Atomistry » Magnesium » PDB 1z6n-1zk2 » 1zbi
Atomistry »
  Magnesium »
    PDB 1z6n-1zk2 »
      1zbi »

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

Go back to Magnesium Binding Sites List in 1zbi
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

Go back to Magnesium Binding Sites List in 1zbi
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

Go back to Magnesium Binding Sites List in 1zbi
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

Go back to Magnesium Binding Sites List in 1zbi
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy