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Magnesium in PDB 2g8h: B. Halodurans Rnase H Catalytic Domain D192N Mutant in Complex with MG2+ and Rna/Dna Hybrid (Non-P Nick at the Active Site)

Enzymatic activity of B. Halodurans Rnase H Catalytic Domain D192N 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 D192N Mutant in Complex with MG2+ and Rna/Dna Hybrid (Non-P Nick at the Active Site):
3.1.26.4;

Protein crystallography data

The structure of B. Halodurans Rnase H Catalytic Domain D192N Mutant in Complex with MG2+ and Rna/Dna Hybrid (Non-P Nick at the Active Site), PDB code: 2g8h 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 (°) 82.441, 36.964, 61.810, 90.00, 96.38, 90.00
R / Rfree (%) 20.6 / 25.4

Other elements in 2g8h:

The structure of B. Halodurans Rnase H Catalytic Domain D192N Mutant in Complex with MG2+ and Rna/Dna Hybrid (Non-P Nick at the Active Site) also contains other interesting chemical elements:

Vanadium (V) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the B. Halodurans Rnase H Catalytic Domain D192N Mutant in Complex with MG2+ and Rna/Dna Hybrid (Non-P Nick at the Active Site) (pdb code 2g8h). 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 D192N Mutant in Complex with MG2+ and Rna/Dna Hybrid (Non-P Nick at the Active Site), PDB code: 2g8h:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 2g8h

Go back to Magnesium Binding Sites List in 2g8h
Magnesium binding site 1 out of 2 in the B. Halodurans Rnase H Catalytic Domain D192N 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 D192N 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:Mg301

b:23.1
occ:1.00
 O B:HOH55 2.0 26.3 1.0
OD1 A:ASP71 2.1 17.6 1.0
OE2 A:GLU109 2.1 15.8 1.0
OD1 A:ASP132 2.2 18.3 1.0
O3' B:A6 2.3 15.8 1.0
OD2 A:ASP132 2.7 19.9 1.0
CG A:ASP132 2.8 17.5 1.0
CD A:GLU109 3.1 14.7 1.0
CG A:ASP71 3.2 19.1 1.0
OE1 A:GLU109 3.3 14.9 1.0
O A:HOH565 3.3 26.9 1.0
MG A:MG302 3.4 27.1 1.0
O A:HOH411 3.4 11.4 1.0
C3' B:A6 3.6 17.6 1.0
OD2 A:ASP71 3.7 18.7 1.0
O2' B:A6 3.9 16.9 1.0
C4' B:A6 3.9 17.4 1.0
CB A:ASP132 4.3 14.4 1.0
C2' B:A6 4.3 18.9 1.0
CG1 A:VAL72 4.4 18.3 1.0
CB A:ASP71 4.5 15.9 1.0
CG A:GLU109 4.5 15.5 1.0
N A:VAL72 4.5 16.4 1.0
O B:HOH78 4.6 37.8 1.0
C5' B:A6 4.6 18.3 1.0
O A:HOH563 4.7 23.9 1.0
CA A:ASP71 4.7 16.0 1.0
O A:HOH457 4.8 20.9 1.0
C A:ASP132 4.9 15.0 1.0
N A:ASP132 4.9 13.7 1.0
CA A:ASP132 4.9 13.4 1.0
N A:SER133 5.0 14.8 1.0
O A:VAL72 5.0 19.0 1.0

Magnesium binding site 2 out of 2 in 2g8h

Go back to Magnesium Binding Sites List in 2g8h
Magnesium binding site 2 out of 2 in the B. Halodurans Rnase H Catalytic Domain D192N 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 D192N 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:Mg302

b:27.1
occ:1.00
 O B:HOH55 1.9 26.3 1.0
O A:HOH565 2.0 26.9 1.0
O A:HOH457 2.0 20.9 1.0
O A:HOH563 2.2 23.9 1.0
OD2 A:ASP71 2.2 18.7 1.0
OD1 A:ASN192 2.3 27.8 1.0
CG A:ASP71 3.0 19.1 1.0
OD1 A:ASP71 3.2 17.6 1.0
MG A:MG301 3.4 23.1 1.0
CG A:ASN192 3.5 28.2 1.0
O3' B:A6 3.8 15.8 1.0
O A:VAL72 3.8 19.0 1.0
O B:HOH78 3.8 37.8 1.0
OE2 A:GLU188 3.9 39.8 1.0
OD2 A:ASP132 4.1 19.9 1.0
CB A:ASN192 4.1 27.0 1.0
N A:TYR193 4.2 29.0 1.0
CA A:ASN192 4.2 25.7 1.0
O A:HOH564 4.3 52.2 1.0
CB A:ASP71 4.5 15.9 1.0
ND2 A:ASN192 4.5 29.0 1.0
N A:GLY194 4.6 40.5 1.0
C A:ASN192 4.8 27.8 1.0
CG2 A:ILE189 4.9 16.9 1.0
C A:VAL72 5.0 20.2 1.0
OE2 A:GLU109 5.0 15.8 1.0

Reference:

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
Page generated: Tue Aug 13 23:24:36 2024

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