Magnesium in PDB 5us2: 2-Se-T2-Dna and Native Rna Hybrid in Complex with Rnase H Catalytic Domain D132N Mutant

All present enzymatic activity of 2-Se-T2-Dna and Native Rna Hybrid in Complex with Rnase H Catalytic Domain D132N Mutant:
3.1.26.4;

The structure of 2-Se-T2-Dna and Native Rna Hybrid in Complex with Rnase H Catalytic Domain D132N Mutant, PDB code: 5us2 was solved by Z.Fang, F.Yang, Z.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	61.49 / 1.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	81.319, 37.252, 61.998, 90.00, 97.37, 90.00
R / Rfree (%)	19.1 / 22.7

The binding sites of Magnesium atom in the 2-Se-T2-Dna and Native Rna Hybrid in Complex with Rnase H Catalytic Domain D132N Mutant (pdb code 5us2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the 2-Se-T2-Dna and Native Rna Hybrid in Complex with Rnase H Catalytic Domain D132N Mutant, PDB code: 5us2:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the 2-Se-T2-Dna and Native Rna Hybrid in Complex with Rnase H Catalytic Domain D132N Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 2-Se-T2-Dna and Native Rna Hybrid in Complex with Rnase H Catalytic Domain D132N Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:20.8 occ:1.00 O A:HOH308 2.0 19.4 1.0 OP1 B:A6 2.0 19.6 1.0 OD1 A:ASP192 2.1 19.4 1.0 O A:HOH305 2.1 17.9 1.0 OD2 A:ASP71 2.1 22.0 1.0 O A:HOH311 2.2 19.5 1.0 CG A:ASP71 3.1 18.2 1.0 CG A:ASP192 3.2 21.6 1.0 P B:A6 3.3 17.9 1.0 OD1 A:ASP71 3.4 22.1 1.0 OP2 B:A6 3.8 15.0 1.0 MG B:MG202 4.0 19.9 1.0 OD2 A:ASP192 4.0 24.9 1.0 O A:VAL72 4.0 17.4 1.0 CA A:ASP192 4.1 20.1 1.0 CB A:ASP192 4.1 21.1 1.0 O5' B:A6 4.1 17.3 1.0 O A:HOH301 4.1 29.2 1.0 N A:TYR193 4.2 17.6 1.0 OE1 A:GLU188 4.3 38.5 1.0 ND2 A:ASN132 4.3 19.2 1.0 O3' B:C5 4.4 15.7 1.0 CB A:ASP71 4.5 17.3 1.0 C5' B:A6 4.5 16.4 1.0 C A:ASP192 4.7 20.9 1.0 CG2 A:ILE189 4.8 18.8 1.0

Magnesium binding site 2 out of 2 in the 2-Se-T2-Dna and Native Rna Hybrid in Complex with Rnase H Catalytic Domain D132N Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of 2-Se-T2-Dna and Native Rna Hybrid in Complex with Rnase H Catalytic Domain D132N Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:19.9 occ:1.00 OD1 A:ASP71 2.2 22.1 1.0 OD1 A:ASN132 2.2 23.3 1.0 OE2 A:GLU109 2.2 17.1 1.0 OP1 B:A6 2.5 19.6 1.0 O3' B:C5 2.6 15.7 1.0 CG A:ASN132 2.9 17.5 1.0 ND2 A:ASN132 3.0 19.2 1.0 CD A:GLU109 3.0 18.3 1.0 OE1 A:GLU109 3.0 21.2 1.0 P B:A6 3.1 17.9 1.0 O A:HOH313 3.2 19.8 1.0 CG A:ASP71 3.2 18.2 1.0 OD2 A:ASP71 3.7 22.0 1.0 C3' B:C5 3.8 17.2 1.0 O A:HOH305 3.9 17.9 1.0 MG B:MG201 4.0 20.8 1.0 C5' B:A6 4.0 16.4 1.0 O5' B:A6 4.1 17.3 1.0 O2' B:C5 4.2 17.9 1.0 C4' B:C5 4.2 15.4 1.0 CB A:ASN132 4.4 16.5 1.0 OP2 B:A6 4.4 15.0 1.0 CB A:ASP71 4.4 17.3 1.0 CG A:GLU109 4.5 17.7 1.0 N A:VAL72 4.5 16.8 1.0 C2' B:C5 4.5 17.2 1.0 CG1 A:VAL72 4.6 17.1 1.0 CA A:ASP71 4.7 18.0 1.0 O A:VAL72 4.8 17.4 1.0 C5' B:C5 4.8 16.4 1.0 O A:HOH308 4.9 19.4 1.0 CA A:ASN132 4.9 15.1 1.0 N A:ASN132 4.9 14.9 1.0 C A:ASN132 5.0 16.1 1.0

Z.Fang, F.Yang, Z.Huang. 2-Se-T-Modified-Dna and Native Rna Hybrid in Complex with Rnase H Catalytic Domain D132N Mutant To Be Published.