Magnesium in PDB 6dp4: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 20 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 20 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 20 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 20 Mm MG2+ and 75 Mm K+ For 40 S at 21 C, PDB code: 6dp4
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)
|
19.92 /
1.37
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
81.525,
37.674,
62.050,
90.00,
96.52,
90.00
|
R / Rfree (%)
|
15.7 /
17.6
|
Other elements in 6dp4:
The structure of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 20 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 20 Mm MG2+ and 75 Mm K+ For 40 S at 21 C
(pdb code 6dp4). 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 20 Mm MG2+ and 75 Mm K+ For 40 S at 21 C, PDB code: 6dp4:
Jump to Magnesium binding site number:
1;
2;
Magnesium binding site 1 out
of 2 in 6dp4
Go back to
Magnesium Binding Sites List in 6dp4
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 20 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 20 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:21.4
occ:1.00
|
OD2
|
A:ASP71
|
2.0
|
21.9
|
1.0
|
OP3
|
b:C5
|
2.0
|
26.5
|
0.8
|
O
|
A:HOH301
|
2.0
|
26.2
|
0.2
|
OD1
|
A:ASP192
|
2.1
|
24.0
|
1.0
|
O
|
A:HOH311
|
2.1
|
23.1
|
1.0
|
O
|
A:HOH310
|
2.1
|
24.6
|
1.0
|
OP1
|
b:C5
|
2.3
|
30.7
|
0.2
|
OP1
|
b:C5
|
2.4
|
26.4
|
0.8
|
P
|
b:C5
|
2.8
|
24.1
|
0.8
|
CG
|
A:ASP71
|
3.0
|
17.6
|
1.0
|
HA
|
A:ASP192
|
3.2
|
27.7
|
1.0
|
CG
|
A:ASP192
|
3.2
|
24.0
|
1.0
|
P
|
b:C5
|
3.4
|
25.1
|
0.2
|
OD1
|
A:ASP71
|
3.4
|
18.5
|
1.0
|
HB2
|
A:ASP192
|
3.6
|
28.3
|
1.0
|
H
|
A:TYR193
|
3.6
|
29.6
|
1.0
|
OP2
|
b:C5
|
3.7
|
30.0
|
0.2
|
CB
|
A:ASP192
|
3.7
|
23.6
|
1.0
|
MG
|
A:MG202
|
3.8
|
20.6
|
1.0
|
NZ
|
A:LYS196
|
3.8
|
31.8
|
0.8
|
CA
|
A:ASP192
|
3.9
|
23.1
|
1.0
|
OP2
|
b:C5
|
3.9
|
26.3
|
0.8
|
O5'
|
b:C5
|
3.9
|
20.7
|
0.8
|
K
|
A:K203
|
3.9
|
27.2
|
0.1
|
OP2
|
b:G6
|
4.0
|
27.1
|
1.0
|
OE2
|
A:GLU188
|
4.0
|
50.6
|
1.0
|
OD2
|
A:ASP132
|
4.0
|
32.2
|
1.0
|
O
|
A:VAL72
|
4.0
|
20.6
|
1.0
|
O
|
b:HOH101
|
4.1
|
29.2
|
0.9
|
HG22
|
A:ILE189
|
4.1
|
26.3
|
1.0
|
O5'
|
b:C5
|
4.2
|
28.1
|
0.2
|
C5'
|
b:C5
|
4.2
|
23.4
|
1.0
|
OD2
|
A:ASP192
|
4.2
|
25.6
|
1.0
|
N
|
A:TYR193
|
4.3
|
24.7
|
1.0
|
CB
|
A:ASP71
|
4.4
|
18.7
|
1.0
|
HB3
|
A:ASP71
|
4.5
|
22.5
|
1.0
|
K
|
A:K204
|
4.5
|
28.5
|
0.4
|
HD1
|
A:TYR193
|
4.5
|
25.9
|
1.0
|
O3'
|
B:U4
|
4.7
|
21.0
|
0.2
|
HB3
|
A:ASP192
|
4.7
|
28.3
|
1.0
|
HG21
|
A:ILE189
|
4.7
|
26.3
|
1.0
|
HB2
|
A:ASP71
|
4.7
|
22.5
|
1.0
|
C
|
