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Iodine in PDB 6dp2: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 7.5 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 7.5 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 7.5 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 7.5 Mm MG2+ and 75 Mm K+ For 40 S at 21 C, PDB code: 6dp2 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) 20.02 / 1.66
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 81.396, 37.309, 62.340, 90.00, 96.62, 90.00
R / Rfree (%) 15.7 / 19.6

Other elements in 6dp2:

The structure of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 7.5 Mm MG2+ and 75 Mm K+ For 40 S at 21 C also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Potassium (K) 2 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 7.5 Mm MG2+ and 75 Mm K+ For 40 S at 21 C (pdb code 6dp2). 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 7.5 Mm MG2+ and 75 Mm K+ For 40 S at 21 C, PDB code: 6dp2:
Jump to Iodine binding site number: 1; 2; 3; 4;

Iodine binding site 1 out of 4 in 6dp2

Go back to Iodine Binding Sites List in 6dp2
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 7.5 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 7.5 Mm MG2+ and 75 Mm K+ For 40 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I204

b:29.3
occ:0.45
 HH A:TYR83 2.4 39.5 1.0
HD22 A:LEU161 3.0 43.9 1.0
OH A:TYR83 3.2 32.9 1.0
HD13 A:LEU161 3.3 39.3 1.0
O A:HOH330 3.3 44.7 1.0
HB3 A:LEU161 3.3 29.0 1.0
HD22 A:LEU111 3.3 30.9 1.0
HD13 A:LEU111 3.4 30.2 1.0
HE2 A:TYR83 3.4 33.4 1.0
HD3 A:ARG97 3.5 38.1 1.0
O A:HOH378 3.5 34.0 1.0
HB3 A:LEU111 3.5 27.8 1.0
O A:HOH348 3.6 26.5 1.0
C1 A:GOL210 3.8 55.3 1.0
HH11 A:ARG97 3.8 46.9 1.0
CD2 A:LEU161 3.9 36.6 1.0
CE2 A:TYR83 4.1 27.9 1.0
CD1 A:LEU161 4.1 32.8 1.0
CZ A:TYR83 4.1 25.3 1.0
CB A:LEU161 4.2 24.2 1.0
CG A:LEU161 4.3 28.2 1.0
CD2 A:LEU111 4.3 25.8 1.0
CD1 A:LEU111 4.3 25.2 1.0
O1 A:GOL210 4.3 36.1 1.0
NH1 A:ARG97 4.3 39.1 1.0
HG2 A:ARG97 4.3 32.5 1.0
HD21 A:LEU161 4.4 43.9 1.0
CB A:LEU111 4.4 23.2 1.0
CD A:ARG97 4.4 31.8 1.0
HD23 A:LEU161 4.5 43.9 1.0
CG A:LEU111 4.5 24.2 1.0
HD11 A:LEU161 4.6 39.3 1.0
O A:HOH390 4.6 47.1 1.0
HH12 A:ARG97 4.6 46.9 1.0
HB2 A:LEU161 4.7 29.0 1.0
HB2 A:HIS115 4.7 27.4 1.0
HD21 A:LEU111 4.7 30.9 1.0
HD11 A:LEU111 4.8 30.2 1.0
HD12 A:LEU161 4.8 39.3 1.0
HD11 A:ILE100 4.8 38.1 1.0
HD23 A:LEU111 4.8 30.9 1.0
HD12 A:LEU111 4.9 30.2 1.0
CG A:ARG97 4.9 27.1 1.0
O A:HOH392 4.9 31.8 1.0
HB2 A:LEU111 5.0 27.8 1.0
CZ A:ARG97 5.0 39.4 1.0
HD2 A:ARG97 5.0 38.1 1.0
O A:HOH320 5.0 30.4 1.0
HB2 A:ARG97 5.0 34.5 1.0

