Manganese in PDB 6dpc: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 12 Mm MN2+ and 200 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 12 Mm MN2+ and 200 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 12 Mm MN2+ and 200 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 12 Mm MN2+ and 200 Mm K+ For 40 S at 21 C, PDB code: 6dpc
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)
|
20.01 /
1.34
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
81.821,
37.426,
61.946,
90.00,
96.83,
90.00
|
R / Rfree (%)
|
14.9 /
18
|
Other elements in 6dpc:
The structure of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 12 Mm MN2+ and 200 Mm K+ For 40 S at 21 C also contains other interesting chemical elements:
Manganese Binding Sites:
The binding sites of Manganese atom in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 12 Mm MN2+ and 200 Mm K+ For 40 S at 21 C
(pdb code 6dpc). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 5 binding sites of Manganese where determined in the
Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 12 Mm MN2+ and 200 Mm K+ For 40 S at 21 C, PDB code: 6dpc:
Jump to Manganese binding site number:
1;
2;
3;
4;
5;
Manganese binding site 1 out
of 5 in 6dpc
Go back to
Manganese Binding Sites List in 6dpc
Manganese binding site 1 out
of 5 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 12 Mm MN2+ and 200 Mm K+ For 40 S at 21 C
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 1 of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 12 Mm MN2+ and 200 Mm K+ For 40 S at 21 C within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn201
b:17.4
occ:1.00
|
OD2
|
A:ASP71
|
2.1
|
16.3
|
1.0
|
OD1
|
A:ASP192
|
2.1
|
18.8
|
1.0
|
O
|
B:HOH201
|
2.1
|
17.3
|
0.3
|
OP3
|
b:C5
|
2.1
|
21.7
|
0.7
|
O
|
A:HOH358
|
2.1
|
18.2
|
1.0
|
O
|
A:HOH325
|
2.2
|
17.8
|
1.0
|
OP1
|
b:C5
|
2.3
|
15.2
|
0.3
|
OP1
|
b:C5
|
2.4
|
29.8
|
0.7
|
P
|
b:C5
|
2.9
|
15.9
|
0.7
|
HA
|
A:ASP192
|
3.1
|
21.6
|
1.0
|
CG
|
A:ASP71
|
3.1
|
16.7
|
1.0
|
CG
|
A:ASP192
|
3.2
|
18.9
|
1.0
|
OD1
|
A:ASP71
|
3.4
|
15.4
|
1.0
|
P
|
b:C5
|
3.5
|
17.9
|
0.3
|
HB2
|
A:ASP192
|
3.5
|
23.6
|
1.0
|
H
|
A:TYR193
|
3.6
|
23.0
|
1.0
|
CB
|
A:ASP192
|
3.7
|
19.7
|
1.0
|
MN
|
A:MN202
|
3.8
|
16.1
|
1.0
|
CA
|
A:ASP192
|
3.8
|
18.0
|
1.0
|
OP2
|
b:C5
|
3.8
|
17.3
|
0.3
|
K
|
A:K205
|
3.9
|
20.4
|
0.1
|
O5'
|
b:C5
|
3.9
|
14.7
|
0.7
|
OP2
|
b:C5
|
3.9
|
18.7
|
0.7
|
OP2
|
b:G6
|
4.0
|
20.5
|
1.0
|
NZ
|
A:LYS196
|
4.0
|
22.2
|
0.7
|
OD2
|
A:ASP132
|
4.0
|
22.7
|
1.0
|
HG22
|
A:ILE189
|
4.1
|
20.7
|
1.0
|
O
|
A:HOH364
|
4.1
|
20.6
|
0.7
|
O
|
A:VAL72
|
4.2
|
16.1
|
1.0
|
C5'
|
b:C5
|
4.2
|
18.9
|
1.0
|
OE2
|
A:GLU188
|
4.3
|
30.4
|
1.0
|
O5'
|
b:C5
|
4.3
|
17.2
|
0.3
|
OD2
|
A:ASP192
|
4.3
|
22.7
|
1.0
|
N
|
A:TYR193
|
4.3
|
19.2
|
1.0
|
CB
|
A:ASP71
|
4.5
|
13.8
|
1.0
|
HD1
|
A:TYR193
|
4.6
|
23.4
|
1.0
|
O
|
A:HOH305
|
4.6
|
17.3
|
0.3
|
O3'
|
B:U4
|
4.6
|
18.2
|
