Iodine in PDB 6doh: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Soak in 0.5 Mm Egta and 200 Mm K+ at 21 C

Enzymatic activity of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Soak in 0.5 Mm Egta and 200 Mm K+ at 21 C

All present enzymatic activity of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Soak in 0.5 Mm Egta and 200 Mm K+ 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: Soak in 0.5 Mm Egta and 200 Mm K+ at 21 C, PDB code: 6doh 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) 19.81 / 1.36
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 81.194, 37.843, 61.829, 90.00, 96.15, 90.00
R / Rfree (%) 16.8 / 20

Other elements in 6doh:

The structure of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Soak in 0.5 Mm Egta and 200 Mm K+ at 21 C also contains other interesting chemical elements:

Potassium (K) 3 atoms
Calcium (Ca) 1 atom

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: Soak in 0.5 Mm Egta and 200 Mm K+ at 21 C (pdb code 6doh). 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: Soak in 0.5 Mm Egta and 200 Mm K+ at 21 C, PDB code: 6doh:
Jump to Iodine binding site number: 1; 2; 3; 4;

Iodine binding site 1 out of 4 in 6doh

Go back to Iodine Binding Sites List in 6doh
Iodine binding site 1 out of 4 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Soak in 0.5 Mm Egta and 200 Mm K+ 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: Soak in 0.5 Mm Egta and 200 Mm K+ at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I204

b:16.7
occ:0.35
 HH A:TYR83 2.4 29.0 1.0
HD22 A:LEU161 3.1 33.4 1.0
HD13 A:LEU161 3.2 34.4 1.0
OH A:TYR83 3.2 24.1 1.0
HD22 A:LEU111 3.3 18.6 1.0
O A:HOH397 3.4 30.3 1.0
HB3 A:LEU161 3.4 25.0 1.0
HB3 A:LEU111 3.4 17.9 1.0
HE2 A:TYR83 3.5 22.7 1.0
HD13 A:LEU111 3.5 22.3 1.0
HD3 A:ARG97 3.5 30.7 1.0
O A:HOH334 3.8 19.2 1.0
HH11 A:ARG97 3.9 38.1 1.0
CD2 A:LEU161 4.0 27.8 1.0
CD1 A:LEU161 4.1 28.7 1.0
CE2 A:TYR83 4.2 18.9 1.0
CZ A:TYR83 4.2 19.7 1.0
CD2 A:LEU111 4.2 15.5 1.0
CB A:LEU161 4.3 20.8 1.0
O A:HOH331 4.3 30.6 1.0
CB A:LEU111 4.3 14.9 1.0
CG A:LEU161 4.4 21.1 1.0
NH1 A:ARG97 4.4 31.8 1.0
CD1 A:LEU111 4.4 18.6 1.0
HG2 A:ARG97 4.5 24.2 1.0
CD A:ARG97 4.5 25.6 1.0
O A:HOH310 4.5 43.1 1.0
HD21 A:LEU161 4.5 33.4 1.0
CG A:LEU111 4.5 16.1 1.0
HD11 A:LEU161 4.6 34.4 1.0
HD23 A:LEU161 4.6 33.4 1.0
HD11 A:ILE100 4.7 29.0 1.0
HH12 A:ARG97 4.7 38.1 1.0
HD12 A:LEU161 4.7 34.4 1.0
HD23 A:LEU111 4.7 18.6 1.0
HD21 A:LEU111 4.8 18.6 1.0
HB2 A:LEU161 4.8 25.0 1.0
HB2 A:LEU111 4.8 17.9 1.0
HD11 A:LEU111 4.9 22.3 1.0
O A:HOH381 5.0 21.2 1.0
HD12 A:LEU111 5.0 22.3 1.0
CG A:ARG97 5.0 20.2 1.0

