Chlorine 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:
Chlorine Binding Sites:
The binding sites of Chlorine 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 Chlorine atom.
In total 3 binding sites of Chlorine 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 Chlorine binding site number:
1;
2;
3;
Chlorine binding site 1 out
of 3 in 6dpp
Go back to
Chlorine Binding Sites List in 6dpp
Chlorine binding site 1 out
of 3 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
![](/pictures/CL/pdb/dp/6dpp-CL-sphere_01.jpg) Mono view
![](/pictures/CL/pdb/dp/6dpp-CL-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl 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:Cl206
b:29.3
occ:0.65
|
HH
|
A:TYR83
|
2.3
|
28.4
|
1.0
|
HD22
|
A:LEU111
|
2.9
|
21.8
|
1.0
|
HB3
|
A:LEU111
|
3.1
|
18.9
|
1.0
|
OH
|
A:TYR83
|
3.1
|
23.7
|
1.0
|
HD13
|
A:LEU111
|
3.1
|
21.4
|
1.0
|
O
|
A:HOH384
|
3.2
|
29.4
|
1.0
|
HD22
|
A:LEU161
|
3.2
|
29.8
|
1.0
|
HE2
|
A:TYR83
|
3.3
|
24.3
|
1.0
|
HB3
|
A:LEU161
|
3.3
|
22.2
|
1.0
|
HD13
|
A:LEU161
|
3.3
|
29.5
|
1.0
|
O
|
A:HOH370
|
3.5
|
22.0
|
1.0
|
O
|
A:HOH343
|
3.5
|
41.9
|
1.0
|
C3
|
A:GOL211
|
3.5
|
51.6
|
1.0
|
CD2
|
A:LEU111
|
3.8
|
18.2
|
1.0
|
HD3
|
A:ARG97
|
3.9
|
28.7
|
1.0
|
CE2
|
A:TYR83
|
3.9
|
20.3
|
1.0
|
CZ
|
A:TYR83
|
4.0
|
19.7
|
1.0
|
CB
|
A:LEU111
|
4.0
|
15.8
|
1.0
|
CD1
|
A:LEU111
|
4.0
|
17.8
|
1.0
|
CD2
|
A:LEU161
|
4.1
|
24.8
|
1.0
|
CG
|
A:LEU111
|
4.1
|
16.3
|
1.0
|
CB
|
A:LEU161
|
4.2
|
18.5
|
1.0
|
CD1
|
A:LEU161
|
4.2
|
24.6
|
1.0
|
HH11
|
A:ARG97
|
4.3
|
49.4
|
1.0
|
HD21
|
A:LEU111
|
4.3
|
21.8
|
1.0
|
O3
|
A:GOL211
|
4.3
|
38.1
|
1.0
|
HD23
|
A:LEU111
|
4.4
|
21.8
|
1.0
|
CG
|
A:LEU161
|
4.4
|
22.2
|
1.0
|
HD11
|
A:LEU111
|
4.5
|
21.4
|
1.0
|
C2
|
A:GOL211
|
4.5
|
71.6
|
1.0
|
HB2
|
A:HIS115
|
4.6
|
19.5
|
1.0
|
O
|
A:HOH401
|
4.6
|
24.6
|
1.0
|
HB2
|
A:LEU111
|
4.6
|
18.9
|
1.0
|
HD12
|
A:LEU111
|
4.6
|
21.4
|
1.0
|
HG2
|
A:ARG97
|
4.6
|
25.5
|
1.0
|
HD21
|
A:LEU161
|
4.6
|
29.8
|
1.0
|
HB2
|
A:LEU161
|
4.7
|
22.2
|
1.0
|
HD23
|
A:LEU161
|
4.7
|
29.8
|
1.0
|
HD11
|
A:LEU161
|
4.7
|
29.5
|
1.0
|
HA
|
A:LEU111
|
4.7
|
17.8
|
1.0
|
NH1
|
A:ARG97
|
4.7
|
41.2
|
1.0
|
HD12
|
A:LEU161
|
4.8
|
29.5
|
1.0
|
O
|
A:HOH422
|
4.8
|
38.5
|
1.0
|
CD
|
A:ARG97
|
4.9
|
23.9
|
1.0
|
O
|
A:LEU111
|
4.9
|
14.6
|
1.0
|
CA
|
A:LEU111
|
4.9
|
14.8
|
1.0
|
HD11
|
A:ILE100
|
4.9
|
29.1
|
1.0
|
O2
|
A:GOL211
|
4.9
|
77.3
|
1.0
|
HB2
|
A:ALA165
|
5.0
|
22.1
|
1.0
|
|
Chlorine binding site 2 out
of 3 in 6dpp
Go back to
Chlorine Binding Sites List in 6dpp
Chlorine binding site 2 out
of 3 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
![](/pictures/CL/pdb/dp/6dpp-CL-sphere_02.jpg) Mono view
