Magnesium in PDB 6c6k: Structural Basis For Preferential Recognition of Cap 0 Rna By A Human IFIT1-IFIT3 Protein Complex

The structure of Structural Basis For Preferential Recognition of Cap 0 Rna By A Human IFIT1-IFIT3 Protein Complex, PDB code: 6c6k was solved by G.K.Amarasinghe, D.W.Leung, B.Johnson, W.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	84.96 / 2.54
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	51.957, 80.484, 88.054, 79.82, 78.81, 90.04
R / Rfree (%)	16.9 / 23.7

The binding sites of Magnesium atom in the Structural Basis For Preferential Recognition of Cap 0 Rna By A Human IFIT1-IFIT3 Protein Complex (pdb code 6c6k). 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 Basis For Preferential Recognition of Cap 0 Rna By A Human IFIT1-IFIT3 Protein Complex, PDB code: 6c6k:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structural Basis For Preferential Recognition of Cap 0 Rna By A Human IFIT1-IFIT3 Protein Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structural Basis For Preferential Recognition of Cap 0 Rna By A Human IFIT1-IFIT3 Protein Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:49.7 occ:1.00 OP1 F:A2 2.3 21.7 1.0 OH B:TYR159 2.6 21.9 1.0 O B:LEU152 3.0 19.1 1.0 N B:GLY155 3.1 24.9 1.0 CA B:GLY155 3.4 22.8 1.0 O2B F:M7G1 3.4 21.3 1.0 P F:A2 3.5 21.5 1.0 C B:LYS153 3.6 22.6 1.0 O B:LYS153 3.6 23.4 1.0 CZ B:TYR159 3.6 22.4 1.0 CE1 B:TYR159 3.7 22.5 1.0 NH1 B:ARG189 3.7 19.6 1.0 O1B F:M7G1 3.9 23.3 1.0 CA B:LYS153 3.9 21.5 1.0 C B:LEU152 3.9 19.9 1.0 O5' F:A2 3.9 21.3 1.0 N B:CYS154 4.0 23.5 1.0 C B:GLY155 4.1 22.2 1.0 PB F:M7G1 4.1 21.9 1.0 NH1 B:ARG40 4.2 32.2 1.0 C B:CYS154 4.2 26.0 1.0 C8 F:A2 4.3 25.0 1.0 N B:LYS153 4.3 20.7 1.0 N B:GLY156 4.5 21.5 1.0 CA B:CYS154 4.6 25.2 1.0 O B:GLY155 4.7 20.7 1.0 CZ B:ARG40 4.7 28.6 1.0 NH2 B:ARG40 4.8 28.8 1.0 N7 F:A2 4.8 24.0 1.0 O3B F:M7G1 4.8 21.6 1.0 OP2 F:A2 4.8 21.7 1.0 CE2 B:TYR159 4.9 22.6 1.0

Magnesium binding site 2 out of 4 in the Structural Basis For Preferential Recognition of Cap 0 Rna By A Human IFIT1-IFIT3 Protein Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structural Basis For Preferential Recognition of Cap 0 Rna By A Human IFIT1-IFIT3 Protein Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg101 b:55.9 occ:1.00 OP1 E:A2 2.7 19.7 1.0 N3 E:U3 3.3 24.0 1.0 OD2 A:ASP36 3.4 29.2 1.0 CG2 A:VAL287 3.5 15.6 1.0 CE A:LYS338 3.5 36.2 1.0 P E:A2 3.6 20.9 1.0 NE A:ARG40 3.7 22.8 1.0 OP2 E:A2 3.7 20.6 1.0 NZ A:LYS338 3.7 39.0 1.0 O2 E:U3 3.7 24.4 1.0 O E:HOH211 3.9 44.5 1.0 CD A:LYS338 3.9 32.6 1.0 C2 E:U3 4.0 24.1 1.0 CD A:ARG40 4.0 22.4 1.0 O4 E:U3 4.2 25.8 1.0 C4 E:U3 4.2 23.7 1.0 CZ A:ARG40 4.3 23.6 1.0 O5' E:A2 4.3 21.0 1.0 CG A:ASP36 4.4 28.4 1.0 O A:HOH558 4.4 19.0 1.0 OD1 A:ASP36 4.6 31.5 1.0 O A:HOH507 4.6 27.1 1.0 NH2 A:ARG40 4.6 23.6 1.0 O E:HOH204 4.7 44.6 1.0 C5' E:A2 4.7 20.3 1.0 O3B E:M7G1 4.8 21.7 1.0 O4' E:A2 4.9 21.0 1.0 CG A:LYS338 5.0 29.7 1.0

