Magnesium in PDB 5vaj: Bhrnase H - Amide-Rna/Dna Complex

All present enzymatic activity of Bhrnase H - Amide-Rna/Dna Complex:
3.1.26.4;

The structure of Bhrnase H - Amide-Rna/Dna Complex, PDB code: 5vaj was solved by P.S.Pallan, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	79.90 / 1.95
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	137.180, 37.513, 93.863, 90.00, 121.65, 90.00
R / Rfree (%)	16.6 / 21.7

The binding sites of Magnesium atom in the Bhrnase H - Amide-Rna/Dna Complex (pdb code 5vaj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Bhrnase H - Amide-Rna/Dna Complex, PDB code: 5vaj:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Bhrnase H - Amide-Rna/Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Bhrnase H - Amide-Rna/Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg206 b:21.8 occ:1.00 OD1 A:ASN132 2.2 15.6 1.0 OD1 A:ASP71 2.2 19.9 1.0 OE2 A:GLU109 2.3 14.1 1.0 O A:HOH336 2.7 16.0 1.0 OP1 C:URU10 2.8 17.2 1.0 OE1 A:GLU109 2.8 14.9 1.0 CD A:GLU109 2.9 14.2 1.0 CG A:ASN132 3.0 15.6 1.0 O3' C:A9 3.0 14.1 1.0 CG A:ASP71 3.3 21.9 1.0 ND2 A:ASN132 3.3 14.7 1.0 P C:URU10 3.5 16.0 1.0 OD2 A:ASP71 3.9 24.8 1.0 C5' C:URU10 4.0 14.5 1.0 MG A:MG207 4.2 23.6 1.0 O2' C:A9 4.2 14.4 1.0 O5' C:URU10 4.3 16.0 1.0 C3' C:A9 4.3 14.6 1.0 N A:VAL72 4.3 15.9 1.0 CB A:ASP71 4.4 19.2 1.0 CA A:ASP71 4.4 18.5 1.0 CB A:ASN132 4.4 14.4 1.0 CG A:GLU109 4.4 13.8 1.0 C4' C:A9 4.7 14.7 1.0 N A:ASN132 4.7 15.0 1.0 C2' C:A9 4.8 14.2 1.0 OP2 C:URU10 4.8 15.7 1.0 CA A:ASN132 4.9 14.8 1.0 N A:SER133 4.9 14.9 1.0 C A:ASN132 4.9 15.6 1.0 C A:ASP71 4.9 16.7 1.0 CG2 A:VAL72 5.0 14.6 0.5

Magnesium binding site 2 out of 4 in the Bhrnase H - Amide-Rna/Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Bhrnase H - Amide-Rna/Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg207 b:23.6 occ:1.00 OP1 C:URU10 2.1 17.2 1.0 OD2 A:ASP71 2.1 24.8 1.0 O A:HOH334 2.3 27.6 1.0 OD1 A:ASP192 2.4 31.0 1.0 CG A:ASP71 3.0 21.9 1.0 OD1 A:ASP71 3.2 19.9 1.0 CG A:ASP192 3.4 32.8 1.0 P C:URU10 3.4 16.0 1.0 OP2 C:URU10 4.0 15.7 1.0 CA A:ASP192 4.0 26.0 1.0 CB A:ASP192 4.0 29.6 1.0 MG A:MG206 4.2 21.8 1.0 ND2 A:ASN132 4.2 14.7 1.0 O5' C:URU10 4.3 16.0 1.0 O A:VAL72 4.4 16.3 1.0 N A:TYR193 4.4 26.1 1.0 OD2 A:ASP192 4.4 38.2 1.0 CB A:ASP71 4.5 19.2 1.0 CG2 A:ILE189 4.5 21.9 1.0 O A:HOH345 4.6 17.4 0.5 O3' C:A9 4.6 14.1 1.0 C5' C:URU10 4.7 14.5 1.0 O A:TYR193 4.7 40.8 1.0 C A:ASP192 4.8 27.1 1.0

