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Magnesium in PDB 1zbl: Bacillus Halodurans Rnase H Catalytic Domain Mutant D192N in Complex with 12-Mer Rna/Dna Hybrid

Enzymatic activity of Bacillus Halodurans Rnase H Catalytic Domain Mutant D192N in Complex with 12-Mer Rna/Dna Hybrid

All present enzymatic activity of Bacillus Halodurans Rnase H Catalytic Domain Mutant D192N in Complex with 12-Mer Rna/Dna Hybrid:
3.1.26.4;

Protein crystallography data

The structure of Bacillus Halodurans Rnase H Catalytic Domain Mutant D192N in Complex with 12-Mer Rna/Dna Hybrid, PDB code: 1zbl was solved by M.Nowotny, S.A.Gaidamakov, R.J.Crouch, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 36.897, 44.983, 62.280, 83.63, 89.90, 65.69
R / Rfree (%) 21.7 / 25.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Bacillus Halodurans Rnase H Catalytic Domain Mutant D192N in Complex with 12-Mer Rna/Dna Hybrid (pdb code 1zbl). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Bacillus Halodurans Rnase H Catalytic Domain Mutant D192N in Complex with 12-Mer Rna/Dna Hybrid, PDB code: 1zbl:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1zbl

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Magnesium binding site 1 out of 4 in the Bacillus Halodurans Rnase H Catalytic Domain Mutant D192N in Complex with 12-Mer Rna/Dna Hybrid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Bacillus Halodurans Rnase H Catalytic Domain Mutant D192N in Complex with 12-Mer Rna/Dna Hybrid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:33.9
occ:1.00
 OD1 A:ASP71 2.1 30.5 1.0
OD1 A:ASP132 2.3 24.2 1.0
OE2 A:GLU109 2.4 30.3 1.0
OP1 C:C5 2.8 38.7 0.5
OD2 A:ASP132 2.8 24.7 1.0
CG A:ASP132 2.9 24.1 1.0
O A:HOH206 2.9 21.6 1.0
O3' C:A4 2.9 37.2 0.5
OE1 A:GLU109 3.1 27.3 1.0
CD A:GLU109 3.1 30.2 1.0
CG A:ASP71 3.3 28.8 1.0
O C:HOH19 3.4 35.9 1.0
P C:C5 3.5 38.0 0.5
OD2 A:ASP71 3.9 33.3 1.0
MG A:MG202 4.1 33.4 1.0
C3' C:A4 4.2 37.4 0.5
C5' C:C5 4.3 36.2 0.5
CB A:ASP132 4.3 24.2 1.0
O2' C:A4 4.3 39.3 0.5
CB A:ASP71 4.4 29.4 1.0
C4' C:A4 4.4 37.4 0.5
N A:VAL72 4.4 30.1 1.0
O5' C:C5 4.4 36.7 0.5
CA A:ASP71 4.5 28.1 1.0
CG1 A:VAL72 4.6 30.4 1.0
CG A:GLU109 4.6 26.7 1.0
OP2 C:C5 4.6 38.4 0.5
N A:ASP132 4.7 25.5 1.0
N A:SER133 4.7 25.1 1.0
O C:HOH14 4.8 32.1 1.0
C A:ASP132 4.9 25.7 1.0
CA A:ASP132 4.9 25.2 1.0
C2' C:A4 4.9 38.4 0.5
C5' C:A4 4.9 36.4 0.5
O A:VAL72 5.0 29.5 1.0

Magnesium binding site 2 out of 4 in 1zbl

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Magnesium binding site 2 out of 4 in the Bacillus Halodurans Rnase H Catalytic Domain Mutant D192N in Complex with 12-Mer Rna/Dna Hybrid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Bacillus Halodurans Rnase H Catalytic Domain Mutant D192N in Complex with 12-Mer Rna/Dna Hybrid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:33.4
occ:1.00
 O C:HOH14 1.9 32.1 1.0
OD1 A:ASN192 2.1 46.3 1.0
OP1 C:C5 2.1 38.7 0.5
O C:HOH19 2.2 35.9 1.0
OD2 A:ASP71 2.2 33.3 1.0
O A:HOH203 2.7 47.0 1.0
CG A:ASN192 3.1 45.4 1.0
CG A:ASP71 3.2 28.8 1.0
P C:C5 3.3 38.0 0.5
OD1 A:ASP71 3.4 30.5 1.0
OP2 C:C5 3.7 38.4 0.5
CB A:ASN192 3.8 44.0 1.0
ND2 A:ASN192 4.0 44.7 1.0
CA A:ASN192 4.0 43.6 1.0
OP2 C:C6 4.1 36.9 0.5
MG A:MG201 4.1 33.9 1.0
N A:TYR193 4.1 48.0 1.0
O5' C:C5 4.1 36.7 0.5
O A:VAL72 4.2 29.5 1.0
OD2 A:ASP132 4.4 24.7 1.0
O3' C:A4 4.5 37.2 0.5
CB A:ASP71 4.5 29.4 1.0
C A:ASN192 4.6 46.0 1.0
C5' C:C5 4.7 36.2 0.5
CG2 A:ILE189 4.8 36.1 1.0
O A:TYR193 4.9 49.3 1.0