Magnesium binding site 3 out of 4 in the Structural Basis For Preferential Recognition of Cap 0 Rna By A Human IFIT1-IFIT3 Protein Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structural Basis For Preferential Recognition of Cap 0 Rna By A Human IFIT1-IFIT3 Protein Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg102 b:53.9 occ:1.00 O3' E:A4 2.5 53.9 1.0 OP1 E:G5 2.7 58.9 1.0 OD2 A:ASP347 2.9 32.0 1.0 P E:G5 3.2 54.8 1.0 OD1 A:ASP347 3.3 33.5 1.0 CG A:ASP347 3.5 30.6 1.0 CG1 A:VAL343 3.6 21.8 1.0 C4' E:A4 3.6 42.3 1.0 C3' E:A4 3.6 49.9 1.0 C5' E:A4 3.8 33.5 1.0 CD2 A:LEU295 3.9 19.2 1.0 OP2 E:G5 4.1 51.7 1.0 NE2 A:HIS291 4.1 18.0 1.0 CE1 A:HIS291 4.3 18.7 1.0 O5' E:G5 4.4 64.3 1.0 O2' E:A4 4.5 48.7 1.0 C2' E:A4 4.6 49.7 1.0 CD1 A:LEU295 4.7 19.6 1.0 C5' E:G5 4.7 64.4 1.0 O5' E:A4 4.7 29.8 1.0 CG A:LEU295 4.9 19.1 1.0 O4' E:A4 5.0 45.3 1.0

Magnesium binding site 4 out of 4 in the Structural Basis For Preferential Recognition of Cap 0 Rna By A Human IFIT1-IFIT3 Protein Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structural Basis For Preferential Recognition of Cap 0 Rna By A Human IFIT1-IFIT3 Protein Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg103 b:65.7 occ:1.00 OP2 E:G5 1.9 51.7 1.0 N2 E:G5 2.7 80.5 1.0 NH1 A:ARG264 3.2 24.9 1.0 P E:G5 3.3 54.8 1.0 NH2 A:ARG264 3.4 26.8 1.0 C5' E:A4 3.4 33.5 1.0 C3' E:A4 3.5 49.9 1.0 CZ A:ARG264 3.7 25.2 1.0 O3' E:A4 3.9 53.9 1.0 C2 E:G5 3.9 73.0 1.0 OP1 E:A4 4.0 25.8 1.0 CD1 A:LEU295 4.0 19.6 1.0 C4' E:A4 4.0 42.3 1.0 O5' E:G5 4.1 64.3 1.0 C8 E:A4 4.2 50.0 1.0 N3 E:G5 4.4 69.1 1.0 OP1 E:G5 4.4 58.9 1.0 O5' E:A4 4.6 29.8 1.0 N9 E:A4 4.6 50.4 1.0 O4' E:A4 4.7 45.3 1.0 N7 E:A4 4.7 49.5 1.0 C2' E:A4 4.7 49.7 1.0 CG A:ARG265 4.9 26.4 1.0 P E:A4 4.9 29.2 1.0 N1 E:G5 4.9 73.0 1.0 C1' E:A4 5.0 47.2 1.0 NE A:ARG264 5.0 25.4 1.0

B.Johnson, L.A.Vanblargan, W.Xu, J.P.White, C.Shan, P.Y.Shi, R.Zhang, J.Adhikari, M.L.Gross, D.W.Leung, M.S.Diamond, G.K.Amarasinghe. Human IFIT3 Modulates IFIT1 Rna Binding Specificity and Protein Stability. Immunity V. 48 487 2018.
ISSN: ISSN 1097-4180
PubMed: 29525521
DOI: 10.1016/J.IMMUNI.2018.01.014