Magnesium in PDB 2g8v: B. Halodurans Rnase H Catalytic Domain E188A Mutant in Complex with MG2+ and Rna/Dna Hybrid (Reaction Product)

All present enzymatic activity of B. Halodurans Rnase H Catalytic Domain E188A Mutant in Complex with MG2+ and Rna/Dna Hybrid (Reaction Product):
3.1.26.4;

The structure of B. Halodurans Rnase H Catalytic Domain E188A Mutant in Complex with MG2+ and Rna/Dna Hybrid (Reaction Product), PDB code: 2g8v 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 / 1.85
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	81.871, 36.809, 62.144, 90.00, 97.17, 90.00
R / Rfree (%)	19.8 / 24

The binding sites of Magnesium atom in the B. Halodurans Rnase H Catalytic Domain E188A Mutant in Complex with MG2+ and Rna/Dna Hybrid (Reaction Product) (pdb code 2g8v). 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 E188A Mutant in Complex with MG2+ and Rna/Dna Hybrid (Reaction Product), PDB code: 2g8v:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the B. Halodurans Rnase H Catalytic Domain E188A Mutant in Complex with MG2+ and Rna/Dna Hybrid (Reaction Product)


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 E188A Mutant in Complex with MG2+ and Rna/Dna Hybrid (Reaction Product) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:35.5 occ:1.00 OE2 A:GLU109 2.2 26.2 1.0 OD1 A:ASP71 2.4 27.1 1.0 O A:HOH537 2.5 32.7 1.0 O3' B:A6 2.6 34.4 1.0 O A:HOH506 2.6 34.7 1.0 OD1 A:ASP132 2.7 25.5 1.0 OD2 A:ASP132 3.2 24.3 1.0 CD A:GLU109 3.3 22.9 1.0 CG A:ASP132 3.3 23.9 1.0 O2' B:A6 3.5 33.9 1.0 CG A:ASP71 3.5 25.1 1.0 C3' B:A6 3.6 31.6 1.0 OE1 A:GLU109 3.7 24.2 1.0 C4' B:A6 3.9 29.9 1.0 OD2 A:ASP71 3.9 26.4 1.0 O A:HOH512 3.9 20.5 1.0 C2' B:A6 4.1 31.5 1.0 CG1 A:VAL72 4.2 29.3 1.0 O B:HOH7 4.4 66.2 1.0 N A:VAL72 4.6 23.5 1.0 CG A:GLU109 4.6 20.4 1.0 C5' B:A6 4.7 30.4 1.0 CB A:ASP71 4.7 22.1 1.0 O A:HOH503 4.8 43.5 1.0 MG A:MG402 4.8 76.6 1.0 O A:VAL72 4.8 24.3 1.0 CB A:ASP132 4.8 20.0 1.0 CA A:ASP71 5.0 22.2 1.0

Magnesium binding site 2 out of 2 in the B. Halodurans Rnase H Catalytic Domain E188A Mutant in Complex with MG2+ and Rna/Dna Hybrid (Reaction Product)


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 E188A Mutant in Complex with MG2+ and Rna/Dna Hybrid (Reaction Product) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:76.6 occ:1.00 O A:HOH503 2.1 43.5 1.0 OD2 A:ASP192 2.2 34.6 1.0 O A:HOH505 2.3 46.1 1.0 O A:HOH507 2.3 46.3 1.0 O B:HOH7 2.4 66.2 1.0 O A:HOH506 2.4 34.7 1.0 CG A:ASP192 3.5 34.0 1.0 O A:HOH508 3.9 53.4 1.0 O A:HOH504 4.1 30.0 1.0 OD2 A:ASP71 4.1 26.4 1.0 O3' B:A6 4.1 34.4 1.0 CB A:ASP192 4.3 30.4 1.0 O A:HOH535 4.3 25.3 1.0 OD1 A:ASP192 4.3 31.8 1.0 OD2 A:ASP132 4.4 24.3 1.0 O A:HOH537 4.7 32.7 1.0 MG A:MG401 4.8 35.5 1.0 CG A:ASP71 5.0 25.1 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