Magnesium in PDB 6dop: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 200 Mm K+ For 120 S at 21 C (Dataset 1)
Enzymatic activity of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 200 Mm K+ For 120 S at 21 C (Dataset 1)
All present enzymatic activity of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 200 Mm K+ For 120 S at 21 C (Dataset 1):
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 2 Mm MG2+ and 200 Mm K+ For 120 S at 21 C (Dataset 1), PDB code: 6dop
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)
|
19.87 /
1.25
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
81.535,
37.625,
61.837,
90.00,
95.84,
90.00
|
R / Rfree (%)
|
16.2 /
17.8
|
Other elements in 6dop:
The structure of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 200 Mm K+ For 120 S at 21 C (Dataset 1) 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 2 Mm MG2+ and 200 Mm K+ For 120 S at 21 C (Dataset 1)
(pdb code 6dop). 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 2 Mm MG2+ and 200 Mm K+ For 120 S at 21 C (Dataset 1), PDB code: 6dop:
Jump to Magnesium binding site number:
1;
2;
Magnesium binding site 1 out
of 2 in 6dop
Go back to
Magnesium Binding Sites List in 6dop
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 2 Mm MG2+ and 200 Mm K+ For 120 S at 21 C (Dataset 1)
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 2 Mm MG2+ and 200 Mm K+ For 120 S at 21 C (Dataset 1) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg201
b:24.4
occ:1.00
|
OD1
|
A:ASP71
|
2.1
|
23.7
|
1.0
|
OP1
|
b:C5
|
2.2
|
27.6
|
0.3
|
OP1
|
b:C5
|
2.2
|
22.8
|
0.5
|
OE1
|
A:GLU109
|
2.4
|
27.7
|
1.0
|
OD1
|
A:ASP132
|
2.4
|
20.8
|
1.0
|
O3'
|
B:U4
|
2.6
|
19.6
|
0.5
|
OP1
|
b:C5
|
2.7
|
35.2
|
0.2
|
O3'
|
B:U4
|
2.7
|
19.8
|
0.2
|
OD2
|
A:ASP132
|
3.0
|
24.8
|
1.0
|
CG
|
A:ASP132
|
3.1
|
21.8
|
1.0
|
P
|
b:C5
|
3.1
|
23.6
|
0.5
|
CG
|
A:ASP71
|
3.1
|
22.7
|
1.0
|
CD
|
A:GLU109
|
3.2
|
22.5
|
1.0
|
P
|
b:C5
|
3.3
|
20.8
|
0.2
|
O
|
A:HOH350
|
3.3
|
18.8
|
1.0
|
OE2
|
A:GLU109
|
3.4
|
20.8
|
1.0
|
O
|
A:HOH313
|
3.5
|
30.4
|
1.0
|
C3'
|
B:U4
|
3.5
|
40.3
|
0.3
|
HG12
|
A:VAL72
|
3.5
|
24.9
|
1.0
|
OD2
|
A:ASP71
|
3.5
|
26.6
|
1.0
|
P
|
b:C5
|
3.6
|
71.8
|
0.3
|
H
|
A:VAL72
|
3.6
|
22.8
|
1.0
|
O3'
|
B:U4
|
3.7
|
33.6
|
0.3
|
MG
|
A:MG214
|
3.8
|
26.6
|
1.0
|
C3'
|
B:U4
|
3.9
|
19.4
|
0.5
|
C3'
|
B:U4
|
4.0
|
19.4
|
0.2
|
C5'
|
b:C5
|
4.1
|
21.9
|
1.0
|
O5'
|
b:C5
|
4.1
|
20.9
|
0.5
|
O2'
|
B:U4
|
4.1
|
19.3
|
0.2
|
O2'
|
B:U4
|
4.1
|
18.5
|
0.5
|
O5'
|
b:C5
|
4.2
|
20.9
|
0.2
|
OP2
|
b:C5
|
4.2
|
21.4
|
0.3
|
OP2
|
b:C5
|
4.2
|
40.1
|
0.5
|
O5'
|
b:C5
|
4.3
|
54.3
|
0.3
|
C4'
|
B:U4
|
4.3
|
19.9
|
0.5
|
C4'
|
B:U4
|
4.3
|
19.4
|
0.2
|
CB
|
A:ASP71
|
4.3
|
18.6
|
1.0
|
C4'
|
B:U4
|
4.4
|
26.0
|
0.3
|
HB2
|
A:SER133
|
4.4
|
19.5
|
1.0
|
CG1
|
A:VAL72
|
4.4
|
20.8
|
1.0
|
HG21
|
A:ILE189
|
4.5
|
28.4
