119 4.2 22.6 1.0 O B:ALA367 4.3 14.9 1.0 O B:VAL276 4.4 16.1 1.0 CA B:PRO277 4.5 15.7 1.0 CB B:ASP214 4.5 14.6 1.0 CG B:ASP275 4.6 19.9 1.0 CB B:ALA217 4.8 17.9 1.0

Magnesium binding site 5 out of 5 in the Major Tropism Determinant U1 Variant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Major Tropism Determinant U1 Variant within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg2005 b:32.7 occ:1.00 O C:HOH2155 2.1 25.6 1.0 O C:HOH2071 2.1 21.4 1.0 OD2 C:ASP214 2.2 22.9 1.0 O C:HOH2197 2.4 26.3 1.0 CG C:ASP214 3.2 22.7 1.0 OD1 C:ASP214 3.4 23.2 1.0 OD1 C:ASP275 3.8 28.1 1.0 O C:HOH2195 3.8 33.4 1.0 OD2 C:ASP275 3.9 28.3 1.0 O C:ILE212 4.2 20.1 1.0 CG C:ASP275 4.3 26.2 1.0 CA C:PRO277 4.4 21.8 1.0 O C:VAL276 4.5 22.6 1.0 O C:ALA367 4.5 20.9 1.0 CB C:ALA217 4.6 23.5 1.0 CB C:ASP214 4.6 21.7 1.0 CB C:PRO277 5.0 21.8 1.0

S.A.Mcmahon, J.L.Miller, J.A.Lawton, D.E.Kerkow, A.Hodes, M.A.Marti-Renom, S.Doulatov, E.Narayanan, A.Sali, J.F.Miller, P.Ghosh. The C-Type Lectin Fold As An Evolutionary Solution For Massive Sequence Variation Nat.Struct.Mol.Biol. V. 12 886 2005.
ISSN: ISSN 1545-9993
PubMed: 16170324
DOI: 10.1038/NSMB992