![](/pictures/CL/pdb/dp/6dpp-CL-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl 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:Cl207
b:38.4
occ:0.50
|
O
|
A:HOH440
|
2.7
|
39.0
|
1.0
|
O
|
A:HOH360
|
2.9
|
26.5
|
1.0
|
HB2
|
A:LYS180
|
3.1
|
25.4
|
1.0
|
HA
|
A:GLN134
|
3.2
|
24.7
|
1.0
|
HD12
|
A:ILE137
|
3.2
|
24.3
|
1.0
|
HD3
|
A:LYS180
|
3.3
|
28.6
|
1.0
|
HG21
|
A:ILE137
|
3.4
|
27.7
|
1.0
|
HG3
|
A:GLN134
|
3.4
|
33.3
|
1.0
|
HD13
|
A:ILE137
|
3.5
|
24.3
|
1.0
|
HB
|
A:ILE137
|
3.6
|
22.6
|
1.0
|
CD1
|
A:ILE137
|
3.8
|
20.3
|
1.0
|
CB
|
A:LYS180
|
4.1
|
21.2
|
1.0
|
CG2
|
A:ILE137
|
4.1
|
23.1
|
1.0
|
CA
|
A:GLN134
|
4.1
|
20.6
|
1.0
|
HG22
|
A:ILE137
|
4.2
|
27.7
|
1.0
|
O
|
A:HOH368
|
4.2
|
35.0
|
1.0
|
CD
|
A:LYS180
|
4.2
|
23.8
|
1.0
|
CB
|
A:ILE137
|
4.2
|
18.9
|
1.0
|
HG2
|
A:LYS180
|
4.2
|
30.0
|
1.0
|
CG
|
A:GLN134
|
4.3
|
27.8
|
1.0
|
O
|
A:HOH439
|
4.4
|
51.9
|
1.0
|
CG
|
A:LYS180
|
4.4
|
25.0
|
1.0
|
HB3
|
A:LYS180
|
4.5
|
25.4
|
1.0
|
HB2
|
A:GLN134
|
4.5
|
29.0
|
1.0
|
CB
|
A:GLN134
|
4.5
|
24.1
|
1.0
|
O
|
A:GLN134
|
4.6
|
21.7
|
1.0
|
HD11
|
A:ILE137
|
4.6
|
24.3
|
1.0
|
HG2
|
A:GLN134
|
4.6
|
33.3
|
1.0
|
O
|
A:HOH434
|
4.6
|
45.2
|
1.0
|
CG1
|
A:ILE137
|
4.6
|
17.7
|
1.0
|
O
|
A:HOH419
|
4.8
|
34.5
|
1.0
|
HD2
|
A:LYS180
|
4.8
|
28.6
|
1.0
|
C
|
A:GLN134
|
4.9
|
21.8
|
1.0
|
HE3
|
A:LYS180
|
4.9
|
29.9
|
1.0
|
HG23
|
A:ILE137
|
4.9
|
27.7
|
1.0
|
HA
|
A:LYS180
|
4.9
|
22.0
|
1.0
|
CE
|
A:LYS180
|
5.0
|
24.9
|
1.0
|
HE2
|
A:LYS180
|
5.0
|
29.9
|
1.0
|
|
Chlorine binding site 3 out
of 3 in 6dpp
Go back to
Chlorine Binding Sites List in 6dpp
Chlorine binding site 3 out
of 3 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
![](/pictures/CL/pdb/dp/6dpp-CL-sphere_03.jpg) Mono view
![](/pictures/CL/pdb/dp/6dpp-CL-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 3 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:Cl208
b:39.7
occ:0.75
|
O
|
A:HOH447
|
2.8
|
36.6
|
1.0
|
HG3
|
A:PRO128
|
3.2
|
29.7
|
1.0
|
HD11
|
A:LEU179
|
3.2
|
25.6
|
1.0
|
HB3
|
A:PRO128
|
3.2
|
24.0
|
1.0
|
CG
|
A:PRO177
|
3.6
|
22.4
|
1.0
|
HD21
|
A:LEU179
|
3.7
|
28.4
|
1.0
|
CB
|
A:PRO177
|
3.7
|
21.4
|
1.0
|
CD1
|
A:ILE64
|
3.8
|
36.1
|
1.0
|
CG
|
A:PRO128
|
3.9
|
24.8
|
1.0
|
CB
|
A:PRO128
|
3.9
|
20.0
|
1.0
|
CD1
|
A:LEU179
|
4.2
|
21.3
|
1.0
|
HD3
|
A:PRO128
|
4.3
|
20.0
|
1.0
|
HB2
|
A:PRO128
|
4.3
|
24.0
|
1.0
|
CD2
|
A:LEU179
|
4.5
|
23.6
|
1.0
|
HD13
|
A:LEU179
|
4.5
|
25.6
|
1.0
|
HG2
|
A:PRO128
|
4.7
|
29.7
|
1.0
|
CD
|
A:PRO128
|
4.7
|
16.6
|
1.0
|
CD
|
A:PRO177
|
4.7
|
19.3
|
1.0
|
HD12
|
A:LEU179
|
4.7
|
25.6
|
1.0
|
HG
|
A:LEU179
|
4.7
|
25.1
|
1.0
|
CG
|
A:LEU179
|
4.8
|
20.9
|
1.0
|
HD22
|
A:LEU179
|
4.8
|
28.4
|
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: Sat Jul 27 21:45:42 2024
|