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Magnesium in PDB 1zbi: Bacillus Halodurans Rnase H Catalytic Domain Mutant D132N in Complex with 12-Mer Rna/Dna Hybrid

Enzymatic activity of Bacillus Halodurans Rnase H Catalytic Domain Mutant D132N in Complex with 12-Mer Rna/Dna Hybrid

All present enzymatic activity of Bacillus Halodurans Rnase H Catalytic Domain Mutant D132N 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 D132N in Complex with 12-Mer Rna/Dna Hybrid, PDB code: 1zbi 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 / 1.85
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 136.393, 36.964, 93.202, 90.00, 121.51, 90.00
R / Rfree (%) 20.6 / 24.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Bacillus Halodurans Rnase H Catalytic Domain Mutant D132N in Complex with 12-Mer Rna/Dna Hybrid (pdb code 1zbi). 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 D132N in Complex with 12-Mer Rna/Dna Hybrid, PDB code: 1zbi:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1zbi

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Magnesium binding site 1 out of 4 in the Bacillus Halodurans Rnase H Catalytic Domain Mutant D132N 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 D132N in Complex with 12-Mer Rna/Dna Hybrid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:36.8
occ:1.00
 OD1 A:ASP71 2.0 25.7 1.0
OD1 A:ASN132 2.2 22.7 1.0
OE2 A:GLU109 2.3 28.2 1.0
OP1 C:U10 2.8 24.7 1.0
OE1 A:GLU109 2.8 24.4 1.0
O A:HOH339 2.9 27.8 1.0
CG A:ASN132 2.9 23.3 1.0
CD A:GLU109 2.9 27.4 1.0
O3' C:A9 3.0 22.0 1.0
ND2 A:ASN132 3.0 22.9 1.0
CG A:ASP71 3.2 25.8 1.0
P C:U10 3.6 21.7 1.0
OD2 A:ASP71 3.8 26.7 1.0
C5' C:U10 4.0 23.1 1.0
O2' C:A9 4.1 21.5 1.0
C3' C:A9 4.2 19.3 1.0
CB A:ASP71 4.3 22.7 1.0
O5' C:U10 4.3 21.8 1.0
N A:VAL72 4.3 21.2 1.0
CB A:ASN132 4.3 20.4 1.0
CG1 A:VAL72 4.4 21.4 1.0
CA A:ASP71 4.4 21.4 1.0
CG A:GLU109 4.4 23.6 1.0
MG A:MG302 4.5 16.5 1.0
C4' C:A9 4.5 19.1 1.0
N A:ASN132 4.7 19.7 1.0
C2' C:A9 4.8 20.4 1.0
N A:SER133 4.8 20.2 1.0
C A:ASN132 4.8 21.5 1.0
OP2 C:U10 4.8 24.6 1.0
CA A:ASN132 4.8 21.8 1.0
O A:HOH335 4.9 19.5 1.0
C A:ASP71 5.0 21.3 1.0
CB A:SER133 5.0 20.2 1.0

Magnesium binding site 2 out of 4 in 1zbi

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Magnesium binding site 2 out of 4 in the Bacillus Halodurans Rnase H Catalytic Domain Mutant D132N 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 D132N in Complex with 12-Mer Rna/Dna Hybrid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:16.5
occ:1.00
 O A:HOH304 2.0 23.6 1.0
O A:HOH303 2.1 30.1 1.0
OD2 A:ASP192 2.2 32.2 1.0
OP1 C:U10 2.3 24.7 1.0
OD2 A:ASP71 2.3 26.7 1.0
OE2 A:GLU188 2.7 43.8 1.0
CG A:ASP192 3.3 31.9 1.0
CG A:ASP71 3.3 25.8 1.0
P C:U10 3.5 21.7 1.0
OD1 A:ASP71 3.7 25.7 1.0
OP2 C:U10 3.9 24.6 1.0
CD A:GLU188 3.9 43.8 1.0
CB A:ASP192 4.0 30.7 1.0
CA A:ASP192 4.1 28.4 1.0
O5' C:U10 4.1 21.8 1.0
OP2 C:U11 4.3 26.5 1.0
O A:VAL72 4.3 19.4 1.0
OD1 A:ASP192 4.3 34.2 1.0
N A:TYR193 4.4 29.3 1.0
ND2 A:ASN132 4.5 22.9 1.0
MG A:MG301 4.5 36.8 1.0
CG2 A:ILE189 4.6 27.2 1.0
C5' C:U10 4.7 23.1 1.0
CB A:ASP71 4.7 22.7 1.0
O3' C:A9 4.7 22.0 1.0
CG A:GLU188 4.7 40.4 1.0
C A:ASP192 4.8 28.7 1.0
OE1 A:GLU188 4.8 44.3 1.0

