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
Go back to
Magnesium Binding Sites List in 1zbl
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
Go back to
Magnesium Binding Sites List in 1zbl
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
Go back to
Magnesium Binding Sites List in 1zbl
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: Tue Aug 13 20:05:57 2024
|