A:ASP192
|
4.7
|
24.9
|
1.0
|
CG2
|
A:ILE189
|
4.8
|
21.9
|
1.0
|
HB2
|
A:TYR193
|
4.9
|
34.3
|
1.0
|
N
|
A:ASP192
|
5.0
|
22.6
|
1.0
|
HG23
|
A:ILE189
|
5.0
|
26.3
|
1.0
|
CE
|
A:LYS196
|
5.0
|
36.3
|
0.8
|
|
Magnesium binding site 2 out
of 2 in 6dp4
Go back to
Magnesium Binding Sites List in 6dp4
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 20 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 20 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:20.6
occ:1.00
|
OD1
|
A:ASP71
|
2.0
|
18.5
|
1.0
|
OE1
|
A:GLU109
|
2.1
|
21.3
|
1.0
|
OP1
|
b:C5
|
2.1
|
26.4
|
0.8
|
OP1
|
b:C5
|
2.1
|
30.7
|
0.2
|
OD1
|
A:ASP132
|
2.2
|
22.8
|
1.0
|
OD2
|
A:ASP132
|
2.4
|
32.2
|
1.0
|
CG
|
A:ASP132
|
2.6
|
25.6
|
1.0
|
O3'
|
B:U4
|
2.6
|
21.0
|
0.2
|
P
|
b:C5
|
2.9
|
25.1
|
0.2
|
CD
|
A:GLU109
|
3.0
|
18.6
|
1.0
|
CG
|
A:ASP71
|
3.0
|
17.6
|
1.0
|
O
|
A:HOH349
|
3.1
|
18.9
|
1.0
|
OE2
|
A:GLU109
|
3.2
|
19.0
|
1.0
|
P
|
b:C5
|
3.4
|
24.1
|
0.8
|
OD2
|
A:ASP71
|
3.5
|
21.9
|
1.0
|
HG12
|
A:VAL72
|
3.5
|
23.2
|
1.0
|
C3'
|
B:U4
|
3.6
|
23.1
|
0.8
|
O3'
|
B:U4
|
3.7
|
25.5
|
0.8
|
H
|
A:VAL72
|
3.7
|
22.5
|
1.0
|
MG
|
A:MG201
|
3.8
|
21.4
|
1.0
|
O
|
A:HOH311
|
3.8
|
23.1
|
1.0
|
HA
|
A:ASP71
|
3.9
|
18.9
|
1.0
|
O5'
|
b:C5
|
4.0
|
28.1
|
0.2
|
C3'
|
B:U4
|
4.0
|
28.2
|
0.2
|
OP2
|
b:C5
|
4.0
|
30.0
|
0.2
|
OP2
|
b:C5
|
4.1
|
26.3
|
0.8
|
CB
|
A:ASP132
|
4.1
|
20.8
|
1.0
|
H
|
A:ASP132
|
4.1
|
22.1
|
1.0
|
C5'
|
b:C5
|
4.2
|
23.4
|
1.0
|
CB
|
A:ASP71
|
4.2
|
18.7
|
1.0
|
O5'
|
b:C5
|
4.2
|
20.7
|
0.8
|
HB2
|
A:SER133
|
4.3
|
23.0
|
1.0
|
OP3
|
b:C5
|
4.3
|
26.5
|
0.8
|
HG21
|
A:ILE189
|
4.3
|
26.3
|
1.0
|
CG
|
A:GLU109
|
4.4
|
17.4
|
1.0
|
C4'
|
B:U4
|
4.5
|
26.7
|
0.2
|
N
|
A:VAL72
|
4.5
|
18.7
|
1.0
|
HB2
|
A:ASP71
|
4.5
|
22.5
|
1.0
|
CG1
|
A:VAL72
|
4.5
|
19.4
|
1.0
|
HB3
|
A:ASP132
|
4.5
|
24.9
|
1.0
|
CA
|
A:ASP71
|
4.5
|
15.8
|
1.0
|
O2'
|
B:U4
|
4.5
|
18.5
|
0.2
|
HB2
|
A:ASP132
|
4.5
|
24.9
|
1.0
|
C4'
|
B:U4
|
4.6
|
27.7
|
0.8
|
HG3
|
A:GLU109
|
4.6
|
20.8
|
1.0
|
C5'
|
B:U4
|
4.7
|
31.2
|
0.2
|
HG2
|
A:GLU109
|
4.7
|
20.8
|
1.0
|
C5'
|
B:U4
|
4.8
|
27.1
|
0.8
|
C2'
|
B:U4
|
4.8
|
21.2
|
0.8
|
N
|
A:ASP132
|
4.8
|
18.4
|
1.0
|
CA
|
A:ASP132
|
4.8
|
19.8
|
1.0
|
O
|
A:HOH310
|
4.8
|
24.6
|
1.0
|
HG13
|
A:VAL72
|
4.8
|
23.2
|
1.0
|
HG22
|
A:ILE189
|
4.8
|
26.3
|
1.0
|
C2'
|
B:U4
|
4.8
|
25.6
|
0.2
|
HG11
|
A:VAL72
|
4.9
|
23.2
|
1.0
|
O
|
A:HOH301
|
4.9
|
26.2
|
0.2
|
O
|
A:VAL72
|
4.9
|
20.6
|
1.0
|
C
|
A:ASP132
|
4.9
|
18.1
|
1.0
|
HB3
|
A:ASP71
|
5.0
|
22.5
|
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 22:36:19 2020
|