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

Iodine in PDB 6dph: Crystal Structure of Bacillus Halodurans Ribonuclease H1 E188A in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MN2+ and 200 Mm K+ For 120 S at 21 C

Enzymatic activity of Crystal Structure of Bacillus Halodurans Ribonuclease H1 E188A in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MN2+ and 200 Mm K+ For 120 S at 21 C

All present enzymatic activity of Crystal Structure of Bacillus Halodurans Ribonuclease H1 E188A in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MN2+ and 200 Mm K+ For 120 S at 21 C:
3.1.26.4;

Protein crystallography data

The structure of Crystal Structure of Bacillus Halodurans Ribonuclease H1 E188A in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MN2+ and 200 Mm K+ For 120 S at 21 C, PDB code: 6dph 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) 23.20 / 1.34
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 80.867, 37.063, 61.789, 90.00, 96.33, 90.00
R / Rfree (%) 16 / 19.2

Other elements in 6dph:

The structure of Crystal Structure of Bacillus Halodurans Ribonuclease H1 E188A in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MN2+ and 200 Mm K+ For 120 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 E188A in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MN2+ and 200 Mm K+ For 120 S at 21 C (pdb code 6dph). 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 E188A in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MN2+ and 200 Mm K+ For 120 S at 21 C, PDB code: 6dph:
Jump to Iodine binding site number: 1; 2; 3; 4;

Iodine binding site 1 out of 4 in 6dph

Go back to Iodine Binding Sites List in 6dph
Iodine binding site 1 out of 4 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 E188A in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MN2+ and 200 Mm K+ 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 E188A in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MN2+ and 200 Mm K+ For 120 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I205

b:16.5
occ:0.50
HH A:TYR83 2.5 27.3 1.0
HD22 A:LEU161 3.2 29.5 1.0
HD13 A:LEU161 3.2 39.7 1.0
HD3 A:ARG97 3.3 33.3 1.0
HD22 A:LEU111 3.3 21.0 1.0
HB3 A:LEU161 3.3 24.2 1.0
OH A:TYR83 3.3 22.8 1.0
HE2 A:TYR83 3.4 22.2 1.0
HB3 A:LEU111 3.4 18.0 1.0
O A:HOH377 3.5 22.9 1.0
HD13 A:LEU111 3.5 20.6 1.0
O A:HOH364 3.6 19.2 1.0
HH11 A:ARG97 3.7 37.3 1.0
CD2 A:LEU161 4.1 24.6 1.0
CE2 A:TYR83 4.1 18.5 1.0
CD1 A:LEU161 4.1 33.1 1.0
CZ A:TYR83 4.2 19.4 1.0
CB A:LEU161 4.2 20.2 1.0
CD2 A:LEU111 4.2 17.5 1.0
O A:HOH332 4.2 30.0 1.0
CD A:ARG97 4.3 27.8 1.0
NH1 A:ARG97 4.3 31.1 1.0
CB A:LEU111 4.3 15.0 1.0
CD1 A:LEU111 4.3 17.1 1.0
CG A:LEU161 4.4 24.3 1.0
HG2 A:ARG97 4.4 22.5 1.0
CG A:LEU111 4.5 16.0 1.0
HB2 A:HIS115 4.5 18.2 1.0
HD21 A:LEU161 4.6 29.5 1.0
HD11 A:LEU161 4.6 39.7 1.0
HH12 A:ARG97 4.6 37.3 1.0
HD23 A:LEU161 4.6 29.5 1.0
HD11 A:ILE100 4.7 25.9 1.0
HB2 A:LEU161 4.7 24.2 1.0
HD12 A:LEU161 4.7 39.7 1.0
HD21 A:LEU111 4.7 21.0 1.0
HD23 A:LEU111 4.7 21.0 1.0
HD2 A:ARG97 4.8 33.3 1.0
O A:HOH403 4.8 21.9 1.0
HB2 A:LEU111 4.8 18.0 1.0
O A:HOH338 4.8 45.7 1.0
HD11 A:LEU111 4.9 20.6 1.0
CG A:ARG97 4.9 18.7 1.0
NE A:ARG97 4.9 26.1 1.0
CZ A:ARG97 4.9 28.3 1.0
HD12 A:LEU111 4.9 20.6 1.0
O A:HOH344 5.0 25.4 1.0

