Calcium in PDB 2g8w: B. Halodurans Rnase H Catalytic Domain E188A Mutant in Complex with CA2+ and Rna/Dna Hybrid

All present enzymatic activity of B. Halodurans Rnase H Catalytic Domain E188A Mutant in Complex with CA2+ and Rna/Dna Hybrid:
3.1.26.4;

The structure of B. Halodurans Rnase H Catalytic Domain E188A Mutant in Complex with CA2+ and Rna/Dna Hybrid, PDB code: 2g8w 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 / 2.05
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	81.671, 37.091, 61.980, 90.00, 96.74, 90.00
R / Rfree (%)	21.5 / 24.2

The binding sites of Calcium atom in the B. Halodurans Rnase H Catalytic Domain E188A Mutant in Complex with CA2+ and Rna/Dna Hybrid (pdb code 2g8w). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the B. Halodurans Rnase H Catalytic Domain E188A Mutant in Complex with CA2+ and Rna/Dna Hybrid, PDB code: 2g8w:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the B. Halodurans Rnase H Catalytic Domain E188A Mutant in Complex with CA2+ and Rna/Dna Hybrid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of B. Halodurans Rnase H Catalytic Domain E188A Mutant in Complex with CA2+ and Rna/Dna Hybrid within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:20.9 occ:1.00 OD1 A:ASP71 2.2 15.4 1.0 OE2 A:GLU109 2.3 20.4 1.0 OD1 A:ASP132 2.4 20.1 1.0 OD2 A:ASP132 2.5 17.8 1.0 CG A:ASP132 2.8 19.8 1.0 O A:HOH403 3.0 17.5 1.0 O A:HOH410 3.0 55.1 0.5 CD A:GLU109 3.1 20.3 1.0 OE1 A:GLU109 3.1 18.5 1.0 CG A:ASP71 3.2 18.2 1.0 OD2 A:ASP71 3.8 19.6 1.0 CA A:CA402 4.0 34.4 1.0 CB A:ASP132 4.3 18.8 1.0 CB A:ASP71 4.3 15.7 1.0 CG A:GLU109 4.5 17.9 1.0 N A:VAL72 4.6 16.6 1.0 CA A:ASP71 4.6 16.6 1.0 CG1 A:VAL72 4.6 15.0 1.0 O A:HOH446 4.9 17.5 1.0 N A:ASP132 4.9 16.8 1.0 N A:SER133 4.9 17.4 1.0 CG2 A:ILE189 4.9 18.9 1.0 O A:HOH444 5.0 28.4 1.0 CA A:ASP132 5.0 19.5 1.0

Calcium binding site 2 out of 2 in the B. Halodurans Rnase H Catalytic Domain E188A Mutant in Complex with CA2+ and Rna/Dna Hybrid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of B. Halodurans Rnase H Catalytic Domain E188A Mutant in Complex with CA2+ and Rna/Dna Hybrid within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:34.4 occ:1.00 O A:HOH444 2.1 28.4 1.0 O A:HOH404 2.3 30.7 1.0 O A:HOH410 2.3 55.1 0.5 OD2 A:ASP71 2.4 19.6 1.0 OD2 A:ASP192 2.4 29.2 1.0 O A:HOH407 2.9 38.1 1.0 CG A:ASP71 3.3 18.2 1.0 CG A:ASP192 3.4 30.2 1.0 OD1 A:ASP71 3.6 15.4 1.0 O A:HOH406 4.0 43.3 1.0 CA A:CA401 4.0 20.9 1.0 OD1 A:ASP192 4.1 33.8 1.0 CB A:ASP192 4.1 26.7 1.0 CA A:ASP192 4.2 26.6 1.0 O A:HOH405 4.2 59.6 1.0 O A:VAL72 4.3 19.1 1.0 N A:TYR193 4.5 28.6 1.0 OD2 A:ASP132 4.6 17.8 1.0 CB A:ASP71 4.7 15.7 1.0 CG2 A:ILE189 4.8 18.9 1.0 O A:HOH446 4.8 17.5 1.0 C A:ASP192 4.9 27.6 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