Magnesium in PDB 3twh: Selenium Derivatized Rna/Dna Hybrid in Complex with Rnase H Catalytic Domain D132N Mutant

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

The structure of Selenium Derivatized Rna/Dna Hybrid in Complex with Rnase H Catalytic Domain D132N Mutant, PDB code: 3twh was solved by A.Rob, O.Gerlits, J.S.Jiang, J.H.Gan, Z.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 1.79
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 (%)	17.5 / 20.8

The binding sites of Magnesium atom in the Selenium Derivatized Rna/Dna Hybrid in Complex with Rnase H Catalytic Domain D132N Mutant (pdb code 3twh). 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 D132N Mutant, PDB code: 3twh:
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 D132N Mutant


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 D132N Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:23.8 occ:1.00 OD2 A:ASP192 2.2 30.9 1.0 O A:HOH36 2.2 27.1 1.0 O A:HOH55 2.3 35.5 1.0 OD2 A:ASP71 2.3 22.9 1.0 OP1 B:C5 2.3 20.3 1.0 O B:HOH56 2.4 30.3 1.0 CG A:ASP192 3.2 32.3 1.0 CG A:ASP71 3.3 18.2 1.0 P B:C5 3.4 17.9 1.0 OD1 A:ASP71 3.6 17.5 1.0 CB A:ASP192 3.7 27.2 1.0 OP2 B:C5 3.8 19.1 1.0 CA A:ASP192 3.9 26.6 1.0 OP2 B:A6 3.9 30.8 1.0 O5' B:C5 4.0 18.8 1.0 N A:TYR193 4.2 29.2 1.0 OD1 A:ASP192 4.3 33.8 1.0 O A:VAL72 4.3 18.0 1.0 ND2 A:ASN132 4.4 20.3 1.0 MG A:MG402 4.4 32.3 1.0 OE2 A:GLU188 4.5 47.9 1.0 C5' B:C5 4.5 19.1 1.0 C A:ASP192 4.6 27.4 1.0 CB A:ASP71 4.6 15.5 1.0 O3' B:A4 4.6 16.7 1.0 O A:HOH209 4.7 30.8 1.0 CG2 A:ILE189 4.8 19.5 1.0 N A:ASP192 5.0 24.9 1.0

Magnesium binding site 2 out of 2 in the Selenium Derivatized Rna/Dna 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 Selenium Derivatized Rna/Dna Hybrid in Complex with Rnase H Catalytic Domain D132N Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:32.3 occ:1.00 OE2 A:GLU109 2.0 19.3 1.0 OD1 A:ASP71 2.1 17.5 1.0 OD1 A:ASN132 2.4 19.2 1.0 OP1 B:C5 2.7 20.3 1.0 O3' B:A4 2.8 16.7 1.0 CD A:GLU109 2.8 25.7 1.0 OE1 A:GLU109 2.9 21.5 1.0 CG A:ASN132 3.1 17.1 1.0 ND2 A:ASN132 3.2 20.3 1.0 O A:HOH4 3.2 17.1 1.0 CG A:ASP71 3.2 18.2 1.0 P B:C5 3.3 17.9 1.0 C5' B:C5 3.7 19.1 1.0 OD2 A:ASP71 3.9 22.9 1.0 O2' B:A4 3.9 17.2 1.0 C3' B:A4 4.1 17.1 1.0 O5' B:C5 4.1 18.8 1.0 CG1 A:VAL72 4.2 19.1 1.0 CG A:GLU109 4.2 18.4 1.0 N A:VAL72 4.3 17.4 1.0 C4' B:A4 4.4 17.1 1.0 CB A:ASP71 4.4 15.5 1.0 MG A:MG401 4.4 23.8 1.0 CA A:ASP71 4.5 16.8 1.0 C2' B:A4 4.5 19.7 1.0 CB A:ASN132 4.6 14.5 1.0 OP2 B:C5 4.7 19.1 1.0 O A:VAL72 4.8 18.0 1.0 CB A:SER133 4.9 14.6 1.0 N A:ASN132 4.9 14.3 1.0 O A:HOH8 4.9 25.3 1.0 C A:ASP71 5.0 16.3 1.0

R.Abdur, O.O.Gerlits, J.Gan, J.Jiang, J.Salon, A.Y.Kovalevsky, A.A.Chumanevich, I.T.Weber, Z.Huang. Novel Complex Mad Phasing and Rnase H Structural Insights Using Selenium Oligonucleotides. Acta Crystallogr.,Sect.D V. 70 354 2014.
ISSN: ISSN 0907-4449
PubMed: 24531469
DOI: 10.1107/S1399004713027922