|
1.0
|
N
|
A:VAL72
|
4.5
|
19.0
|
1.0
|
OP2
|
b:C5
|
4.5
|
21.7
|
0.2
|
OP3
|
b:C5
|
4.5
|
39.6
|
0.3
|
CB
|
A:ASP132
|
4.5
|
17.5
|
1.0
|
C5'
|
B:U4
|
4.5
|
30.8
|
0.3
|
C2'
|
B:U4
|
4.5
|
23.5
|
0.3
|
O
|
A:HOH310
|
4.6
|
28.6
|
1.0
|
C2'
|
B:U4
|
4.6
|
19.0
|
0.5
|
C2'
|
B:U4
|
4.7
|
19.0
|
0.2
|
CA
|
A:ASP71
|
4.7
|
16.5
|
1.0
|
CG
|
A:GLU109
|
4.7
|
18.6
|
1.0
|
HG13
|
A:VAL72
|
4.7
|
24.9
|
1.0
|
HG11
|
A:VAL72
|
4.8
|
24.9
|
1.0
|
O2'
|
B:U4
|
4.8
|
40.3
|
0.3
|
HG3
|
A:GLU109
|
4.9
|
22.3
|
1.0
|
C5'
|
B:U4
|
4.9
|
20.0
|
0.5
|
O
|
A:VAL72
|
4.9
|
19.9
|
1.0
|
C5'
|
B:U4
|
4.9
|
20.0
|
0.2
|
HG2
|
A:GLU109
|
4.9
|
22.3
|
1.0
|
|
Magnesium binding site 2 out
of 2 in 6dop
Go back to
Magnesium Binding Sites List in 6dop
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 2 Mm MG2+ and 200 Mm K+ For 120 S at 21 C (Dataset 1)
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 2 Mm MG2+ and 200 Mm K+ For 120 S at 21 C (Dataset 1) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg214
b:26.6
occ:1.00
|
O
|
A:HOH310
|
2.0
|
28.6
|
1.0
|
OD1
|
A:ASP192
|
2.0
|
31.1
|
1.0
|
OP1
|
b:C5
|
2.0
|
35.2
|
0.2
|
O
|
A:HOH304
|
2.0
|
28.8
|
0.7
|
OD2
|
A:ASP71
|
2.1
|
26.6
|
1.0
|
OP3
|
b:C5
|
2.1
|
39.6
|
0.3
|
OP1
|
b:C5
|
2.2
|
22.8
|
0.5
|
O
|
A:HOH313
|
2.2
|
30.4
|
1.0
|
OP1
|
b:C5
|
2.4
|
27.6
|
0.3
|
P
|
b:C5
|
2.8
|
71.8
|
0.3
|
CG
|
A:ASP71
|
3.1
|
22.7
|
1.0
|
CG
|
A:ASP192
|
3.2
|
30.6
|
1.0
|
P
|
b:C5
|
3.3
|
23.6
|
0.5
|
HA
|
A:ASP192
|
3.3
|
31.2
|
1.0
|
P
|
b:C5
|
3.3
|
20.8
|
0.2
|
OD1
|
A:ASP71
|
3.5
|
23.7
|
1.0
|
K
|
A:K202
|
3.5
|
44.5
|
0.2
|
OP2
|
b:C5
|
3.6
|
40.1
|
0.5
|
H
|
A:TYR193
|
3.6
|
38.0
|
1.0
|
MG
|
A:MG201
|
3.8
|
24.4
|
1.0
|
OP2
|
b:C5
|
3.8
|
21.4
|
0.3
|
HB2
|
A:ASP192
|
3.9
|
35.2
|
1.0
|
OP2
|
b:C5
|
3.9
|
21.7
|
0.2
|
CB
|
A:ASP192
|
3.9
|
29.3
|
1.0
|
O5'
|
b:C5
|
4.0
|
54.3
|
0.3
|
OP2
|
b:G6
|
4.0
|
32.7
|
1.0
|
O
|
A:HOH319
|
4.0
|
35.1
|
0.4
|
CA
|
A:ASP192
|
4.0
|
26.0
|
1.0
|
O
|
A:VAL72
|
4.1
|
19.9
|
1.0
|
OD2
|
A:ASP192
|
4.1
|
37.2
|
1.0
|
OE2
|
A:GLU188
|
4.2
|
81.9
|
1.0
|
O5'
|
b:C5
|
4.2
|
20.9
|
0.5
|
O
|
A:HOH308
|
4.2
|
37.1
|
0.6
|
O5'
|
b:C5
|
4.2
|
20.9
|
0.2
|
HG22
|
A:ILE189
|
4.3
|
28.4
|
1.0
|
N
|
A:TYR193
|
4.4
|
31.7
|
1.0
|
O3'
|
B:U4
|
4.4
|
19.8
|
0.2
|
CB
|
A:ASP71
|
4.4
|
18.6
|
1.0
|
O3'
|
B:U4
|
4.4
|
19.6
|
0.5
|
OD2
|
A:ASP132
|
4.5
|
24.8
|
1.0
|
O
|
b:HOH102
|
4.5
|
31.5
|
0.6
|
C5'
|
b:C5
|
4.6
|
21.9
|
1.0
|
HD1
|
A:TYR193
|
4.7
|
31.5
|
1.0
|
HG21
|
A:ILE189
|
4.7
|
28.4
|
1.0
|
OE1
|
A:GLU188
|
4.7
|
76.8
|
1.0
|
C
|
A:ASP192
|
4.8
|
26.5
|
1.0
|
CD
|
A:GLU188
|
4.8
|
77.3
|
1.0
|
HB3
|
A:ASP192
|
4.8
|
35.2
|
1.0
|
HB2
|
A:TYR193
|
4.8
|
38.6
|
1.0
|
CG2
|
A:ILE189
|
4.9
|
23.7
|
1.0
|
H
|
A:VAL72
|
4.9
|
22.8
|
1.0
|
H
|
A:GLY194
|
4.9
|
45.6
|
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 22:36:09 2020
|