Manganese in PDB 6dp7: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 500 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 500 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 500 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 500 Mm MN2+ and 200 Mm K+ For 40 S at 21 C, PDB code: 6dp7 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) 17.98 / 1.38
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 82.013, 37.557, 61.932, 90.00, 96.79, 90.00
R / Rfree (%) 16.9 / 19.2

Other elements in 6dp7:

The structure of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 500 Mm MN2+ and 200 Mm K+ For 40 S at 21 C also contains other interesting chemical elements:

Potassium (K) 1 atom
Iodine (I) 3 atoms

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 500 Mm MN2+ and 200 Mm K+ For 40 S at 21 C (pdb code 6dp7). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 500 Mm MN2+ and 200 Mm K+ For 40 S at 21 C, PDB code: 6dp7:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 6dp7

Go back to Manganese Binding Sites List in 6dp7
Manganese binding site 1 out of 4 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 500 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 500 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:18.7
occ:1.00
 OD1 A:ASP192 2.1 22.6 1.0
OD2 A:ASP71 2.1 18.5 1.0
O b:HOH201 2.2 19.0 1.0
O A:HOH341 2.2 21.8 1.0
OP3 b:C5 2.2 20.9 1.0
OP1 b:C5 2.5 18.8 1.0
P b:C5 2.9 20.6 1.0
HA A:ASP192 3.1 23.6 1.0
CG A:ASP71 3.1 18.4 1.0
CG A:ASP192 3.2 22.5 1.0
OD1 A:ASP71 3.5 17.3 1.0
HB2 A:ASP192 3.5 23.7 1.0
H A:TYR193 3.6 27.9 1.0
CB A:ASP192 3.7 19.8 1.0
MN A:MN202 3.8 17.9 1.0
CA A:ASP192 3.8 19.7 1.0
O b:HOH205 3.9 31.4 1.0
MN b:MN101 3.9 22.2 0.3
OP2 b:C5 4.0 20.7 1.0
OP2 b:G6 4.0 24.7 1.0
O5' b:C5 4.0 18.6 1.0
O b:HOH204 4.0 28.3 0.5
HG22 A:ILE189 4.1 23.7 1.0
OD2 A:ASP132 4.1 23.1 1.0
O A:VAL72 4.1 19.2 1.0
OD2 A:ASP192 4.2 25.1 1.0
C5' b:C5 4.3 19.3 1.0
N A:TYR193 4.3 23.3 1.0
OE2 A:GLU188 4.3 40.7 1.0
CB A:ASP71 4.4 14.5 1.0
HD1 A:TYR193 4.6 22.0 1.0
HB3 A:ASP192 4.6 23.7 1.0
C A:ASP192 4.6 22.9 1.0
K A:K204 4.7 32.8 0.4
HG21 A:ILE189 4.7 23.7 1.0
CG2 A:ILE189 4.8 19.7 1.0
N A:ASP192 4.9 17.5 1.0
HG23 A:ILE189 4.9 23.7 1.0
HB2 A:TYR193 5.0 27.3 1.0

Manganese binding site 2 out of 4 in 6dp7

Go back to Manganese Binding Sites List in 6dp7
Manganese binding site 2 out of 4 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 500 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 500 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:17.9
occ:1.00
 OP1 b:C5 2.1 18.8 1.0
OD1 A:ASP71 2.1 17.3 1.0
OE1 A:GLU109 2.1 18.9 1.0
OD1 A:ASP132 2.1 19.1 1.0
OD2 A:ASP132 2.6 23.1 1.0
CG A:ASP132 2.7 19.6 1.0
CD A:GLU109 3.1 16.6 1.0
CG A:ASP71 3.1 18.4 1.0
OE2 A:GLU109 3.3 18.4 1.0
O A:HOH345 3.3 18.0 1.0
P b:C5 3.5 20.6 1.0
O3' B:U4 3.5 37.7 1.0
OD2 A:ASP71 3.5 18.5 1.0
HG12 A:VAL72 3.5 20.0 1.0
C3' B:U4 3.5 23.2 1.0
H A:VAL72 3.8 19.4 1.0
MN A:MN201 3.8 18.7 1.0
O A:HOH341 3.9 21.8 1.0
C5' b:C5 4.0 19.3 1.0
OP2 b:C5 4.1 20.7 1.0
O5' b:C5 4.1 18.6 1.0
CB A:ASP132 4.2 16.7 1.0
H A:ASP132 4.2 18.7 1.0
HB2 A:SER133 4.3 20.2 1.0
CB A:ASP71 4.4 14.5 1.0
OP3 b:C5 4.4 20.9 1.0
HG21 A:ILE189 4.5 23.7 1.0
CG A:GLU109 4.5 18.0 1.0
CG1 A:VAL72 4.5 16.7 1.0
C4' B:U4 4.5 22.5 1.0
N A:VAL72 4.6 16.2 1.0
HG3 A:GLU109 4.6 21.6 1.0
HB2 A:ASP132 4.6 20.0 1.0
HB3 A:ASP132 4.6 20.0 1.0
C2' B:U4 4.7 20.9 1.0
CA A:ASP71 4.7 13.7 1.0
HG13 A:VAL72 4.7 20.0 1.0
HG2 A:GLU109 4.8 21.6 1.0
C5' B:U4 4.8 20.0 1.0
HG11 A:VAL72 4.8 20.0 1.0
CA A:ASP132 4.8 16.8 1.0
O2' B:U4 4.9 28.3 1.0
N A:ASP132 4.9 15.6 1.0
HG22 A:ILE189 4.9 23.7 1.0
C A:ASP132 4.9 16.1 1.0
O A:VAL72 4.9 19.2 1.0
O b:HOH201 5.0 19.0 1.0