Magnesium binding site 3 out of 4 in the Bhrnase H - Amide-Rna/Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Bhrnase H - Amide-Rna/Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg203 b:32.0 occ:1.00 OD1 B:ASP71 2.0 24.1 1.0 OE2 B:GLU109 2.3 23.2 1.0 OD1 B:ASN132 2.5 15.0 1.0 OP1 C:C5 2.7 18.1 1.0 O B:HOH326 2.8 14.9 1.0 OE1 B:GLU109 3.0 18.9 1.0 CD B:GLU109 3.0 20.5 1.0 CG B:ASP71 3.1 25.1 1.0 CG B:ASN132 3.2 13.7 1.0 O3' C:A4 3.2 16.1 1.0 ND2 B:ASN132 3.2 13.1 1.0 P C:C5 3.5 17.6 1.0 OD2 B:ASP71 3.8 27.0 1.0 C5' C:C5 3.9 17.9 1.0 N B:VAL72 4.1 20.8 1.0 MG B:MG204 4.1 34.5 1.0 CB B:ASP71 4.2 22.4 1.0 CA B:ASP71 4.2 21.5 1.0 O5' C:C5 4.3 18.0 1.0 O2' C:A4 4.3 14.8 1.0 CG1 B:VAL72 4.4 24.9 1.0 C3' C:A4 4.4 14.7 1.0 CG B:GLU109 4.5 18.1 1.0 CB B:ASN132 4.6 13.0 1.0 O B:VAL72 4.8 20.0 1.0 C B:ASP71 4.8 21.2 1.0 C4' C:A4 4.8 14.1 1.0 N B:ASN132 4.8 12.0 1.0 OP2 C:C5 4.8 15.2 1.0 O B:VAL70 4.9 19.6 1.0 CG2 B:ILE189 4.9 21.5 1.0 C2' C:A4 5.0 14.8 1.0

Magnesium binding site 4 out of 4 in the Bhrnase H - Amide-Rna/Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Bhrnase H - Amide-Rna/Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg204 b:34.5 occ:1.00 OD1 B:ASP192 2.2 45.6 1.0 OD2 B:ASP71 2.2 27.0 1.0 OP1 C:C5 2.2 18.1 1.0 O B:HOH310 2.4 31.8 1.0 CG B:ASP71 3.1 25.1 1.0 CG B:ASP192 3.3 50.5 1.0 OD1 B:ASP71 3.3 24.1 1.0 P C:C5 3.4 17.6 1.0 CB B:ASP192 3.8 48.4 1.0 O5' C:C5 3.9 18.0 1.0 CA B:ASP192 3.9 45.2 1.0 OP2 C:C5 3.9 15.2 1.0 O B:VAL72 4.0 20.0 1.0 MG B:MG203 4.1 32.0 1.0 OD2 B:ASP192 4.3 62.3 1.0 OE2 B:GLU188 4.3 49.4 0.5 N B:TYR193 4.3 52.2 1.0 C5' C:C5 4.3 17.9 1.0 OP2 C:C6 4.5 19.2 1.0 CB B:ASP71 4.5 22.4 1.0 ND2 B:ASN132 4.6 13.1 1.0 CG2 B:ILE189 4.6 21.5 1.0 C B:ASP192 4.7 51.0 1.0 O3' C:A4 4.7 16.1 1.0 CG B:GLU188 4.9 35.8 0.5 N B:ASP192 5.0 41.0 1.0

D.Mutisya, T.Hardcastle, S.K.Cheruiyot, P.S.Pallan, S.D.Kennedy, M.Egli, M.L.Kelley, A.V.B.Smith, E.Rozners. Amide Linkages Mimic Phosphates in Rna Interactions with Proteins and Are Well Tolerated in the Guide Strand of Short Interfering Rnas. Nucleic Acids Res. V. 45 8142 2017.
ISSN: ESSN 1362-4962
PubMed: 28854734
DOI: 10.1093/NAR/GKX558