Iodine binding site 2 out of 4 in 6dp2

Go back to Iodine Binding Sites List in 6dp2
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 7.5 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 7.5 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:69.0
occ:0.40
 O A:HOH352 3.0 29.7 1.0
O A:HOH429 3.1 46.2 1.0
HB2 A:LYS180 3.2 36.3 1.0
HD3 A:LYS180 3.2 36.1 1.0
HG3 A:GLN134 3.2 50.9 1.0
HA A:GLN134 3.2 33.7 1.0
HD12 A:ILE137 3.5 35.5 1.0
HG21 A:ILE137 3.8 33.4 1.0
HD13 A:ILE137 3.8 35.5 1.0
HB A:ILE137 3.9 30.0 1.0
HG2 A:LYS180 4.0 39.2 1.0
O A:HOH427 4.0 60.4 1.0
O A:HOH336 4.0 42.0 1.0
CD A:LYS180 4.0 30.1 1.0
CB A:LYS180 4.1 30.2 1.0
CG A:GLN134 4.1 42.4 1.0
CD1 A:ILE137 4.1 29.6 1.0
CA A:GLN134 4.1 28.1 1.0
CG A:LYS180 4.3 32.6 1.0
O A:HOH424 4.3 49.1 1.0
HG2 A:GLN134 4.4 50.9 1.0
HB2 A:GLN134 4.4 39.8 1.0
CB A:GLN134 4.4 33.2 1.0
CG2 A:ILE137 4.5 27.8 1.0
HE3 A:LYS180 4.5 35.2 1.0
HB3 A:LYS180 4.5 36.3 1.0
HG22 A:ILE137 4.5 33.4 1.0
CB A:ILE137 4.6 25.0 1.0
CE A:LYS180 4.7 29.3 1.0
O A:GLN134 4.7 29.4 1.0
HD2 A:LYS180 4.7 36.1 1.0
HE2 A:LYS180 4.8 35.2 1.0
HD11 A:ILE137 4.9 35.5 1.0
HE21 A:GLN134 4.9 41.5 1.0
C A:GLN134 5.0 31.7 1.0
O A:HOH412 5.0 38.7 1.0
CG1 A:ILE137 5.0 27.4 1.0

Iodine binding site 3 out of 4 in 6dp2

Go back to Iodine Binding Sites List in 6dp2
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 7.5 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 7.5 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:46.4
occ:0.25
 O A:HOH432 2.8 31.8 0.8
HG2 A:PRO177 2.9 36.0 1.0
HD11 A:LEU179 3.1 36.4 1.0
HG3 A:PRO128 3.1 36.8 1.0
HB3 A:PRO128 3.3 31.4 1.0
HB2 A:PRO177 3.4 36.9 1.0
HD21 A:LEU179 3.7 38.5 1.0
CD1 A:ILE64 3.7 42.2 1.0
CG A:PRO177 3.7 30.0 1.0
CB A:PRO177 3.8 30.8 1.0
HB3 A:PRO177 3.8 36.9 1.0
CG A:PRO128 4.0 30.7 1.0
CB A:PRO128 4.0 26.2 1.0
CD1 A:LEU179 4.1 30.3 1.0
HG3 A:PRO177 4.2 36.0 1.0
HD3 A:PRO128 4.3 29.7 1.0
HB2 A:PRO128 4.4 31.4 1.0
HD13 A:LEU179 4.4 36.4 1.0
CD2 A:LEU179 4.5 32.1 1.0
HD2 A:PRO177 4.6 28.5 1.0
HD12 A:LEU179 4.6 36.4 1.0
HG2 A:PRO128 4.7 36.8 1.0
CD A:PRO128 4.7 24.7 1.0
CG A:LEU179 4.7 27.7 1.0
HG A:LEU179 4.7 33.2 1.0
CD A:PRO177 4.8 23.7 1.0
HD22 A:LEU179 4.8 38.5 1.0

Iodine binding site 4 out of 4 in 6dp2

Go back to Iodine Binding Sites List in 6dp2
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 7.5 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 4 of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 7.5 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:0.0
occ:0.35
 HD2 A:HIS172 2.8 39.7 1.0
O A:HOH422 3.0 56.5 1.0
CD2 A:HIS172 3.5 33.1 1.0
O A:HOH307 3.5 50.4 1.0
NE2 A:HIS172 3.8 34.3 1.0
HE3 A:LYS121 3.9 51.1 1.0
O A:HOH420 4.0 58.3 1.0
HE2 A:LYS121 4.0 51.1 1.0
O A:HOH399 4.2 39.7 1.0
O A:HOH375 4.2 44.8 1.0
CE A:LYS121 4.4 42.6 1.0
HD3 A:LYS121 4.8 40.6 1.0
CG A:HIS172 4.8 28.3 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 22:59:17 2024

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