Magnesium in PDB 2g8u: B. Halodurans Rnase H Catalytic Domain D132N Mutant in Complex with MG2+ and Rna/Dna Hybrid (Non-P Nick at the Active Site)

All present enzymatic activity of B. Halodurans Rnase H Catalytic Domain D132N Mutant in Complex with MG2+ and Rna/Dna Hybrid (Non-P Nick at the Active Site):
3.1.26.4;

The structure of B. Halodurans Rnase H Catalytic Domain D132N Mutant in Complex with MG2+ and Rna/Dna Hybrid (Non-P Nick at the Active Site), PDB code: 2g8u was solved by M.Nowotny, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	83.878, 35.412, 63.839, 90.00, 98.66, 90.00
R / Rfree (%)	22.3 / 28.8

The binding sites of Magnesium atom in the B. Halodurans Rnase H Catalytic Domain D132N Mutant in Complex with MG2+ and Rna/Dna Hybrid (Non-P Nick at the Active Site) (pdb code 2g8u). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the B. Halodurans Rnase H Catalytic Domain D132N Mutant in Complex with MG2+ and Rna/Dna Hybrid (Non-P Nick at the Active Site), PDB code: 2g8u:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the B. Halodurans Rnase H Catalytic Domain D132N Mutant in Complex with MG2+ and Rna/Dna Hybrid (Non-P Nick at the Active Site)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of B. Halodurans Rnase H Catalytic Domain D132N Mutant in Complex with MG2+ and Rna/Dna Hybrid (Non-P Nick at the Active Site) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:35.0 occ:1.00 OE2 A:GLU109 2.0 45.2 1.0 OD1 A:ASN132 2.3 33.3 1.0 OD1 A:ASP71 2.4 49.3 1.0 CD A:GLU109 2.9 44.1 1.0 O A:HOH4 2.9 19.5 1.0 O3' B:A6 3.0 40.6 1.0 OE1 A:GLU109 3.0 44.6 1.0 CG A:ASN132 3.4 32.6 1.0 CG A:ASP71 3.6 48.6 1.0 ND2 A:ASN132 3.7 30.6 1.0 O2' B:A6 3.9 43.6 1.0 C3' B:A6 4.0 40.2 1.0 CG1 A:VAL72 4.0 48.8 1.0 C4' B:A6 4.1 39.7 1.0 CG A:GLU109 4.3 41.1 1.0 N A:VAL72 4.3 45.4 1.0 CB A:ASP71 4.5 45.9 1.0 MG A:MG402 4.5 26.9 1.0 C2' B:A6 4.5 40.4 1.0 OD2 A:ASP71 4.5 53.3 1.0 CA A:ASP71 4.5 44.6 1.0 N A:SER133 4.7 27.1 1.0 CB A:ASN132 4.7 30.8 1.0 N A:ASN132 4.7 30.9 1.0 C A:ASN132 4.7 28.6 1.0 C5' B:A6 4.8 39.1 1.0 CB A:SER133 4.8 27.5 1.0 O A:VAL72 4.9 45.5 1.0 C A:ASP71 5.0 44.5 1.0

Magnesium binding site 2 out of 2 in the B. Halodurans Rnase H Catalytic Domain D132N Mutant in Complex with MG2+ and Rna/Dna Hybrid (Non-P Nick at the Active Site)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of B. Halodurans Rnase H Catalytic Domain D132N Mutant in Complex with MG2+ and Rna/Dna Hybrid (Non-P Nick at the Active Site) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:26.9 occ:1.00 OD2 A:ASP192 2.4 55.5 1.0 O A:HOH1 2.4 30.4 1.0 OD2 A:ASP71 2.9 53.3 1.0 OD1 A:ASP71 3.4 49.3 1.0 CG A:ASP71 3.4 48.6 1.0 CG A:ASP192 3.4 56.3 1.0 OE2 A:GLU188 3.8 59.5 1.0 O3' B:A6 4.0 40.6 1.0 CB A:ASP192 4.2 55.9 1.0 OD1 A:ASP192 4.3 58.4 1.0 O A:VAL72 4.4 45.5 1.0 MG A:MG401 4.5 35.0 1.0 ND2 A:ASN132 4.5 30.6 1.0 CA A:ASP192 4.5 56.1 1.0 CD A:GLU188 4.7 56.6 1.0 CG2 A:ILE189 4.8 42.4 1.0 CB A:ASP71 4.8 45.9 1.0 N A:TYR193 5.0 60.6 1.0

M.Nowotny, W.Yang. Stepwise Analyses of Metal Ions in Rnase H Catalysis From Substrate Destabilization to Product Release. Embo J. V. 25 1924 2006.
ISSN: ISSN 0261-4189
PubMed: 16601679
DOI: 10.1038/SJ.EMBOJ.7601076