Magnesium in PDB 6dp6: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 80 Mm MG2+ and 75 Mm K+ For 40 S at 21 C
Enzymatic activity of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 80 Mm MG2+ and 75 Mm K+ For 40 S at 21 C
All present enzymatic activity of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 80 Mm MG2+ and 75 Mm K+ For 40 S at 21 C:
3.1.26.4;
Protein crystallography data
The structure of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 80 Mm MG2+ and 75 Mm K+ For 40 S at 21 C, PDB code: 6dp6
was solved by
N.L.Samara,
W.Yang,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.08 /
1.40
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
81.832,
37.292,
62.607,
90.00,
96.71,
90.00
|
R / Rfree (%)
|
16.3 /
18.6
|
Other elements in 6dp6:
The structure of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 80 Mm MG2+ and 75 Mm K+ For 40 S at 21 C also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 80 Mm MG2+ and 75 Mm K+ For 40 S at 21 C
(pdb code 6dp6). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the
Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 80 Mm MG2+ and 75 Mm K+ For 40 S at 21 C, PDB code: 6dp6:
Jump to Magnesium binding site number:
1;
2;
Magnesium binding site 1 out
of 2 in 6dp6
Go back to
Magnesium Binding Sites List in 6dp6
Magnesium binding site 1 out
of 2 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 80 Mm MG2+ and 75 Mm K+ For 40 S at 21 C
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 80 Mm MG2+ and 75 Mm K+ For 40 S at 21 C within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg201
b:18.9
occ:1.00
|
OD2
|
A:ASP71
|
2.0
|
18.3
|
1.0
|
OP3
|
b:C5
|
2.0
|
23.3
|
0.8
|
O
|
A:HOH302
|
2.0
|
19.1
|
0.1
|
OD1
|
A:ASP192
|
2.1
|
22.3
|
1.0
|
O
|
A:HOH309
|
2.1
|
21.5
|
1.0
|
O
|
A:HOH332
|
2.1
|
19.8
|
1.0
|
OP1
|
b:C5
|
2.3
|
28.4
|
0.1
|
OP1
|
b:C5
|
2.4
|
23.2
|
0.8
|
P
|
b:C5
|
2.8
|
20.4
|
0.8
|
CG
|
A:ASP71
|
3.0
|
17.2
|
1.0
|
CG
|
A:ASP192
|
3.2
|
25.1
|
1.0
|
HA
|
A:ASP192
|
3.2
|
22.2
|
1.0
|
OD1
|
A:ASP71
|
3.4
|
18.1
|
1.0
|
P
|
b:C5
|
3.5
|
26.5
|
0.1
|
HB2
|
A:ASP192
|
3.5
|
25.2
|
1.0
|
H
|
A:TYR193
|
3.6
|
25.3
|
1.0
|
CB
|
A:ASP192
|
3.7
|
21.0
|
1.0
|
OP2
|
b:C5
|
3.8
|
17.9
|
0.1
|
MG
|
A:MG202
|
3.8
|
18.8
|
1.0
|
CA
|
A:ASP192
|
3.9
|
18.5
|
1.0
|
OP2
|
b:C5
|
3.9
|
24.6
|
0.8
|
NZ
|
A:LYS196
|
3.9
|
31.1
|
0.8
|
O5'
|
b:C5
|
3.9
|
18.5
|
0.8
|
K
|
A:K203
|
3.9
|
16.6
|
0.1
|
OP2
|
b:G6
|
4.0
|
20.6
|
1.0
|
OD2
|
A:ASP132
|
4.0
|
29.7
|
1.0
|
O
|
A:VAL72
|
4.0
|
19.7
|
1.0
|
HG22
|
A:ILE189
|
4.1
|
22.9
|
1.0
|
OE2
|
A:GLU188
|
4.1
|
40.9
|
1.0
|
O
|
b:HOH101
|
4.2
|
27.9
|
0.9
|
C5'
|
b:C5
|
4.2
|
20.3
|
1.0
|
OD2
|
A:ASP192
|
4.2
|
23.6
|
1.0
|
CB
|
A:ASP71
|
4.3
|
14.8
|
1.0
|
O5'
|
b:C5
|
4.3
|
25.8
|
0.1
|
N
|
A:TYR193
|
4.4
|
21.1
|
1.0
|
HB3
|
A:ASP71
|
4.4
|
17.8
|
1.0
|
HD1
|
A:TYR193
|
4.5
|
27.1
|
1.0
|
K
|
A:K204
|
4.6
|
28.1
|
0.4
|
HB3
|
A:ASP192
|
4.6
|
25.2
|
1.0
|
