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Iodine in PDB 6dp4: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 20 Mm MG2+ and 75 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 20 Mm MG2+ and 75 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 20 Mm MG2+ and 75 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 20 Mm MG2+ and 75 Mm K+ For 40 S at 21 C, PDB code: 6dp4 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) 19.92 / 1.37
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 81.525, 37.674, 62.050, 90.00, 96.52, 90.00
R / Rfree (%) 15.7 / 17.6

Other elements in 6dp4:

The structure of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 20 Mm MG2+ and 75 Mm K+ For 40 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 20 Mm MG2+ and 75 Mm K+ For 40 S at 21 C (pdb code 6dp4). 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 20 Mm MG2+ and 75 Mm K+ For 40 S at 21 C, PDB code: 6dp4:
Jump to Iodine binding site number: 1; 2; 3;

Iodine binding site 1 out of 3 in 6dp4

Go back to Iodine Binding Sites List in 6dp4
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 20 Mm MG2+ and 75 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 20 Mm MG2+ and 75 Mm K+ For 40 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I205

b:19.4
occ:0.50
HH A:TYR83 2.5 23.6 1.0
HD22 A:LEU161 3.2 28.3 1.0
O A:HOH342 3.2 34.5 1.0
HE2 A:TYR83 3.3 20.3 1.0
OH A:TYR83 3.3 19.7 1.0
HD22 A:LEU111 3.3 20.0 1.0
HB3 A:LEU161 3.4 20.7 1.0
HD13 A:LEU161 3.4 27.0 1.0
HD13 A:LEU111 3.4 19.1 1.0
HB3 A:LEU111 3.4 18.2 1.0
HD3 A:ARG97 3.5 27.6 1.0
O A:HOH386 3.5 21.0 1.0
O A:HOH366 3.6 19.2 1.0
C3 A:GOL212 3.8 68.7 1.0
HH11 A:ARG97 3.8 36.6 1.0
CE2 A:TYR83 4.0 16.9 1.0
CZ A:TYR83 4.1 16.9 1.0
CD2 A:LEU161 4.1 23.6 1.0
CD2 A:LEU111 4.2 16.6 1.0
CD1 A:LEU161 4.2 22.5 1.0
CB A:LEU161 4.3 17.2 1.0
CD1 A:LEU111 4.3 15.9 1.0
O3 A:GOL212 4.3 30.1 1.0
NH1 A:ARG97 4.3 30.5 1.0
CB A:LEU111 4.3 15.2 1.0
CG A:LEU161 4.4 19.9 1.0
CD A:ARG97 4.4 23.0 1.0
HG2 A:ARG97 4.4 23.2 1.0
CG A:LEU111 4.5 15.4 1.0
O A:HOH356 4.6 37.2 1.0
HD21 A:LEU161 4.6 28.3 1.0
HH12 A:ARG97 4.6 36.6 1.0
HD23 A:LEU161 4.7 28.3 1.0
HB2 A:HIS115 4.7 17.6 1.0
HD11 A:LEU161 4.7 27.0 1.0
HD21 A:LEU111 4.7 20.0 1.0
HB2 A:LEU161 4.8 20.7 1.0
HD11 A:LEU111 4.8 19.1 1.0
HD11 A:ILE100 4.8 27.4 1.0
HD23 A:LEU111 4.8 20.0 1.0
HD12 A:LEU161 4.9 27.0 1.0
HB2 A:LEU111 4.9 18.2 1.0
HD12 A:LEU111 4.9 19.1 1.0
O A:HOH401 4.9 21.6 1.0
O A:HOH353 5.0 21.9 1.0
CG A:ARG97 5.0 19.3 1.0
C2 A:GOL212 5.0 0.1 1.0
HD2 A:ARG97 5.0 27.6 1.0

