Atomistry » Iodine » PDB 6dof-6ep1 » 6doy
Atomistry »
  Iodine »
    PDB 6dof-6ep1 »
      6doy »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy