Magnesium in PDB 6dpp: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 5 Mm MG2+ and 200 Mm Rb+ For 240 S at 21 C
Enzymatic activity of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 5 Mm MG2+ and 200 Mm Rb+ For 240 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 5 Mm MG2+ and 200 Mm Rb+ For 240 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 5 Mm MG2+ and 200 Mm Rb+ For 240 S at 21 C, PDB code: 6dpp
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)
|
19.94 /
1.45
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
81.468,
37.992,
62.477,
90.00,
96.81,
90.00
|
R / Rfree (%)
|
15.1 /
17.1
|
Other elements in 6dpp:
The structure of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 5 Mm MG2+ and 200 Mm Rb+ For 240 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 5 Mm MG2+ and 200 Mm Rb+ For 240 S at 21 C
(pdb code 6dpp). 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 5 Mm MG2+ and 200 Mm Rb+ For 240 S at 21 C, PDB code: 6dpp:
Jump to Magnesium binding site number:
1;
2;
Magnesium binding site 1 out
of 2 in 6dpp
Go back to
Magnesium Binding Sites List in 6dpp
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 5 Mm MG2+ and 200 Mm Rb+ For 240 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 5 Mm MG2+ and 200 Mm Rb+ For 240 S at 21 C within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg201
b:20.8
occ:1.00
|
OD2
|
A:ASP71
|
2.0
|
18.7
|
1.0
|
OD1
|
A:ASP192
|
2.0
|
20.9
|
1.0
|
O
|
A:HOH321
|
2.1
|
21.7
|
1.0
|
O
|
A:HOH313
|
2.1
|
22.3
|
1.0
|
OP3
|
b:C5
|
2.1
|
23.1
|
0.7
|
OP1
|
b:C5
|
2.2
|
27.2
|
0.3
|
O
|
A:HOH308
|
2.2
|
30.2
|
0.3
|
OP1
|
b:C5
|
2.3
|
23.8
|
0.7
|
P
|
b:C5
|
2.7
|
21.9
|
0.7
|
CG
|
A:ASP71
|
3.0
|
18.4
|
1.0
|
HA
|
A:ASP192
|
3.1
|
23.8
|
1.0
|
CG
|
A:ASP192
|
3.1
|
23.0
|
1.0
|
P
|
b:C5
|
3.4
|
17.5
|
0.3
|
OD1
|
A:ASP71
|
3.4
|
19.4
|
1.0
|
HB2
|
A:ASP192
|
3.6
|
27.4
|
1.0
|
H
|
A:TYR193
|
3.6
|
25.4
|
1.0
|
CB
|
A:ASP192
|
3.7
|
22.9
|
1.0
|
OP2
|
b:C5
|
3.8
|
22.5
|
0.3
|
CA
|
A:ASP192
|
3.9
|
19.8
|
1.0
|
MG
|
A:MG202
|
3.9
|
19.9
|
1.0
|
OP2
|
b:C5
|
3.9
|
21.1
|
0.7
|
O5'
|
b:C5
|
3.9
|
20.4
|
0.7
|
NZ
|
A:LYS196
|
3.9
|
34.4
|
0.7
|
OD2
|
A:ASP132
|
4.0
|
28.9
|
1.0
|
RB
|
A:RB204
|
4.0
|
32.5
|
0.1
|
OP2
|
b:G6
|
4.0
|
22.9
|
1.0
|
O
|
b:HOH201
|
4.0
|
22.0
|
0.7
|
O
|
A:VAL72
|
4.1
|
20.4
|
1.0
|
OE1
|
A:GLU188
|
4.1
|
43.8
|
1.0
|
HG22
|
A:ILE189
|
4.1
|
23.9
|
1.0
|
O5'
|
b:C5
|
4.1
|
18.2
|
0.3
|
OD2
|
A:ASP192
|
4.2
|
23.9
|
1.0
|
RB
|
A:RB203
|
4.2
|
32.0
|
0.1
|
C5'
|
b:C5
|
4.2
|
22.3
|
1.0
|
N
|
A:TYR193
|
4.3
|
21.1
|
1.0
|
CB
|
A:ASP71
|
4.4
|
17.5
|
1.0
|
O
|
A:HOH326
|
4.4
|
18.9
|
0.3
|
HB3
|
A:ASP71
|
4.5
|
21.1
|
1.0
|
HD1
|
A:TYR193
|
4.6
|
26.6
|
1.0
|
O3'
|
B:U4
|
4.6
|
19.0
|
0.3
|
HB3