Iodine binding site 2 out of 3 in 6dp4

Go back to Iodine Binding Sites List in 6dp4
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 20 Mm MG2+ and 75 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 20 Mm MG2+ and 75 Mm K+ For 40 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I206

b:46.6
occ:0.40
O A:HOH445 3.1 36.8 1.0
HD3 A:LYS180 3.2 27.1 1.0
O A:HOH361 3.2 24.8 1.0
HB2 A:LYS180 3.2 24.3 1.0
HG3 A:GLN134 3.2 35.6 1.0
HA A:GLN134 3.2 22.8 1.0
O A:HOH370 3.6 37.1 1.0
HD12 A:ILE137 3.7 23.7 1.0
HG2 A:LYS180 3.9 28.9 1.0
HG21 A:ILE137 4.0 24.9 1.0
HD13 A:ILE137 4.0 23.7 1.0
CD A:LYS180 4.0 22.6 1.0
CB A:LYS180 4.0 20.3 1.0
CG A:GLN134 4.1 29.6 1.0
CA A:GLN134 4.1 19.0 1.0
O A:HOH446 4.1 51.4 1.0
HB A:ILE137 4.2 21.1 1.0
HB2 A:GLN134 4.2 31.1 1.0
CG A:LYS180 4.2 24.1 1.0
CD1 A:ILE137 4.3 19.7 1.0
CB A:GLN134 4.3 26.0 1.0
HB3 A:LYS180 4.4 24.3 1.0
O A:HOH444 4.5 39.8 1.0
HE21 A:GLN134 4.6 46.6 1.0
HE3 A:LYS180 4.6 28.1 1.0
HG2 A:GLN134 4.6 35.6 1.0
CG2 A:ILE137 4.7 20.7 1.0
HD2 A:LYS180 4.7 27.1 1.0
CE A:LYS180 4.8 23.4 1.0
HG22 A:ILE137 4.8 24.9 1.0
CB A:ILE137 4.8 17.6 1.0
HE2 A:LYS180 4.8 28.1 1.0
O A:GLN134 4.8 20.6 1.0
HD11 A:ILE137 5.0 23.7 1.0

Iodine binding site 3 out of 3 in 6dp4

Go back to Iodine Binding Sites List in 6dp4
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 20 Mm MG2+ and 75 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 20 Mm MG2+ and 75 Mm K+ For 40 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I207

b:39.8
occ:0.30
O A:HOH457 2.8 31.3 1.0
HG2 A:PRO177 2.9 25.1 1.0
HD13 A:ILE64 3.1 44.8 1.0
HD11 A:LEU179 3.1 26.1 1.0
HG3 A:PRO128 3.2 23.8 1.0
HB3 A:PRO128 3.3 22.2 1.0
HB2 A:PRO177 3.4 23.2 1.0
HD21 A:LEU179 3.7 26.7 1.0
CG A:PRO177 3.7 20.9 1.0
CD1 A:ILE64 3.8 37.3 1.0
HD12 A:ILE64 3.8 44.8 1.0
CB A:PRO177 3.8 19.3 1.0
HB3 A:PRO177 3.8 23.2 1.0
HD11 A:ILE64 3.9 44.8 1.0
CG A:PRO128 4.0 19.9 1.0
CB A:PRO128 4.0 18.5 1.0
CD1 A:LEU179 4.1 21.8 1.0
HG3 A:PRO177 4.2 25.1 1.0
HD3 A:PRO128 4.3 20.5 1.0
HB2 A:PRO128 4.4 22.2 1.0
HG21 A:ILE64 4.4 31.9 1.0
HD13 A:LEU179 4.4 26.1 1.0
CD2 A:LEU179 4.5 22.2 1.0
HD12 A:LEU179 4.6 26.1 1.0
HD2 A:PRO177 4.7 22.1 1.0
HG A:LEU179 4.7 24.2 1.0
CG A:LEU179 4.7 20.1 1.0
HG2 A:PRO128 4.7 23.8 1.0
CD A:PRO128 4.7 17.1 1.0
HD22 A:LEU179 4.8 26.7 1.0
CD A:PRO177 4.8 18.4 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: Sun Dec 13 19:43:31 2020

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