HB2
|
A:ASP71
|
4.6
|
17.8
|
1.0
|
HG21
|
A:ILE189
|
4.7
|
22.9
|
1.0
|
C
|
A:ASP192
|
4.7
|
23.6
|
1.0
|
O3'
|
B:U4
|
4.7
|
22.6
|
0.1
|
CG2
|
A:ILE189
|
4.7
|
19.1
|
1.0
|
HG23
|
A:ILE189
|
4.9
|
22.9
|
1.0
|
HB2
|
A:TYR193
|
4.9
|
27.4
|
1.0
|
N
|
A:ASP192
|
5.0
|
19.3
|
1.0
|
|
Magnesium binding site 2 out
of 2 in 6dp6
Go back to
Magnesium Binding Sites List in 6dp6
Magnesium binding site 2 out
of 2 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 80 Mm MG2+ and 75 Mm K+ For 40 S at 21 C
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 80 Mm MG2+ and 75 Mm K+ For 40 S at 21 C within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg202
b:18.8
occ:1.00
|
OD1
|
A:ASP71
|
2.0
|
18.1
|
1.0
|
OE1
|
A:GLU109
|
2.0
|
19.3
|
1.0
|
OD1
|
A:ASP132
|
2.1
|
20.5
|
1.0
|
OP1
|
b:C5
|
2.1
|
23.2
|
0.8
|
OP1
|
b:C5
|
2.1
|
28.4
|
0.1
|
OD2
|
A:ASP132
|
2.4
|
29.7
|
1.0
|
CG
|
A:ASP132
|
2.6
|
24.2
|
1.0
|
O3'
|
B:U4
|
2.6
|
22.6
|
0.1
|
P
|
b:C5
|
2.8
|
26.5
|
0.1
|
CD
|
A:GLU109
|
3.0
|
16.5
|
1.0
|
CG
|
A:ASP71
|
3.0
|
17.2
|
1.0
|
O
|
A:HOH334
|
3.1
|
19.4
|
1.0
|
OE2
|
A:GLU109
|
3.2
|
19.2
|
1.0
|
P
|
b:C5
|
3.5
|
20.4
|
0.8
|
HG12
|
A:VAL72
|
3.5
|
20.3
|
1.0
|
OD2
|
A:ASP71
|
3.5
|
18.3
|
1.0
|
C3'
|
B:U4
|
3.6
|
24.7
|
0.8
|
O3'
|
B:U4
|
3.7
|
25.3
|
0.8
|
H
|
A:VAL72
|
3.7
|
20.0
|
1.0
|
O5'
|
b:C5
|
3.7
|
25.8
|
0.1
|
MG
|
A:MG201
|
3.8
|
18.9
|
1.0
|
O
|
A:HOH332
|
3.9
|
19.8
|
1.0
|
HA
|
A:ASP71
|
3.9
|
20.3
|
1.0
|
C3'
|
B:U4
|
4.0
|
24.5
|
0.1
|
OP2
|
b:C5
|
4.1
|
17.9
|
0.1
|
CB
|
A:ASP132
|
4.1
|
20.3
|
1.0
|
OP2
|
b:C5
|
4.1
|
24.6
|
0.8
|
H
|
A:ASP132
|
4.1
|
21.3
|
1.0
|
C5'
|
b:C5
|
4.2
|
20.3
|
1.0
|
CB
|
A:ASP71
|
4.2
|
14.8
|
1.0
|
O5'
|
b:C5
|
4.2
|
18.5
|
0.8
|
HB2
|
A:SER133
|
4.3
|
21.7
|
1.0
|
HG21
|
A:ILE189
|
4.3
|
22.9
|
1.0
|
OP3
|
b:C5
|
4.3
|
23.3
|
0.8
|
CG
|
A:GLU109
|
4.4
|
17.3
|
1.0
|
O2'
|
B:U4
|
4.4
|
17.4
|
0.1
|
N
|
A:VAL72
|
4.5
|
16.7
|
1.0
|
CG1
|
A:VAL72
|
4.5
|
16.9
|
1.0
|
HB2
|
A:ASP71
|
4.5
|
17.8
|
1.0
|
CA
|
A:ASP71
|
4.5
|
16.9
|
1.0
|
HG3
|
A:GLU109
|
4.5
|
20.7
|
1.0
|
HB3
|
A:ASP132
|
4.5
|
24.4
|
1.0
|
HB2
|
A:ASP132
|
4.5
|
24.4
|
1.0
|
C4'
|
B:U4
|
4.5
|
25.1
|
0.1
|
C4'
|
B:U4
|
4.6
|
24.9
|
0.8
|
HG2
|
A:GLU109
|
4.7
|
20.7
|
1.0
|
C5'
|
B:U4
|
4.7
|
28.4
|
0.8
|
C2'
|
B:U4
|
4.8
|
19.2
|
0.8
|
CA
|
A:ASP132
|
4.8
|
20.3
|
1.0
|
N
|
A:ASP132
|
4.8
|
17.8
|
1.0
|
C2'
|
B:U4
|
4.8
|
22.6
|
0.1
|
HG13
|
A:VAL72
|
4.8
|
20.3
|
1.0
|
HG22
|
A:ILE189
|
4.8
|
22.9
|
1.0
|
HG11
|
A:VAL72
|
4.9
|
20.3
|
1.0
|
O
|
A:HOH302
|
4.9
|
19.1
|
0.1
|
C
|
A:ASP132
|
4.9
|
16.2
|
1.0
|
C5'
|
B:U4
|
4.9
|
27.7
|
0.1
|
O
|
A:HOH309
|
4.9
|
21.5
|
1.0
|
O
|
A:VAL72
|
4.9
|
19.7
|
1.0
|
HB3
|
A:ASP71
|
5.0
|
17.8
|
1.0
|
|
Reference:
N.L.Samara,
W.Yang.
Cation Trafficking Propels Rna Hydrolysis. Nat. Struct. Mol. Biol. V. 25 715 2018.
ISSN: ESSN 1545-9985
PubMed: 30076410
DOI: 10.1038/S41594-018-0099-4
Page generated: Mon Dec 14 22:36:21 2020
|