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Iodine in PDB 6doy: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 200 Mm Li+ For 120 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 Li+ For 120 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 Li+ For 120 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 Li+ For 120 S at 21 C, PDB code: 6doy 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) 19.27 / 1.45
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 81.898, 37.350, 62.034, 90.00, 96.81, 90.00
R / Rfree (%) 14.8 / 18.7

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 Li+ For 120 S at 21 C (pdb code 6doy). 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 Li+ For 120 S at 21 C, PDB code: 6doy:
Jump to Iodine binding site number: 1; 2; 3; 4;

Iodine binding site 1 out of 4 in 6doy

Go back to Iodine Binding Sites List in 6doy
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 Li+ For 120 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 Li+ For 120 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I201

b:24.5
occ:0.50
 HH A:TYR83 2.5 31.9 1.0
HD22 A:LEU161 3.1 36.2 1.0
HD13 A:LEU161 3.3 36.2 1.0
HD22 A:LEU111 3.3 27.0 1.0
OH A:TYR83 3.4 26.6 1.0
HD3 A:ARG97 3.4 36.8 1.0
HE2 A:TYR83 3.4 30.0 1.0
HD13 A:LEU111 3.4 25.9 1.0
HB3 A:LEU161 3.4 28.8 1.0
HB3 A:LEU111 3.5 22.1 1.0
O A:HOH393 3.6 31.2 1.0
HH11 A:ARG97 3.7 45.1 1.0
O A:HOH356 3.7 27.4 1.0
CD2 A:LEU161 4.1 30.2 1.0
CE2 A:TYR83 4.1 25.0 1.0
CZ A:TYR83 4.2 24.0 1.0
CD1 A:LEU161 4.2 30.1 1.0
O A:HOH327 4.2 38.5 1.0
NH1 A:ARG97 4.2 37.6 1.0
CD2 A:LEU111 4.2 22.5 1.0
CB A:LEU161 4.3 24.0 1.0
CD1 A:LEU111 4.3 21.6 1.0
CD A:ARG97 4.3 30.6 1.0
CB A:LEU111 4.4 18.4 1.0
CG A:LEU161 4.4 28.1 1.0
HG2 A:ARG97 4.5 28.9 1.0
HD21 A:LEU161 4.5 36.2 1.0
O A:HOH429 4.5 44.7 1.0
CG A:LEU111 4.6 18.8 1.0
HH12 A:ARG97 4.6 45.1 1.0
HD23 A:LEU161 4.6 36.2 1.0
HB2 A:HIS115 4.6 22.9 1.0
O A:HOH402 4.6 32.6 1.0
HD11 A:LEU161 4.7 36.2 1.0
HD21 A:LEU111 4.7 27.0 1.0
HD11 A:LEU111 4.8 25.9 1.0
HD23 A:LEU111 4.8 27.0 1.0
HB2 A:LEU161 4.8 28.8 1.0
HD2 A:ARG97 4.8 36.8 1.0
HD12 A:LEU161 4.8 36.2 1.0
HD11 A:ILE100 4.9 32.0 1.0
HD12 A:LEU111 4.9 25.9 1.0
HB2 A:LEU111 4.9 22.1 1.0
CG A:ARG97 5.0 24.1 1.0
CZ A:ARG97 5.0 37.0 1.0
O A:HOH348 5.0 29.0 1.0
HB2 A:ARG97 5.0 29.9 1.0
NE A:ARG97 5.0 31.1 1.0

Iodine binding site 2 out of 4 in 6doy

Go back to Iodine Binding Sites List in 6doy
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 Li+ For 120 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 Li+ For 120 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I202

