Magnesium in PDB 2r7y: Selenium Derivatized Rna/Dna Hybrid in Complex with Rnase H Catalytic Domain Mutant D132N

All present enzymatic activity of Selenium Derivatized Rna/Dna Hybrid in Complex with Rnase H Catalytic Domain Mutant D132N:
3.1.26.4;

The structure of Selenium Derivatized Rna/Dna Hybrid in Complex with Rnase H Catalytic Domain Mutant D132N, PDB code: 2r7y was solved by J.-S.Jiang, O.Gerlits, Z.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.45 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	80.660, 37.819, 61.937, 90.00, 96.60, 90.00
R / Rfree (%)	18.5 / 23.1

The binding sites of Magnesium atom in the Selenium Derivatized Rna/Dna Hybrid in Complex with Rnase H Catalytic Domain Mutant D132N (pdb code 2r7y). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Selenium Derivatized Rna/Dna Hybrid in Complex with Rnase H Catalytic Domain Mutant D132N, PDB code: 2r7y:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Selenium Derivatized Rna/Dna Hybrid in Complex with Rnase H Catalytic Domain Mutant D132N


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Selenium Derivatized Rna/Dna Hybrid in Complex with Rnase H Catalytic Domain Mutant D132N within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:35.8 occ:1.00 OE2 A:GLU109 2.2 21.2 1.0 OD1 A:ASP71 2.2 18.9 1.0 OD1 A:ASN132 2.4 17.8 1.0 OP1 B:C5 2.6 18.3 1.0 O3' B:A4 2.7 18.1 1.0 CD A:GLU109 2.9 22.4 1.0 OE1 A:GLU109 2.9 19.9 1.0 CG A:ASN132 3.0 18.5 1.0 ND2 A:ASN132 3.1 21.4 1.0 O A:HOH412 3.1 18.1 1.0 P B:C5 3.3 18.1 1.0 CG A:ASP71 3.4 19.0 1.0 C5' B:C5 3.8 20.1 1.0 O2' B:A4 3.9 17.2 1.0 C3' B:A4 4.0 17.9 1.0 OD2 A:ASP71 4.0 23.1 1.0 O5' B:C5 4.1 19.7 1.0 CG1 A:VAL72 4.2 20.1 1.0 N A:VAL72 4.3 18.1 1.0 CG A:GLU109 4.3 17.2 1.0 C4' B:A4 4.4 17.9 1.0 MG A:MG402 4.4 25.5 1.0 CB A:ASP71 4.5 16.1 1.0 CB A:ASN132 4.5 14.6 1.0 C2' B:A4 4.5 17.7 1.0 CA A:ASP71 4.5 16.8 1.0 OP2 B:C5 4.6 19.1 1.0 O A:VAL72 4.8 18.4 1.0 N A:ASN132 4.9 14.1 1.0 N A:SER133 5.0 15.0 1.0 CB A:SER133 5.0 15.1 1.0 C A:ASP71 5.0 15.8 1.0

Magnesium binding site 2 out of 2 in the Selenium Derivatized Rna/Dna Hybrid in Complex with Rnase H Catalytic Domain Mutant D132N


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Selenium Derivatized Rna/Dna Hybrid in Complex with Rnase H Catalytic Domain Mutant D132N within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:25.5 occ:1.00 OP1 B:C5 2.2 18.3 1.0 OD1 A:ASP192 2.3 29.2 1.0 OD2 A:ASP71 2.3 23.1 1.0 O A:HOH403 2.3 25.2 1.0 O A:HOH405 2.4 28.8 1.0 O A:HOH404 2.6 31.8 1.0 CG A:ASP71 3.3 19.0 1.0 CG A:ASP192 3.3 32.3 1.0 P B:C5 3.4 18.1 1.0 OD1 A:ASP71 3.6 18.9 1.0 OP2 B:C5 3.8 19.1 1.0 CB A:ASP192 3.9 27.9 1.0 CA A:ASP192 3.9 26.4 1.0 O A:HOH517 4.0 46.1 1.0 O5' B:C5 4.0 19.7 1.0 N A:TYR193 4.2 28.4 1.0 O A:VAL72 4.3 18.4 1.0 OD2 A:ASP192 4.4 31.0 1.0 MG A:MG401 4.4 35.8 1.0 ND2 A:ASN132 4.5 21.4 1.0 C5' B:C5 4.5 20.1 1.0 C A:ASP192 4.6 27.4 1.0 O3' B:A4 4.6 18.1 1.0 CB A:ASP71 4.7 16.1 1.0 CG2 A:ILE189 4.7 20.1 1.0 O B:HOH88 4.7 32.7 1.0 OE2 A:GLU188 4.9 38.8 1.0 N A:ASP192 5.0 25.0 1.0

J.-S.Jiang, O.Gerlits, Z.Huang. Selenium Derivatized Rna/Dna Hybrid in Complex with Rnase H Catalytic Domain Mutant D132N To Be Published.