0.3
|
C
|
A:ASP192
|
4.6
|
19.8
|
1.0
|
HB3
|
A:ASP192
|
4.7
|
23.6
|
1.0
|
HG21
|
A:ILE189
|
4.7
|
20.7
|
1.0
|
CG2
|
A:ILE189
|
4.7
|
17.3
|
1.0
|
K
|
B:K102
|
4.9
|
26.6
|
0.4
|
N
|
A:ASP192
|
4.9
|
16.8
|
1.0
|
HG23
|
A:ILE189
|
4.9
|
20.7
|
1.0
|
HB2
|
A:TYR193
|
4.9
|
27.2
|
1.0
|
|
Manganese binding site 2 out
of 5 in 6dpc
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Manganese Binding Sites List in 6dpc
Manganese binding site 2 out
of 5 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 12 Mm MN2+ and 200 Mm K+ For 40 S at 21 C
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 2 of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 12 Mm MN2+ and 200 Mm K+ For 40 S at 21 C within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn202
b:16.1
occ:1.00
|
OD1
|
A:ASP71
|
2.1
|
15.4
|
1.0
|
OD1
|
A:ASP132
|
2.1
|
17.7
|
1.0
|
OE1
|
A:GLU109
|
2.1
|
17.4
|
1.0
|
OP1
|
b:C5
|
2.3
|
15.2
|
0.3
|
OP1
|
b:C5
|
2.4
|
29.8
|
0.7
|
OD2
|
A:ASP132
|
2.5
|
22.7
|
1.0
|
CG
|
A:ASP132
|
2.6
|
18.7
|
1.0
|
O3'
|
B:U4
|
2.6
|
18.2
|
0.3
|
CD
|
A:GLU109
|
3.0
|
15.5
|
1.0
|
P
|
b:C5
|
3.0
|
17.9
|
0.3
|
CG
|
A:ASP71
|
3.1
|
16.7
|
1.0
|
OE2
|
A:GLU109
|
3.2
|
16.2
|
1.0
|
O
|
A:HOH346
|
3.2
|
16.3
|
1.0
|
OD2
|
A:ASP71
|
3.5
|
16.3
|
1.0
|
O3'
|
B:U4
|
3.6
|
17.5
|
0.7
|
HG12
|
A:VAL72
|
3.6
|
19.7
|
1.0
|
C3'
|
B:U4
|
3.6
|
15.9
|
0.7
|
P
|
b:C5
|
3.6
|
15.9
|
0.7
|
MN
|
A:MN201
|
3.8
|
17.4
|
1.0
|
H
|
A:VAL72
|
3.8
|
17.9
|
1.0
|
C3'
|
B:U4
|
3.9
|
29.7
|
0.3
|
O5'
|
b:C5
|
4.0
|
17.2
|
0.3
|
O
|
A:HOH358
|
4.0
|
18.2
|
1.0
|
C5'
|
b:C5
|
4.1
|
18.9
|
1.0
|
CB
|
A:ASP132
|
4.1
|
16.6
|
1.0
|
OP2
|
b:C5
|
4.1
|
18.7
|
0.7
|
H
|
A:ASP132
|
4.1
|
17.5
|
1.0
|
OP2
|
b:C5
|
4.2
|
17.3
|
0.3
|
HB2
|
A:SER133
|
4.3
|
18.6
|
1.0
|
O5'
|
b:C5
|
4.3
|
14.7
|
0.7
|
CB
|
A:ASP71
|
4.4
|
13.8
|
1.0
|
CG
|
A:GLU109
|
4.4
|
13.6
|
1.0
|
HG21
|
A:ILE189
|
4.4
|
20.7
|
1.0
|
C4'
|
B:U4
|
4.4
|
25.6
|
0.3
|
O2'
|
B:U4
|
4.4
|
20.7
|
0.3
|
OP3
|
b:C5
|
4.5
|
21.7
|
0.7
|
CG1
|
A:VAL72
|
4.5
|
16.4
|
1.0
|
HB2
|
A:ASP132
|
4.6
|
19.9
|
1.0
|
HG3
|
A:GLU109
|
4.6
|
16.3
|
1.0
|
HB3
|
A:ASP132
|
4.6
|
19.9
|
1.0
|
C4'
|
B:U4
|
4.6
|
18.7
|
0.7
|
N
|
A:VAL72
|
4.6
|
14.9
|
1.0
|
CA
|
A:ASP71
|
4.7
|
14.7
|
1.0
|
O
|
B:HOH201
|
4.7
|
17.3
|
0.3
|
C2'
|
B:U4
|
4.7
|
16.8
|
0.7
|
HG2
|
A:GLU109
|
4.7
|
16.3
|
1.0
|
C5'
|
B:U4
|
4.7
|
25.0
|
0.3
|
C2'
|
B:U4
|
4.8
|
22.3
|
0.3
|
CA
|
A:ASP132
|
4.8
|
15.7
|
1.0
|
C5'
|
B:U4
|
4.8
|
16.2
|
0.7
|
N
|
A:ASP132
|
4.8
|
14.6
|
1.0
|
HG13
|
A:VAL72
|
4.8
|
19.7
|
1.0
|
C
|
A:ASP132
|
4.9
|
17.1
|
1.0
|
HG22
|
A:ILE189
|
4.9
|
20.7
|
1.0
|
O2'
|
B:U4
|
4.9
|
17.7
|
0.7
|
HG11
|
A:VAL72
|
4.9
|
19.7
|
1.0
|
O
|
A:VAL72
|
4.9
|
16.1
|
1.0
|
K
|
B:K102
|
5.0
|
26.6
|
0.4
|
O
|
A:HOH325
|
5.0
|
17.8
|
1.0
|
|
Manganese binding site 3 out
of 5 in 6dpc
Go back to
Manganese Binding Sites List in 6dpc
Manganese binding site 3 out