Magnesium binding site 3 out of 4 in 1zbl

Go back to Magnesium Binding Sites List in 1zbl
Magnesium binding site 3 out of 4 in the Bacillus Halodurans Rnase H Catalytic Domain Mutant D192N in Complex with 12-Mer Rna/Dna Hybrid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Bacillus Halodurans Rnase H Catalytic Domain Mutant D192N in Complex with 12-Mer Rna/Dna Hybrid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg203

b:31.7
occ:1.00
 OD1 B:ASP71 2.1 29.9 1.0
OD1 B:ASP132 2.2 29.3 1.0
OE2 B:GLU109 2.5 31.4 1.0
OP1 C:U11 2.7 38.8 0.5
O B:HOH205 2.8 16.6 1.0
OD2 B:ASP132 2.8 27.6 1.0
CG B:ASP132 2.8 26.3 1.0
O3' C:U10 2.9 35.2 0.5
OE1 B:GLU109 3.1 30.9 1.0
CD B:GLU109 3.2 30.9 1.0
CG B:ASP71 3.3 31.0 1.0
O B:HOH232 3.3 25.5 1.0
P C:U11 3.4 38.6 0.5
OD2 B:ASP71 3.9 30.5 1.0
MG B:MG204 4.1 30.2 1.0
C3' C:U10 4.2 32.6 0.5
CB B:ASP132 4.3 25.3 1.0
CB B:ASP71 4.3 29.1 1.0
O2' C:U10 4.4 31.6 0.5
C5' C:U11 4.4 42.6 0.5
C4' C:U10 4.4 31.8 0.5
N B:VAL72 4.4 29.1 1.0
O5' C:U11 4.4 39.4 0.5
CA B:ASP71 4.5 28.1 1.0
OP2 C:U11 4.5 39.5 0.5
CG B:GLU109 4.7 29.3 1.0
N B:ASP132 4.7 24.5 1.0
CG1 B:VAL72 4.7 28.1 1.0
N B:SER133 4.7 25.6 1.0
CA B:ASP132 4.8 25.2 1.0
C B:ASP132 4.8 25.1 1.0
C2' C:U10 4.9 32.4 0.5
C5' C:U10 4.9 31.1 0.5

Magnesium binding site 4 out of 4 in 1zbl

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Magnesium binding site 4 out of 4 in the Bacillus Halodurans Rnase H Catalytic Domain Mutant D192N in Complex with 12-Mer Rna/Dna Hybrid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Bacillus Halodurans Rnase H Catalytic Domain Mutant D192N in Complex with 12-Mer Rna/Dna Hybrid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg204

b:30.2
occ:1.00
 O C:HOH59 2.0 38.9 1.0
O B:HOH232 2.1 25.5 1.0
OD1 B:ASN192 2.1 45.7 1.0
OP1 C:U11 2.2 38.8 0.5
OD2 B:ASP71 2.3 30.5 1.0
O B:HOH215 2.5 41.0 1.0
CG B:ASN192 3.1 44.8 1.0
CG B:ASP71 3.2 31.0 1.0
P C:U11 3.2 38.6 0.5
OD1 B:ASP71 3.4 29.9 1.0
OP2 C:U11 3.5 39.5 0.5
CB B:ASN192 3.9 43.2 1.0
ND2 B:ASN192 4.0 44.6 1.0
CA B:ASN192 4.0 42.9 1.0
OP2 C:C12 4.1 48.9 0.5
MG B:MG203 4.1 31.7 1.0
O5' C:U11 4.2 39.4 0.5
N B:TYR193 4.2 47.7 1.0
O B:VAL72 4.2 29.6 1.0
OD2 B:ASP132 4.4 27.6 1.0
O3' C:U10 4.4 35.2 0.5
CB B:ASP71 4.5 29.1 1.0
C B:ASN192 4.7 45.4 1.0
O C:HOH85 4.7 29.7 1.0
O B:TYR193 4.8 50.2 1.0
CG2 B:ILE189 4.8 34.4 1.0
C5' C:U11 4.8 42.6 0.5

Reference:

M.Nowotny, S.A.Gaidamakov, R.J.Crouch, W.Yang. Crystal Structures of Rnase H Bound to An Rna/Dna Hybrid: Substrate Specificity and Metal-Dependent Catalysis. Cell(Cambridge,Mass.) V. 121 1005 2005.
ISSN: ISSN 0092-8674
PubMed: 15989951
DOI: 10.1016/J.CELL.2005.04.024
Page generated: Mon Dec 14 07:11:40 2020

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