Iodine binding site 2 out of 4 in 6dph

Go back to Iodine Binding Sites List in 6dph
Iodine binding site 2 out of 4 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 E188A in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MN2+ and 200 Mm K+ 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 E188A in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MN2+ and 200 Mm K+ For 120 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I206

b:38.2
occ:0.40
HD3 A:LYS180 3.1 27.3 1.0
HB2 A:LYS180 3.1 25.4 1.0
HA A:GLN134 3.2 24.7 1.0
O A:HOH348 3.2 24.2 1.0
HG3 A:GLN134 3.2 31.5 1.0
O A:HOH457 3.3 39.5 1.0
HD12 A:ILE137 3.7 22.8 1.0
HG2 A:LYS180 3.7 27.2 1.0
O A:HOH322 3.7 32.4 1.0
CD A:LYS180 3.9 22.7 1.0
CB A:LYS180 3.9 21.2 1.0
HG21 A:ILE137 4.0 23.3 1.0
CG A:LYS180 4.0 22.7 1.0
HD13 A:ILE137 4.1 22.8 1.0
HB A:ILE137 4.1 20.8 1.0
CA A:GLN134 4.1 20.6 1.0
CG A:GLN134 4.1 26.2 1.0
O A:HOH450 4.3 37.6 1.0
HB3 A:LYS180 4.3 25.4 1.0
CD1 A:ILE137 4.3 19.0 1.0
HB2 A:GLN134 4.4 26.6 1.0
HE3 A:LYS180 4.4 29.0 1.0
CB A:GLN134 4.4 22.1 1.0
HG2 A:GLN134 4.6 31.5 1.0
HD2 A:LYS180 4.6 27.3 1.0
HE21 A:GLN134 4.6 35.0 1.0
CE A:LYS180 4.6 24.2 1.0
CG2 A:ILE137 4.7 19.4 1.0
O A:GLN134 4.8 20.9 1.0
CB A:ILE137 4.8 17.3 1.0
HE2 A:LYS180 4.8 29.0 1.0
HG22 A:ILE137 4.8 23.3 1.0
C A:GLN134 5.0 18.3 1.0
N A:GLN134 5.0 18.7 1.0
HG3 A:LYS180 5.0 27.2 1.0
HA A:LYS180 5.0 20.5 1.0

Iodine binding site 3 out of 4 in 6dph

Go back to Iodine Binding Sites List in 6dph
Iodine binding site 3 out of 4 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 E188A in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MN2+ and 200 Mm K+ 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 E188A in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MN2+ and 200 Mm K+ For 120 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I207

b:33.0
occ:0.30
O A:HOH465 2.9 40.7 1.0
O A:HOH459 3.0 36.8 1.0
HD11 A:LEU179 3.1 24.8 1.0
HG3 A:PRO128 3.2 23.9 1.0
HB3 A:PRO128 3.4 20.3 1.0
CD1 A:ILE64 3.6 33.2 1.0
HD21 A:LEU179 3.7 27.3 1.0
CG A:PRO177 3.9 17.2 1.0
CB A:PRO177 3.9 16.8 1.0
CG A:PRO128 4.0 19.9 1.0
CD1 A:LEU179 4.0 20.7 1.0
CB A:PRO128 4.1 16.9 1.0
O A:HOH464 4.2 49.5 1.0
HD3 A:PRO128 4.3 20.7 1.0
HD13 A:LEU179 4.3 24.8 1.0
O A:HOH466 4.4 55.5 1.0
HB2 A:PRO128 4.4 20.3 1.0
CD2 A:LEU179 4.5 22.8 1.0
HD12 A:LEU179 4.5 24.8 1.0
HG2 A:PRO128 4.7 23.9 1.0
CG A:LEU179 4.7 19.3 1.0
HG A:LEU179 4.7 23.2 1.0
CD A:PRO128 4.7 17.3 1.0
HD22 A:LEU179 4.8 27.3 1.0
CD A:PRO177 4.9 16.3 1.0
CG1 A:ILE64 4.9 27.3 1.0
O A:HOH460 4.9 35.9 1.0

Iodine binding site 4 out of 4 in 6dph

Go back to Iodine Binding Sites List in 6dph
Iodine binding site 4 out of 4 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 E188A in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MN2+ and 200 Mm K+ 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 E188A in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MN2+ and 200 Mm K+ For 120 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I208

b:29.5
occ:0.20
HD2 A:HIS172 2.9 24.6 1.0
O A:HOH449 2.9 52.5 1.0
HE3 A:LYS121 3.5 37.8 1.0
CD2 A:HIS172 3.6 20.5 1.0
HE2 A:LYS121 3.7 37.8 1.0
O A:HOH438 3.9 41.7 1.0
O A:HOH413 4.0 39.8 1.0
NE2 A:HIS172 4.0 24.6 1.0
CE A:LYS121 4.1 31.5 1.0
O A:HOH378 4.2 38.4 1.0
HD3 A:LYS121 4.6 29.0 1.0
CG A:HIS172 4.9 19.4 1.0
CD A:LYS121 4.9 24.1 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 19:43:41 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy