Potassium in PDB 6dor: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 300 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 300 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 300 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 300 Mm K+ For 120 S at 21 C (Dataset 1), PDB code: 6dor
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 /
1.50
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
81.544,
37.711,
62.779,
90.00,
96.56,
90.00
|
R / Rfree (%)
|
15.5 /
19.4
|
Other elements in 6dor:
The structure of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 300 Mm K+ For 120 S at 21 C (Dataset 1) also contains other interesting chemical elements:
Potassium Binding Sites:
The binding sites of Potassium atom in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 300 Mm K+ For 120 S at 21 C (Dataset 1)
(pdb code 6dor). This binding sites where shown within
5.0 Angstroms radius around Potassium atom.
In total 3 binding sites of Potassium where determined in the
Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 300 Mm K+ For 120 S at 21 C (Dataset 1), PDB code: 6dor:
Jump to Potassium binding site number:
1;
2;
3;
Potassium binding site 1 out
of 3 in 6dor
Go back to
Potassium Binding Sites List in 6dor
Potassium binding site 1 out
of 3 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 300 Mm K+ For 120 S at 21 C (Dataset 1)
 Mono view
 Stereo pair view
|
A full contact list of Potassium with other atoms in the K 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 300 Mm K+ For 120 S at 21 C (Dataset 1) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K202
b:29.6
occ:0.25
|
O
|
b:HOH302
|
0.8
|
27.5
|
0.4
|
H
|
A:ARG195
|
2.2
|
51.5
|
0.7
|
O
|
A:HOH356
|
2.6
|
31.8
|
0.6
|
O
|
A:HOH305
|
2.7
|
29.2
|
0.5
|
OD1
|
A:ASP192
|
2.9
|
29.7
|
1.0
|
OP2
|
b:G6
|
2.9
|
30.8
|
1.0
|
N
|
A:ARG195
|
3.0
|
42.9
|
0.7
|
OP3
|
b:C5
|
3.1
|
44.9
|
0.5
|
HB2
|
A:ARG195
|
3.1
|
68.7
|
0.7
|
H
|
A:GLY194
|
3.2
|
42.4
|
1.0
|
CG
|
A:LYS196
|
3.2
|
42.4
|
0.5
|
O
|
A:HOH315
|
3.3
|
25.8
|
1.0
|
OD2
|
A:ASP192
|
3.5
|
29.0
|
1.0
|
N
|
A:GLY194
|
3.5
|
35.3
|
1.0
|
H
|
A:TYR193
|
3.5
|
32.0
|
1.0
|
CG
|
A:ASP192
|
3.6
|
26.0
|
1.0
|
HB2
|
A:TYR193
|
3.6
|
40.7
|
1.0
|
N
|
A:LYS196
|
3.7
|
56.7
|
0.5
|
CA
|
A:ARG195
|
3.8
|
45.8
|
0.7
|
CD
|
A:LYS196
|
3.8
|
43.6
|
0.5
|
MG
|
b:MG201
|
3.8
|
24.0
|
1.0
|
CB
|
A:ARG195
|
3.8
|
57.2
|
0.7
|
C
|
A:ARG195
|
3.9
|
47.6
|
0.7
|
C
|
A:GLY194
|
4.0
|
63.5
|
1.0
|
P
|
b:G6
|
4.0
|
26.5
|
1.0
|
HA2
|
A:GLY194
|
4.0
|
52.8
|
1.0
|
CA
|
A:GLY194
|
4.0
|
44.0
|
1.0
|
N
|
A:TYR193
|
4.1
|
26.7
|
1.0
|
C
|
A:TYR193
|
4.1
|
40.5
|
1.0
|
CB
|
A:LYS196
|
4.1
|
46.9
|
0.5
|
CE
|
A:LYS196
|
4.1
|
43.8
|
0.5
|
HG3
|
A:ARG195
|
4.2
|
55.5
|
0.7
|
O5'
|
b:G6
|
4.3
|
29.3
|
1.0
|
CB
|
A:TYR193
|
4.3
|
33.9
|
1.0
|
CA
|
A:TYR193
|
4.3
|
29.5
|
1.0
|
OP1
|
b:G6
|
4.4
|
28.3
|
1.0
|
HD2
|
A:ARG195
|
4.4
|
64.6
|
0.7
|
CG
|
A:ARG195
|
4.5
|
46.3
|
0.7
|
P
|
b:C5
|
4.5
|
65.1
|
0.5
|
CA
|
A:LYS196
|
4.5
|
65.0
|
0.5
|
HB3
|
A:TYR193
|
4.6
|
40.7
|
1.0
|
HB3
|
A:ARG195
|
4.6
|
68.7
|
0.7
|
HA
|
A:ARG195
|
4.7
|
55.0
|
0.7
|
OP1
|
b:C5
|
4.8
|
40.2
|
0.1
|
O
|
A:ARG195
|
4.9
|
61.5
|
0.7
|
O
|
A:TYR193
|
4.9
|
42.1
|
1.0
|
CB
|
A:ASP192
|
5.0
|
27.2
|
1.0
|
HA3
|
A:GLY194
|
5.0
|
52.8
|
1.0
|
OE1
|
A:GLU188
|
5.0
|
73.8
|
1.0
|
|
Potassium binding site 2 out
of 3 in 6dor
Go back to
Potassium Binding Sites List in 6dor
Potassium binding site 2 out
of 3 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 300 Mm K+ For 120 S at 21 C (Dataset 1)
 Mono view
 Stereo pair view
|
A full contact list of Potassium with other atoms in the K 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 300 Mm K+ For 120 S at 21 C (Dataset 1) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K203
b:25.0
occ:0.25
|
O
|
A:HOH317
|
0.9
|
31.3
|
0.6
|
OP2
|
b:C5
|
2.5
|
24.2
|
0.4
|
O
|
B:HOH110
|
2.6
|
33.7
|
1.0
|
C5'
|
B:U4
|
2.7
|
21.2
|
0.1
|
C5'
|
B:U4
|
2.7
|
21.0
|
0.4
|
OP2
|
b:C5
|
2.7
|
46.4
|
0.5
|
OP2
|
b:C5
|
2.8
|
22.8
|
0.1
|
OD2
|
A:ASP132
|
3.3
|
33.4
|
1.0
|
C5'
|
B:U4
|
3.3
|
31.4
|
0.5
|
O
|
A:HOH301
|
3.4
|
45.5
|
1.0
|
OE2
|
A:GLU188
|
3.4
|
49.4
|
1.0
|
O
|
A:HOH350
|
3.5
|
23.6
|
1.0
|
P
|
b:C5
|
3.5
|
22.4
|
0.1
|
O
|
b:HOH301
|
3.6
|
23.1
|
1.0
|
P
|
b:C5
|
3.6
|
22.2
|
0.4
|
O3'
|
B:U4
|
3.6
|
30.8
|
0.1
|
HG21
|
A:THR183
|
3.6
|
33.8
|
1.0
|
HG1
|
A:THR183
|
3.6
|
29.2
|
1.0
|
C4'
|
B:U4
|
3.7
|
23.8
|
0.1
|
O3'
|
B:U4
|
3.7
|
21.1
|
0.4
|
C3'
|
B:U4
|
3.7
|
28.1
|
0.1