Manganese binding site 3 out of 4 in 6dp7

Go back to Manganese Binding Sites List in 6dp7
Manganese binding site 3 out of 4 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 500 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 500 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:14.4
occ:0.55
 O A:HOH355 1.8 32.8 1.0
O A:HOH396 2.1 29.7 1.0
O A:HOH394 2.1 23.2 1.0
O A:HOH332 2.2 28.8 1.0
OE1 A:GLU166 2.2 24.5 1.0
OD1 A:ASP163 2.4 26.9 1.0
CD A:GLU166 3.2 44.6 1.0
HA A:ASP163 3.4 22.8 1.0
OE2 A:GLU166 3.4 24.2 1.0
CG A:ASP163 3.5 52.4 1.0
NH2 A:ARG151 3.9 25.5 1.0
CA A:ASP163 4.2 19.0 1.0
CB A:ASP163 4.2 22.0 1.0
O A:HOH354 4.2 20.5 1.0
HZ3 A:TRP159 4.3 41.5 1.0
HB2 A:GLU166 4.3 22.8 1.0
HB3 A:ASP163 4.3 26.4 1.0
O A:HOH376 4.4 51.3 1.0
OD2 A:ASP163 4.4 30.4 1.0
O A:HOH378 4.5 37.1 1.0
O A:HOH420 4.5 47.1 1.0
HG12 A:VAL162 4.5 24.1 1.0
CG A:GLU166 4.5 19.8 1.0
NZ A:LYS144 4.6 72.7 1.0
CB A:GLU166 4.8 19.0 1.0
HB3 A:GLU166 4.9 22.8 1.0
N A:ASP163 4.9 18.3 1.0
HE3 A:TRP159 5.0 26.9 1.0
HG3 A:GLU166 5.0 23.8 1.0

Manganese binding site 4 out of 4 in 6dp7

Go back to Manganese Binding Sites List in 6dp7
Manganese binding site 4 out of 4 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 500 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 500 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:22.2
occ:0.30
 O b:HOH208 2.1 33.0 0.5
O A:HOH301 2.1 32.5 0.5
O b:HOH204 2.1 28.3 0.5
OP3 b:C5 2.2 20.9 1.0
O b:HOH205 2.5 31.4 1.0
OP2 b:G6 2.6 24.7 1.0
P b:C5 3.4 20.6 1.0
O5' b:C5 3.6 18.6 1.0
O A:ARG195 3.6 73.0 1.0
O A:HOH352 3.6 44.9 1.0
O5' b:G6 3.6 23.2 1.0
P b:G6 3.7 19.9 1.0
OD1 A:ASP192 3.9 22.6 1.0
MN A:MN201 3.9 18.7 1.0
O b:HOH201 3.9 19.0 1.0
OP2 b:C5 3.9 20.7 1.0
C3' b:C5 4.4 19.2 1.0
C5' b:C5 4.4 19.3 1.0
OP1 b:C5 4.5 18.8 1.0
O3' b:C5 4.5 18.9 1.0
C A:ARG195 4.7 47.5 1.0
OP1 b:G6 4.9 19.9 1.0
CG A:ASP192 4.9 22.5 1.0
C4' b:C5 4.9 18.9 1.0
C5' b:G6 4.9 23.6 1.0
N A:ARG195 4.9 34.8 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: Tue Dec 15 04:51:47 2020

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