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Iodine in PDB 6doc: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 200 Mm K+ 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 2 Mm MG2+ and 200 Mm K+ 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 2 Mm MG2+ and 200 Mm K+ 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 2 Mm MG2+ and 200 Mm K+ For 240 S at 21 C, PDB code: 6doc 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) 23.47 / 1.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 81.379, 37.942, 61.905, 90.00, 96.31, 90.00
R / Rfree (%) 18.8 / 22.1

Other elements in 6doc:

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 240 S at 21 C also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Potassium (K) 3 atoms

Iodine Binding Sites:

The binding sites of Iodine 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 240 S at 21 C (pdb code 6doc). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 4 binding sites of Iodine 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 240 S at 21 C, PDB code: 6doc:
Jump to Iodine binding site number: 1; 2; 3; 4;

Iodine binding site 1 out of 4 in 6doc

Go back to Iodine Binding Sites List in 6doc
Iodine binding site 1 out of 4 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 240 S at 21 C


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I 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 240 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I204

b:15.7
occ:0.45
HH A:TYR83 2.5 26.0 1.0
HD22 A:LEU161 3.2 32.1 1.0
OH A:TYR83 3.3 21.6 1.0
HB3 A:LEU161 3.3 23.2 1.0
HE2 A:TYR83 3.4 17.1 1.0
HD22 A:LEU111 3.4 21.8 1.0
HD3 A:ARG97 3.4 23.5 1.0
HD13 A:LEU111 3.5 18.2 1.0
HD13 A:LEU161 3.5 31.0 1.0
O A:HOH385 3.5 24.0 1.0
O A:HOH349 3.5 48.9 1.0
HB3 A:LEU111 3.5 14.9 1.0
O A:HOH345 3.7 18.4 1.0
HH11 A:ARG97 3.8 33.8 1.0
CE2 A:TYR83 4.1 14.3 1.0
CD2 A:LEU161 4.1 26.7 1.0
CZ A:TYR83 4.1 16.6 1.0
O3 A:GOL212 4.2 26.4 1.0
CB A:LEU161 4.2 19.4 1.0
CD2 A:LEU111 4.3 18.2 1.0
NH1 A:ARG97 4.3 28.2 1.0
CD1 A:LEU161 4.3 25.8 1.0
CD1 A:LEU111 4.3 15.2 1.0
C3 A:GOL212 4.4 48.8 1.0
CD A:ARG97 4.4 19.6 1.0
CB A:LEU111 4.4 12.4 1.0
CG A:LEU161 4.4 20.8 1.0
HG2 A:ARG97 4.5 20.2 1.0
O A:HOH326 4.6 40.1 1.0
HD23 A:LEU161 4.6 32.1 1.0
CG A:LEU111 4.6 12.9 1.0
HD21 A:LEU161 4.6 32.1 1.0
HH12 A:ARG97 4.6 33.8 1.0
HB2 A:LEU161 4.7 23.2 1.0
HB2 A:HIS115 4.7 17.2 1.0
HD11 A:ILE100 4.7 24.0 1.0
HD21 A:LEU111 4.8 21.8 1.0
HD11 A:LEU161 4.8 31.0 1.0
HD11 A:LEU111 4.8 18.2 1.0
O A:HOH393 4.8 20.5 1.0
HD23 A:LEU111 4.8 21.8 1.0
HD2 A:ARG97 4.9 23.5 1.0
HD12 A:LEU161 4.9 31.0 1.0
HD12 A:LEU111 4.9 18.2 1.0
CZ A:ARG97 5.0 28.9 1.0
NE A:ARG97 5.0 23.0 1.0
HB2 A:LEU111 5.0 14.9 1.0

Iodine binding site 2 out of 4 in 6doc

Go back to Iodine Binding Sites List in 6doc
Iodine binding site 2 out of 4 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 240 S at 21 C