Iodine binding site 2 out of 4 in 6doh

Go back to Iodine Binding Sites List in 6doh
Iodine binding site 2 out of 4 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Soak in 0.5 Mm Egta and 200 Mm K+ 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: Soak in 0.5 Mm Egta and 200 Mm K+ at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I205

b:50.0
occ:0.40
 HD3 A:LYS180 3.1 25.0 1.0
O A:HOH429 3.1 42.1 1.0
O A:HOH355 3.2 26.3 1.0
HB2 A:LYS180 3.2 26.0 1.0
HA A:GLN134 3.3 21.1 1.0
HG3 A:GLN134 3.3 44.6 1.0
O A:HOH348 3.3 37.4 1.0
HG2 A:LYS180 3.8 27.6 1.0
HD12 A:ILE137 3.8 20.3 1.0
CD A:LYS180 4.0 20.8 1.0
CB A:LYS180 4.1 21.6 1.0
HG21 A:ILE137 4.1 23.9 1.0
HD13 A:ILE137 4.1 20.3 1.0
CG A:LYS180 4.1 23.0 1.0
CG A:GLN134 4.2 37.2 1.0
CA A:GLN134 4.2 17.6 1.0
HB A:ILE137 4.2 17.3 1.0
HE3 A:LYS180 4.4 26.1 1.0
CD1 A:ILE137 4.4 16.9 1.0
HB2 A:GLN134 4.4 26.7 1.0
CB A:GLN134 4.5 22.3 1.0
HB3 A:LYS180 4.5 26.0 1.0
HE21 A:GLN134 4.5 33.9 1.0
HG2 A:GLN134 4.6 44.6 1.0
O A:HOH427 4.6 37.1 1.0
HD2 A:LYS180 4.6 25.0 1.0
CE A:LYS180 4.7 21.8 1.0
CG2 A:ILE137 4.8 19.9 1.0
HE2 A:LYS180 4.8 26.1 1.0
HG22 A:ILE137 4.8 23.9 1.0
O A:GLN134 4.9 18.7 1.0
CB A:ILE137 4.9 14.4 1.0

Iodine binding site 3 out of 4 in 6doh

Go back to Iodine Binding Sites List in 6doh
Iodine binding site 3 out of 4 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Soak in 0.5 Mm Egta and 200 Mm K+ 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: Soak in 0.5 Mm Egta and 200 Mm K+ at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I206

b:38.4
occ:0.30
 HD13 A:ILE64 2.9 42.3 1.0
O A:HOH435 2.9 41.5 1.0
O A:HOH433 3.0 38.3 1.0
HD11 A:LEU179 3.1 25.0 1.0
HG3 A:PRO128 3.1 28.9 1.0
CD1 A:ILE64 3.6 35.3 1.0
HB3 A:PRO128 3.6 18.1 1.0
HD11 A:ILE64 3.6 42.3 1.0
HD12 A:ILE64 3.7 42.3 1.0
HD21 A:LEU179 3.7 26.1 1.0
CG A:PRO177 3.9 17.9 1.0
CB A:PRO177 3.9 19.8 1.0
CG A:PRO128 4.0 24.1 1.0
CD1 A:LEU179 4.0 20.8 1.0
O A:HOH434 4.1 51.0 1.0
HG21 A:ILE64 4.2 30.0 1.0
CB A:PRO128 4.2 15.1 1.0
HD13 A:LEU179 4.3 25.0 1.0
HD3 A:PRO128 4.5 19.0 1.0
CD2 A:LEU179 4.5 21.7 1.0
HD12 A:LEU179 4.6 25.0 1.0
HB2 A:PRO128 4.6 18.1 1.0
HG2 A:PRO128 4.6 28.9 1.0
CG A:LEU179 4.7 21.3 1.0
HG A:LEU179 4.8 25.6 1.0
HD22 A:LEU179 4.8 26.1 1.0
O A:HOH430 4.8 44.0 1.0
CD A:PRO128 4.8 15.8 1.0
CG1 A:ILE64 4.9 27.3 1.0

Iodine binding site 4 out of 4 in 6doh

Go back to Iodine Binding Sites List in 6doh
Iodine binding site 4 out of 4 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Soak in 0.5 Mm Egta and 200 Mm K+ 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: Soak in 0.5 Mm Egta and 200 Mm K+ at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I207

b:33.5
occ:0.20
 HD2 A:HIS172 2.9 25.2 1.0
O A:HOH426 3.0 57.4 1.0
HE3 A:LYS121 3.6 42.7 1.0
CD2 A:HIS172 3.7 21.0 1.0
HE2 A:LYS121 3.8 42.7 1.0
O A:HOH418 3.8 44.6 1.0
O A:HOH376 4.0 43.5 1.0
O A:HOH367 4.1 45.5 1.0
NE2 A:HIS172 4.1 22.9 1.0
CE A:LYS121 4.2 35.6 1.0
HD3 A:LYS121 4.6 24.9 1.0
CG A:HIS172 5.0 17.8 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 19:43:14 2020

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