Magnesium binding site 3 out of 4 in 1zbi

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Magnesium binding site 3 out of 4 in the Bacillus Halodurans Rnase H Catalytic Domain Mutant D132N 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 D132N in Complex with 12-Mer Rna/Dna Hybrid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:29.7
occ:1.00
 OD1 B:ASN132 2.3 19.3 1.0
OE2 B:GLU109 2.3 30.9 1.0
OD1 B:ASP71 2.4 25.1 1.0
O B:HOH341 2.6 15.9 1.0
OE1 B:GLU109 2.9 26.9 1.0
CD B:GLU109 2.9 27.6 1.0
CG B:ASN132 3.0 15.7 1.0
OP1 C:C5 3.0 21.7 1.0
ND2 B:ASN132 3.1 16.0 1.0
O3' C:A4 3.2 19.7 1.0
CG B:ASP71 3.5 29.2 1.0
P C:C5 3.8 19.8 1.0
C5' C:C5 4.0 19.2 1.0
O2' C:A4 4.2 18.7 1.0
OD2 B:ASP71 4.3 29.4 1.0
N B:VAL72 4.3 25.9 1.0
MG B:MG304 4.4 26.6 1.0
CA B:ASP71 4.4 25.6 1.0
CG B:GLU109 4.4 25.2 1.0
CB B:ASN132 4.4 14.4 1.0
O5' C:C5 4.4 18.9 1.0
CB B:ASP71 4.5 27.3 1.0
C3' C:A4 4.5 17.0 1.0
N B:ASN132 4.7 14.1 1.0
C4' C:A4 4.7 18.0 1.0
N B:SER133 4.8 15.9 1.0
O B:VAL70 4.8 22.8 1.0
O B:HOH345 4.9 23.0 1.0
CA B:ASN132 4.9 14.8 1.0
C B:ASN132 4.9 15.9 1.0
C B:ASP71 4.9 26.4 1.0
C2' C:A4 4.9 17.8 1.0
CB B:SER133 5.0 16.4 1.0
O B:HOH305 5.0 33.0 1.0

Magnesium binding site 4 out of 4 in 1zbi

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Magnesium binding site 4 out of 4 in the Bacillus Halodurans Rnase H Catalytic Domain Mutant D132N 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 D132N in Complex with 12-Mer Rna/Dna Hybrid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:26.6
occ:1.00
 O B:HOH305 2.0 33.0 1.0
OP1 C:C5 2.1 21.7 1.0
OD2 B:ASP71 2.3 29.4 1.0
OD1 B:ASP192 2.4 43.8 1.0
OE2 B:GLU188 2.6 41.7 1.0
O C:HOH55 2.6 66.2 1.0
CG B:ASP71 3.1 29.2 1.0
OD1 B:ASP71 3.2 25.1 1.0
P C:C5 3.4 19.8 1.0
CG B:ASP192 3.5 45.4 1.0
CD B:GLU188 3.8 41.3 1.0
O B:HOH380 3.9 50.0 1.0
CB B:ASP192 3.9 44.8 1.0
OP2 C:C5 4.0 19.3 1.0
O5' C:C5 4.0 18.9 1.0
CA B:ASP192 4.3 45.2 1.0
ND2 B:ASN132 4.3 16.0 1.0
MG B:MG303 4.4 29.7 1.0
O B:VAL72 4.4 26.6 1.0
OP2 C:C6 4.4 24.7 1.0
C5' C:C5 4.4 19.2 1.0
CG2 B:ILE189 4.5 25.2 1.0
OD2 B:ASP192 4.5 43.1 1.0
OE1 B:GLU188 4.6 43.4 1.0
O3' C:A4 4.6 19.7 1.0
CB B:ASP71 4.6 27.3 1.0
CG B:GLU188 4.8 38.5 1.0
O B:HOH316 4.8 46.1 1.0

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: Tue Aug 13 20:05:46 2024

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