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Iodine 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
Manganese (Mn) 4 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 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 Iodine atom.
In total 3 binding sites of Iodine 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 Iodine binding site number: 1; 2; 3;

Iodine binding site 1 out of 3 in 6dp7

Go back to Iodine Binding Sites List in 6dp7
Iodine binding site 1 out of 3 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 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 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:I205

b:18.4
occ:0.25
HH A:TYR83 2.4 25.2 1.0
HD22 A:LEU161 3.1 32.4 1.0
HD22 A:LEU111 3.1 20.2 1.0
O A:HOH360 3.2 57.1 1.0
OH A:TYR83 3.3 21.0 1.0
HE2 A:TYR83 3.3 21.3 1.0
O A:HOH362 3.3 20.9 1.0
HB3 A:LEU161 3.3 19.4 1.0
HB3 A:LEU111 3.3 19.4 1.0
HD13 A:LEU111 3.3 20.1 1.0
HD13 A:LEU161 3.4 29.3 1.0
O A:HOH340 3.4 20.0 1.0
HD3 A:ARG97 3.6 29.6 1.0
CE2 A:TYR83 4.0 17.8 1.0
CD2 A:LEU161 4.0 27.0 1.0
CD2 A:LEU111 4.1 16.8 1.0
CZ A:TYR83 4.1 17.8 1.0
O A:HOH342 4.1 41.9 1.0
HH11 A:ARG97 4.1 39.4 1.0
CB A:LEU161 4.2 16.2 1.0
CD1 A:LEU111 4.2 16.7 1.0
CB A:LEU111 4.2 16.1 1.0
CD1 A:LEU161 4.2 24.4 1.0
CG A:LEU161 4.4 20.1 1.0
CG A:LEU111 4.4 15.2 1.0
CD A:ARG97 4.5 24.7 1.0
HG2 A:ARG97 4.6 24.9 1.0
HD21 A:LEU161 4.6 32.4 1.0
HB2 A:HIS115 4.6 18.2 1.0
HD23 A:LEU161 4.6 32.4 1.0
HD21 A:LEU111 4.6 20.2 1.0
HD23 A:LEU111 4.6 20.2 1.0
O A:HOH379 4.6 26.7 1.0
NH1 A:ARG97 4.7 32.8 1.0
HD11 A:LEU111 4.7 20.1 1.0
HD11 A:LEU161 4.7 29.3 1.0
HB2 A:LEU161 4.7 19.4 1.0
HB2 A:LEU111 4.8 19.4 1.0
HD12 A:LEU111 4.8 20.1 1.0
HD12 A:LEU161 4.9 29.3 1.0
HD11 A:ILE100 4.9 29.9 1.0
O A:HOH365 4.9 33.2 1.0
HA A:LEU111 5.0 16.7 1.0
O A:LEU111 5.0 14.3 1.0

Iodine binding site 2 out of 3 in 6dp7

Go back to Iodine Binding Sites List in 6dp7
Iodine binding site 2 out of 3 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 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 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:I206

b:52.8
occ:0.40
O A:HOH347 3.1 24.4 1.0
HG3 A:GLN134 3.1 37.5 1.0
O A:HOH424 3.2 39.0 1.0
HD3 A:LYS180 3.2 26.3 1.0
HA A:GLN134 3.2 23.1 1.0
HB2 A:LYS180 3.2 22.7 1.0
HD12 A:ILE137 3.6 25.7 1.0
O A:HOH337 3.7 39.0 1.0
O A:HOH423 3.8 60.4 1.0
HG21 A:ILE137 3.9 24.4 1.0
HB2 A:GLN134 4.0 30.6 1.0
HG2 A:LYS180 4.0 27.3 1.0
HD13 A:ILE137 4.0 25.7 1.0
CG A:GLN134 4.0 31.3 1.0
HB A:ILE137 4.0 22.6 1.0
CD A:LYS180 4.1 21.9 1.0
CA A:GLN134 4.1 19.2 1.0
CB A:LYS180 4.1 18.9 1.0
O A:HOH417 4.1 49.7 1.0
CB A:GLN134 4.2 25.5 1.0
CD1 A:ILE137 4.2 21.4 1.0
CG A:LYS180 4.2 22.8 1.0
HB3 A:LYS180 4.5 22.7 1.0
HG2 A:GLN134 4.6 37.5 1.0
HE3 A:LYS180 4.6 28.5 1.0
CG2 A:ILE137 4.6 20.4 1.0
CB A:ILE137 4.7 18.9 1.0
HD2 A:LYS180 4.7 26.3 1.0
HG22 A:ILE137 4.7 24.4 1.0
O A:GLN134 4.8 20.5 1.0
CE A:LYS180 4.8 23.8 1.0
CD A:GLN134 4.9 62.4 1.0
HE2 A:LYS180 4.9 28.5 1.0
HD11 A:ILE137 4.9 25.7 1.0
C A:GLN134 5.0 19.7 1.0
N A:GLN134 5.0 18.1 1.0

Iodine binding site 3 out of 3 in 6dp7

Go back to Iodine Binding Sites List in 6dp7
Iodine binding site 3 out of 3 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 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 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:I207

b:36.4
occ:0.25
O A:HOH431 2.9 45.2 1.0
O A:HOH429 3.0 42.8 1.0
HG2 A:PRO177 3.0 32.2 1.0
HD11 A:LEU179 3.2 26.6 1.0
HB2 A:PRO177 3.5 29.7 1.0
CD1 A:ILE64 3.6 51.7 1.0
HD21 A:LEU179 3.7 28.9 1.0
CG A:PRO177 3.8 26.8 1.0
CG A:PRO128 3.9 20.0 1.0
CB A:PRO177 3.9 24.8 1.0
HB3 A:PRO177 4.0 29.7 1.0
CB A:PRO128 4.0 17.9 1.0
CD1 A:LEU179 4.1 22.2 1.0
HG3 A:PRO177 4.3 32.2 1.0
HD13 A:LEU179 4.5 26.6 1.0
CD2 A:LEU179 4.6 24.1 1.0
HD12 A:LEU179 4.6 26.6 1.0
CD A:PRO128 4.7 18.7 1.0
HD2 A:PRO177 4.7 28.9 1.0
HG A:LEU179 4.8 26.0 1.0
CG A:LEU179 4.8 21.6 1.0
CD A:PRO177 4.9 24.1 1.0
HD22 A:LEU179 4.9 28.9 1.0
O A:HOH428 5.0 47.1 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 23:01:04 2024

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