b:32.3
occ:0.55
 HD3 A:LYS180 3.2 27.4 1.0
HB2 A:LYS180 3.3 28.3 1.0
HA A:GLN134 3.3 28.1 1.0
O A:HOH357 3.3 28.5 1.0
HG3 A:GLN134 3.4 37.0 1.0
O A:HOH354 3.4 32.0 1.0
O A:HOH443 3.5 45.5 1.0
HD12 A:ILE137 3.7 29.9 1.0
HG2 A:LYS180 3.8 30.2 1.0
O A:HOH444 4.1 65.8 1.0
CD A:LYS180 4.1 22.8 1.0
CB A:LYS180 4.1 23.6 1.0
HD13 A:ILE137 4.1 29.9 1.0
HG21 A:ILE137 4.1 29.0 1.0
CG A:LYS180 4.2 25.2 1.0
HB2 A:GLN134 4.2 31.5 1.0
CA A:GLN134 4.2 23.4 1.0
CG A:GLN134 4.2 30.9 1.0
HB A:ILE137 4.3 25.0 1.0
CD1 A:ILE137 4.4 24.9 1.0
CB A:GLN134 4.4 26.2 1.0
HE21 A:GLN134 4.4 39.6 1.0
HB3 A:LYS180 4.5 28.3 1.0
HE3 A:LYS180 4.5 28.4 1.0
O A:HOH439 4.6 48.5 1.0
CE A:LYS180 4.8 23.7 1.0
HD2 A:LYS180 4.8 27.4 1.0
HG2 A:GLN134 4.8 37.0 1.0
CG2 A:ILE137 4.8 24.2 1.0
HG22 A:ILE137 4.9 29.0 1.0
HE2 A:LYS180 4.9 28.4 1.0
CB A:ILE137 4.9 20.8 1.0
O A:GLN134 4.9 23.5 1.0

Iodine binding site 3 out of 4 in 6doy

Go back to Iodine Binding Sites List in 6doy
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 Li+ For 120 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 Li+ For 120 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I203

b:33.6
occ:0.30
 O A:HOH453 3.0 37.8 0.8
O A:HOH448 3.1 44.9 1.0
HG2 A:PRO177 3.1 28.8 1.0
HD11 A:LEU179 3.2 28.1 1.0
HG3 A:PRO128 3.3 31.0 1.0
CD1 A:ILE64 3.5 47.5 1.0
HB3 A:PRO128 3.6 24.9 1.0
HB2 A:PRO177 3.7 27.3 1.0
HD21 A:LEU179 3.7 34.7 1.0
CG A:PRO177 3.9 24.0 1.0
HB3 A:PRO177 4.0 27.3 1.0
CB A:PRO177 4.0 22.8 1.0
O A:HOH455 4.1 45.1 1.0
CG A:PRO128 4.1 25.8 1.0
CD1 A:LEU179 4.2 23.4 1.0
O A:HOH454 4.2 57.2 1.0
CB A:PRO128 4.3 20.8 1.0
HG3 A:PRO177 4.3 28.8 1.0
HD13 A:LEU179 4.5 28.1 1.0
HD3 A:PRO128 4.5 25.6 1.0
CD2 A:LEU179 4.6 28.9 1.0
HB2 A:PRO128 4.6 24.9 1.0
HD12 A:LEU179 4.7 28.1 1.0
HG2 A:PRO128 4.8 31.0 1.0
HD22 A:LEU179 4.8 34.7 1.0
CG A:LEU179 4.8 22.4 1.0
HG A:LEU179 4.9 26.9 1.0
O A:HOH447 4.9 50.4 1.0
HD2 A:PRO177 4.9 24.0 1.0
CD A:PRO128 4.9 21.3 1.0
CG1 A:ILE64 4.9 35.1 1.0

Iodine binding site 4 out of 4 in 6doy

Go back to Iodine Binding Sites List in 6doy
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 Li+ For 120 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 Li+ For 120 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I204

b:47.9
occ:0.35
 HD2 A:HIS172 3.0 34.4 1.0
HE3 A:LYS121 3.4 44.4 1.0
CD2 A:HIS172 3.7 28.6 1.0
O A:HOH413 3.8 47.1 1.0
HE2 A:LYS121 3.8 44.4 1.0
CE A:LYS121 4.1 37.0 1.0
NE2 A:HIS172 4.1 34.5 1.0
O A:HOH398 4.4 47.2 1.0
HD3 A:LYS121 4.6 32.6 1.0
CD A:LYS121 4.9 27.2 1.0
HZ1 A:LYS121 5.0 40.6 1.0
CG A:HIS172 5.0 27.4 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 Aug 11 22:58:27 2024

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