of 5 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 12 Mm MN2+ and 200 Mm K+ For 40 S at 21 C
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 3 of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 12 Mm MN2+ and 200 Mm K+ For 40 S at 21 C within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn203
b:18.6
occ:0.40
|
O
|
A:HOH422
|
2.1
|
36.9
|
1.0
|
OE1
|
A:GLU166
|
2.1
|
30.2
|
1.0
|
O
|
A:HOH302
|
2.2
|
63.9
|
1.0
|
OD1
|
A:ASP163
|
2.5
|
25.1
|
1.0
|
O
|
A:HOH331
|
2.6
|
37.7
|
1.0
|
CD
|
A:GLU166
|
3.1
|
23.3
|
1.0
|
HA
|
A:ASP163
|
3.4
|
21.7
|
1.0
|
OE2
|
A:GLU166
|
3.5
|
25.0
|
1.0
|
NZ
|
A:LYS144
|
3.5
|
83.5
|
1.0
|
CG
|
A:ASP163
|
3.6
|
25.3
|
1.0
|
NH2
|
A:ARG151
|
3.8
|
26.3
|
1.0
|
O
|
A:HOH373
|
4.2
|
31.5
|
1.0
|
HZ3
|
A:TRP159
|
4.2
|
25.9
|
1.0
|
HB2
|
A:GLU166
|
4.3
|
21.7
|
1.0
|
CA
|
A:ASP163
|
4.3
|
18.1
|
1.0
|
CB
|
A:ASP163
|
4.3
|
20.2
|
1.0
|
OD2
|
A:ASP163
|
4.4
|
25.1
|
1.0
|
HB3
|
A:ASP163
|
4.4
|
24.2
|
1.0
|
CG
|
A:GLU166
|
4.5
|
19.7
|
1.0
|
HG12
|
A:VAL162
|
4.5
|
24.7
|
1.0
|
CE
|
A:LYS144
|
4.7
|
65.5
|
1.0
|
CB
|
A:GLU166
|
4.8
|
18.1
|
1.0
|
HB3
|
A:GLU166
|
4.8
|
21.7
|
1.0
|
HG3
|
A:GLU166
|
4.8
|
23.7
|
1.0
|
CD
|
A:LYS144
|
4.9
|
64.5
|
1.0
|
HE3
|
A:TRP159
|
5.0
|
24.8
|
1.0
|
CZ3
|
A:TRP159
|
5.0
|
21.6
|
1.0
|
N
|
A:ASP163
|
5.0
|
16.9
|
1.0
|
|
Manganese binding site 4 out
of 5 in 6dpc
Go back to
Manganese Binding Sites List in 6dpc
Manganese binding site 4 out
of 5 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 12 Mm MN2+ and 200 Mm K+ For 40 S at 21 C
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 4 of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 12 Mm MN2+ and 200 Mm K+ For 40 S at 21 C within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn204
b:34.8
occ:0.20
|
O
|
A:LYS196
|
2.5
|
61.5
|
0.7
|
O
|
A:HOH415
|
3.0
|
47.8
|
1.0
|
C
|
A:LYS196
|
3.7
|
52.4
|
0.7
|
MN
|
B:MN101
|
3.9
|
31.0
|
0.2
|
OXT
|
A:LYS196
|
4.2
|
59.0
|
0.7
|
CA
|
A:LYS196
|
4.9
|
44.4
|
0.7
|
|
Manganese binding site 5 out
of 5 in 6dpc
Go back to
Manganese Binding Sites List in 6dpc
Manganese binding site 5 out
of 5 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 12 Mm MN2+ and 200 Mm K+ For 40 S at 21 C
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 5 of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 12 Mm MN2+ and 200 Mm K+ For 40 S at 21 C within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn101
b:31.0
occ:0.20
|
O
|
B:HOH210
|
2.3
|
43.0
|
1.0
|
O6
|
b:G6
|
2.5
|
26.8
|
1.0
|
O
|
B:HOH208
|
2.6
|
48.3
|
1.0
|
C6
|
b:G6
|
3.4
|
25.9
|
1.0
|
N7
|
b:G6
|
3.6
|
27.2
|
1.0
|
C5
|
b:G6
|
3.8
|
22.9
|
1.0
|
MN
|
A:MN204
|
3.9
|
34.8
|
0.2
|
O
|
A:LYS196
|
4.3
|
61.5
|
0.7
|
N4
|
C:DC1
|
4.4
|
28.0
|
1.0
|
O
|
B:HOH213
|
4.6
|
31.7
|
1.0
|
N1
|
b:G6
|
4.7
|
23.3
|
1.0
|
N4
|
b:C5
|
4.8
|
24.8
|
1.0
|
C8
|
b:G6
|
4.8
|
25.3
|
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: Sun Oct 6 04:04:56 2024
|