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I 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 240 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I205

b:33.0
occ:0.40
HD3 A:LYS180 3.1 27.8 1.0
O A:HOH371 3.2 24.1 1.0
HG3 A:GLN134 3.2 27.3 1.0
HB2 A:LYS180 3.3 19.4 1.0
O A:HOH450 3.3 37.5 1.0
HA A:GLN134 3.3 20.2 1.0
O4 A:PGE216 3.5 38.1 1.0
C6 A:PGE216 3.5 59.1 1.0
HD12 A:ILE137 3.7 22.8 1.0
HG2 A:LYS180 3.9 23.6 1.0
O A:HOH454 3.9 50.4 1.0
CD A:LYS180 4.0 23.2 1.0
HG21 A:ILE137 4.0 19.3 1.0
CB A:LYS180 4.1 16.1 1.0
CG A:GLN134 4.1 22.8 1.0
HB A:ILE137 4.2 17.1 1.0
CG A:LYS180 4.2 19.6 1.0
HD13 A:ILE137 4.2 22.8 1.0
CA A:GLN134 4.2 16.8 1.0
HB2 A:GLN134 4.3 21.9 1.0
CD1 A:ILE137 4.4 19.0 1.0
HE21 A:GLN134 4.5 34.7 1.0
CB A:GLN134 4.5 18.2 1.0
O A:HOH449 4.5 41.7 1.0
HE3 A:LYS180 4.5 25.0 1.0
HB3 A:LYS180 4.5 19.4 1.0
HG2 A:GLN134 4.6 27.3 1.0
HD2 A:LYS180 4.7 27.8 1.0
CE A:LYS180 4.7 20.8 1.0
CG2 A:ILE137 4.7 16.1 1.0
HE2 A:LYS180 4.7 25.0 1.0
HG22 A:ILE137 4.8 19.3 1.0
CB A:ILE137 4.8 14.2 1.0
O A:GLN134 4.9 19.4 1.0

Iodine binding site 3 out of 4 in 6doc

Go back to Iodine Binding Sites List in 6doc
Iodine binding site 3 out of 4 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 240 S at 21 C


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I 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 200 Mm K+ For 240 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I206

b:30.5
occ:0.30
O A:HOH456 2.8 37.7 1.0
HD13 A:ILE64 2.9 45.1 1.0
HD11 A:LEU179 3.1 22.3 1.0
HG2 A:PRO177 3.1 21.5 1.0
HG3 A:PRO128 3.3 23.8 1.0
HB3 A:PRO128 3.4 23.0 1.0
HB2 A:PRO177 3.5 19.6 1.0
CD1 A:ILE64 3.5 37.6 1.0
HD11 A:ILE64 3.6 45.1 1.0
HD12 A:ILE64 3.7 45.1 1.0
HD21 A:LEU179 3.8 23.2 1.0
HB3 A:PRO177 3.9 19.6 1.0
CG A:PRO177 3.9 17.9 1.0
CB A:PRO177 3.9 16.4 1.0
CD1 A:LEU179 4.1 18.6 1.0
CG A:PRO128 4.1 19.8 1.0
CB A:PRO128 4.1 19.2 1.0
HG21 A:ILE64 4.2 25.9 1.0
HD13 A:LEU179 4.4 22.3 1.0
HG3 A:PRO177 4.4 21.5 1.0
HB2 A:PRO128 4.4 23.0 1.0
HD3 A:PRO128 4.5 19.7 1.0
CD2 A:LEU179 4.6 19.4 1.0
HD12 A:LEU179 4.6 22.3 1.0
HG2 A:PRO128 4.8 23.8 1.0
HD2 A:PRO177 4.8 20.9 1.0
CG A:LEU179 4.8 18.8 1.0
HG A:LEU179 4.8 22.5 1.0
HD22 A:LEU179 4.8 23.2 1.0
CG1 A:ILE64 4.9 22.8 1.0
CD A:PRO128 4.9 16.4 1.0
CD A:PRO177 5.0 17.4 1.0

Iodine binding site 4 out of 4 in 6doc

Go back to Iodine Binding Sites List in 6doc
Iodine binding site 4 out of 4 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 240 S at 21 C


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 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 240 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I207

b:44.1
occ:0.35
HD2 A:HIS172 2.9 20.1 1.0
O A:HOH336 3.5 37.0 1.0
HE3 A:LYS121 3.7 35.9 1.0
CD2 A:HIS172 3.7 16.7 1.0
HE2 A:LYS121 3.8 35.9 1.0
O A:HOH409 4.0 29.5 1.0
O A:HOH435 4.0 42.4 1.0
NE2 A:HIS172 4.1 21.0 1.0
CE A:LYS121 4.2 29.9 1.0
O A:HOH407 4.2 35.3 1.0
HD3 A:LYS121 4.4 24.1 1.0
CD A:LYS121 4.9 20.1 1.0
CG A:HIS172 5.0 17.5 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 Aug 11 22:53:39 2024

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