|
A:ASP192
|
4.6
|
27.4
|
1.0
|
C
|
A:ASP192
|
4.7
|
23.4
|
1.0
|
HG21
|
A:ILE189
|
4.7
|
23.9
|
1.0
|
HB2
|
A:ASP71
|
4.7
|
21.1
|
1.0
|
CG2
|
A:ILE189
|
4.8
|
19.9
|
1.0
|
HG23
|
A:ILE189
|
4.9
|
23.9
|
1.0
|
N
|
A:ASP192
|
4.9
|
19.9
|
1.0
|
HB2
|
A:TYR193
|
5.0
|
27.1
|
1.0
|
|
Magnesium binding site 2 out
of 2 in 6dpp
Go back to
Magnesium Binding Sites List in 6dpp
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 5 Mm MG2+ and 200 Mm Rb+ For 240 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 5 Mm MG2+ and 200 Mm Rb+ For 240 S at 21 C within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg202
b:19.9
occ:1.00
|
OD1
|
A:ASP71
|
2.0
|
19.4
|
1.0
|
OD1
|
A:ASP132
|
2.0
|
20.9
|
1.0
|
OE1
|
A:GLU109
|
2.0
|
18.3
|
1.0
|
OP1
|
b:C5
|
2.2
|
27.2
|
0.3
|
OP1
|
b:C5
|
2.3
|
23.8
|
0.7
|
OD2
|
A:ASP132
|
2.5
|
28.9
|
1.0
|
CG
|
A:ASP132
|
2.6
|
20.7
|
1.0
|
O3'
|
B:U4
|
2.6
|
19.0
|
0.3
|
P
|
b:C5
|
3.0
|
17.5
|
0.3
|
CD
|
A:GLU109
|
3.0
|
18.9
|
1.0
|
CG
|
A:ASP71
|
3.1
|
18.4
|
1.0
|
O
|
A:HOH346
|
3.1
|
19.9
|
1.0
|
OE2
|
A:GLU109
|
3.3
|
19.8
|
1.0
|
P
|
b:C5
|
3.6
|
21.9
|
0.7
|
OD2
|
A:ASP71
|
3.6
|
18.7
|
1.0
|
HG12
|
A:VAL72
|
3.6
|
22.1
|
1.0
|
C3'
|
B:U4
|
3.6
|
22.6
|
0.7
|
O3'
|
B:U4
|
3.6
|
22.6
|
0.7
|
H
|
A:VAL72
|
3.7
|
20.9
|
1.0
|
HA
|
A:ASP71
|
3.9
|
18.9
|
1.0
|
MG
|
A:MG201
|
3.9
|
20.8
|
1.0
|
C3'
|
B:U4
|
3.9
|
28.2
|
0.3
|
O
|
A:HOH321
|
3.9
|
21.7
|
1.0
|
O5'
|
b:C5
|
4.0
|
18.2
|
0.3
|
CB
|
A:ASP132
|
4.1
|
17.6
|
1.0
|
H
|
A:ASP132
|
4.1
|
20.1
|
1.0
|
OP2
|
b:C5
|
4.1
|
21.1
|
0.7
|
C5'
|
b:C5
|
4.1
|
22.3
|
1.0
|
OP2
|
b:C5
|
4.1
|
22.5
|
0.3
|
HB2
|
A:SER133
|
4.2
|
22.9
|
1.0
|
O5'
|
b:C5
|
4.3
|
20.4
|
0.7
|
CB
|
A:ASP71
|
4.3
|
17.5
|
1.0
|
CG
|
A:GLU109
|
4.3
|
15.4
|
1.0
|
C4'
|
B:U4
|
4.4
|
25.9
|
0.3
|
HG21
|
A:ILE189
|
4.4
|
23.9
|
1.0
|
N
|
A:VAL72
|
4.5
|
17.4
|
1.0
|
HG3
|
A:GLU109
|
4.5
|
18.5
|
1.0
|
CA
|
A:ASP71
|
4.5
|
15.7
|
1.0
|
HB2
|
A:ASP132
|
4.5
|
21.2
|
1.0
|
CG1
|
A:VAL72
|
4.5
|
18.4
|
1.0
|
HB3
|
A:ASP132
|
4.5
|
21.2
|
1.0
|
OP3
|
b:C5
|
4.5
|
23.1
|
0.7
|
O2'
|
B:U4
|
4.5
|
15.6
|
0.3
|
C4'
|
B:U4
|
4.6
|
25.0
|
0.7
|
HB2
|
A:ASP71
|
4.6
|
21.1
|
1.0
|
C5'
|
B:U4
|
4.6
|
29.3
|
0.3
|
HG2
|
A:GLU109
|
4.7
|
18.5
|
1.0
|
C2'
|
B:U4
|
4.7
|
21.9
|
0.7
|
C5'
|
B:U4
|
4.7
|
20.4
|
0.7
|
CA
|
A:ASP132
|
4.7
|
17.2
|
1.0
|
N
|
A:ASP132
|
4.8
|
16.7
|
1.0
|
C
|
A:ASP132
|
4.8
|
17.6
|
1.0
|
C2'
|
B:U4
|
4.8
|
25.0
|
0.3
|
HG13
|
A:VAL72
|
4.9
|
22.1
|
1.0
|
O
|
A:VAL72
|
4.9
|
20.4
|
1.0
|
O
|
A:HOH313
|
4.9
|
22.3
|
1.0
|
HG11
|
A:VAL72
|
4.9
|
22.1
|
1.0
|
HG22
|
A:ILE189
|
4.9
|
23.9
|
1.0
|
N
|
A:SER133
|
5.0
|
16.6
|
1.0
|
O2'
|
B:U4
|
5.0
|
25.4
|
0.7
|
|
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 22:36:28 2020
|