|
O5'
|
B:U4
|
3.7
|
49.9
|
0.5
|
C3'
|
B:U4
|
3.7
|
33.9
|
0.4
|
C4'
|
B:U4
|
3.7
|
24.4
|
0.4
|
O5'
|
B:U4
|
3.8
|
23.7
|
0.1
|
O5'
|
B:U4
|
3.8
|
20.9
|
0.4
|
OP1
|
B:U4
|
3.9
|
28.5
|
1.0
|
P
|
b:C5
|
3.9
|
65.1
|
0.5
|
OP1
|
b:C5
|
3.9
|
40.2
|
0.1
|
CG
|
A:ASP132
|
4.0
|
24.6
|
1.0
|
P
|
B:U4
|
4.1
|
24.9
|
1.0
|
NZ
|
A:LYS196
|
4.2
|
57.5
|
0.5
|
OP1
|
b:C5
|
4.2
|
33.9
|
0.4
|
OP1
|
b:C5
|
4.2
|
26.5
|
0.5
|
OP2
|
B:U4
|
4.3
|
29.6
|
1.0
|
CD
|
A:GLU188
|
4.3
|
69.8
|
1.0
|
OG1
|
A:THR183
|
4.4
|
24.4
|
1.0
|
C4'
|
B:U4
|
4.5
|
27.5
|
0.5
|
CG2
|
A:THR183
|
4.5
|
28.2
|
1.0
|
OP3
|
b:C5
|
4.5
|
44.9
|
0.5
|
O
|
A:HOH305
|
4.5
|
29.2
|
0.5
|
OE1
|
A:GLU188
|
4.6
|
73.8
|
1.0
|
C3'
|
B:U4
|
4.6
|
38.2
|
0.5
|
CB
|
A:ASP132
|
4.6
|
18.6
|
1.0
|
OD1
|
A:ASP132
|
4.6
|
23.4
|
1.0
|
HG23
|
A:THR183
|
4.7
|
33.8
|
1.0
|
O4'
|
B:U4
|
4.8
|
30.9
|
0.1
|
O4'
|
B:U4
|
4.9
|
45.7
|
0.4
|
C2'
|
B:U4
|
4.9
|
33.6
|
0.5
|
CE
|
A:LYS196
|
4.9
|
43.8
|
0.5
|
MG
|
A:MG201
|
4.9
|
22.9
|
1.0
|
MG
|
b:MG201
|
4.9
|
24.0
|
1.0
|
O5'
|
b:C5
|
4.9
|
22.2
|
0.4
|
CB
|
A:THR183
|
5.0
|
26.6
|
1.0
|
|
Potassium binding site 3 out
of 3 in 6dor
Go back to
Potassium Binding Sites List in 6dor
Potassium binding site 3 out
of 3 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 300 Mm K+ For 120 S at 21 C (Dataset 1)
 Mono view
 Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 3 of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 300 Mm K+ For 120 S at 21 C (Dataset 1) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:K101
b:46.1
occ:0.50
|
O
|
C:HOH214
|
2.2
|
25.3
|
0.5
|
O6
|
C:DG5
|
2.6
|
29.8
|
1.0
|
O
|
C:HOH210
|
3.2
|
35.8
|
1.0
|
O4
|
C:DT4
|
3.3
|
27.4
|
1.0
|
C6
|
C:DG5
|
3.7
|
28.6
|
1.0
|
N4
|
B:C2
|
4.0
|
33.8
|
1.0
|
O
|
C:HOH201
|
4.1
|
44.6
|
1.0
|
C4
|
C:DT4
|
4.1
|
26.2
|
1.0
|
N7
|
C:DG5
|
4.1
|
27.1
|
1.0
|
C7
|
C:DT4
|
4.2
|
28.5
|
1.0
|
C5
|
C:DG5
|
4.3
|
27.2
|
1.0
|
O
|
B:HOH105
|
4.4
|
48.4
|
1.0
|
N6
|
B:A3
|
4.5
|
26.2
|
1.0
|
N6
|
B:A1
|
4.5
|
28.5
|
1.0
|
C5
|
C:DT4
|
4.6
|
26.6
|
1.0
|
O
|
B:HOH103
|
4.8
|
67.9
|
1.0
|
N1
|
C:DG5
|
4.9
|
29.3
|
1.0
|
O4
|
C:DT6
|
4.9
|
33.2
|
1.0
|
O
|
B:HOH108
|
4.9
|
43.6
|
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 Aug 12 15:50:01 2024
|