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Iodine in PDB 6dp3: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 10 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 10 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 10 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 10 Mm MG2+ and 75 Mm K+ For 40 S at 21 C, PDB code: 6dp3 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) 19.09 / 1.46
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 81.530, 38.108, 61.723, 90.00, 96.04, 90.00
R / Rfree (%) 17.1 / 19.8

Other elements in 6dp3:

The structure of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 10 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 10 Mm MG2+ and 75 Mm K+ For 40 S at 21 C (pdb code 6dp3). 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 10 Mm MG2+ and 75 Mm K+ For 40 S at 21 C, PDB code: 6dp3:
Jump to Iodine binding site number: 1; 2; 3;

Iodine binding site 1 out of 3 in 6dp3

Go back to Iodine Binding Sites List in 6dp3
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 10 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 10 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:42.1
occ:0.40
O A:HOH370 3.2 43.6 1.0
O A:HOH353 3.3 40.2 1.0
HG3 A:GLN134 3.3 87.6 1.0
HB2 A:LYS180 3.3 26.6 1.0
HA A:GLN134 3.3 23.0 1.0
HD3 A:LYS180 3.3 26.5 1.0
HD12 A:ILE137 3.7 26.0 1.0
HG2 A:LYS180 3.8 31.6 1.0
HB2 A:GLN134 3.8 31.9 1.0
C3 A:GOL220 3.8 57.2 1.0
CD A:LYS180 4.1 22.1 1.0
CB A:LYS180 4.1 22.2 1.0
CG A:GLN134 4.1 73.0 1.0
CA A:GLN134 4.1 19.2 1.0
HD13 A:ILE137 4.1 26.0 1.0
O2 A:GOL220 4.2 69.9 1.0
CB A:GLN134 4.2 26.6 1.0
CG A:LYS180 4.2 26.4 1.0
HG21 A:ILE137 4.2 23.7 1.0
HE3 A:LYS180 4.3 26.9 1.0
HB A:ILE137 4.3 19.5 1.0
CD1 A:ILE137 4.4 21.7 1.0
HE21 A:GLN134 4.4 0.8 1.0
HB3 A:LYS180 4.4 26.6 1.0
C2 A:GOL220 4.7 60.8 1.0
CE A:LYS180 4.7 22.5 1.0
HG2 A:GLN134 4.7 87.6 1.0
HD2 A:LYS180 4.9 26.5 1.0
HE2 A:LYS180 4.9 26.9 1.0
O A:HOH385 4.9 48.7 1.0
O3 A:GOL220 4.9 56.0 1.0
NE2 A:GLN134 4.9 91.5 1.0
CG2 A:ILE137 4.9 19.7 1.0
O A:GLN134 4.9 21.8 1.0
CD A:GLN134 5.0 0.1 1.0
CB A:ILE137 5.0 16.3 1.0

Iodine binding site 2 out of 3 in 6dp3

Go back to Iodine Binding Sites List in 6dp3
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 10 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 10 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:76.5
occ:0.30
HD13 A:ILE64 3.2 53.8 1.0
HG2 A:PRO177 3.5 30.7 1.0
HD11 A:ILE64 3.6 53.8 1.0
HD11 A:LEU179 3.6 27.5 1.0
HG3 A:PRO128 3.7 33.0 1.0
CD1 A:ILE64 3.8 44.8 1.0
HD12 A:ILE64 4.0 53.8 1.0
HB2 A:PRO177 4.1 25.4 1.0
HD21 A:LEU179 4.1 30.4 1.0
HB3 A:PRO128 4.2 25.2 1.0
CG A:PRO177 4.3 25.6 1.0
HB3 A:PRO177 4.3 25.4 1.0
CB A:PRO177 4.4 21.2 1.0
CD1 A:LEU179 4.6 22.9 1.0
CG A:PRO128 4.6 27.5 1.0
HG3 A:PRO177 4.6 30.7 1.0
HG21 A:ILE64 4.7 35.3 1.0
HD13 A:LEU179 4.8 27.5 1.0
CB A:PRO128 4.9 21.0 1.0
CD2 A:LEU179 4.9 25.3 1.0

Iodine binding site 3 out of 3 in 6dp3

Go back to Iodine Binding Sites List in 6dp3
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 10 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 10 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:64.1
occ:0.35
HD2 A:HIS172 3.0 27.6 1.0
HE3 A:LYS121 3.1 38.6 1.0
HE2 A:LYS121 3.6 38.6 1.0
CD2 A:HIS172 3.8 23.0 1.0
CE A:LYS121 3.8 32.2 1.0
O A:HOH373 3.9 46.0 1.0
O A:HOH362 3.9 55.9 1.0
O1 A:EDO214 4.2 58.8 1.0
NE2 A:HIS172 4.2 27.2 1.0
HD3 A:LYS121 4.2 34.2 1.0
CD A:LYS121 4.6 28.5 1.0
HG2 A:LYS121 4.6 30.2 1.0
HZ1 A:LYS121 4.7 35.4 1.0
NZ A:LYS121 4.9 29.5 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 22:59:43 2024

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