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Iodine in PDB 6doa: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 200 Mm K+ For 480 S at 21 C

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 K+ For 480 S at 21 C, PDB code: 6doa 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) 31.14 / 1.47
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 81.731, 37.890, 62.695, 90.00, 96.66, 90.00
R / Rfree (%) 16 / 18.6

Other elements in 6doa:

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 K+ For 480 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 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 200 Mm K+ For 480 S at 21 C (pdb code 6doa). 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 K+ For 480 S at 21 C, PDB code: 6doa:
Jump to Iodine binding site number: 1; 2; 3; 4;

Iodine binding site 1 out of 4 in 6doa

Go back to Iodine Binding Sites List in 6doa
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 K+ For 480 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 K+ For 480 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I204

b:16.3
occ:0.45
HH A:TYR83 2.5 25.6 1.0
HD22 A:LEU161 3.0 24.9 1.0
OH A:TYR83 3.3 21.4 1.0
HD13 A:LEU161 3.4 33.0 1.0
HE2 A:TYR83 3.4 17.6 1.0
HD22 A:LEU111 3.4 19.2 1.0
HB3 A:LEU161 3.4 20.1 1.0
HD13 A:LEU111 3.4 16.5 1.0
HD3 A:ARG97 3.5 25.4 1.0
O A:HOH376 3.6 23.3 1.0
HB3 A:LEU111 3.6 13.5 1.0
O A:HOH351 3.7 16.8 1.0
HH11 A:ARG97 3.8 37.1 1.0
CD2 A:LEU161 3.9 20.8 1.0
CE2 A:TYR83 4.1 14.6 1.0
CZ A:TYR83 4.2 15.9 1.0
CD1 A:LEU161 4.2 27.5 1.0
CB A:LEU161 4.3 16.8 1.0
CD2 A:LEU111 4.3 16.0 1.0
CD1 A:LEU111 4.3 13.8 1.0
NH1 A:ARG97 4.3 30.9 1.0
C3 A:GOL212 4.3 43.7 1.0
CG A:LEU161 4.3 19.1 1.0
HD21 A:LEU161 4.4 24.9 1.0
O3 A:GOL212 4.4 29.4 1.0
CD A:ARG97 4.4 21.2 1.0
CB A:LEU111 4.4 11.2 1.0
O A:HOH304 4.5 35.5 1.0
HG2 A:ARG97 4.5 21.2 1.0
HD23 A:LEU161 4.5 24.9 1.0
CG A:LEU111 4.6 11.2 1.0
HH12 A:ARG97 4.6 37.1 1.0
HD11 A:LEU161 4.7 33.0 1.0
HB2 A:HIS115 4.7 15.9 1.0
HD11 A:ILE100 4.7 23.8 1.0
HD11 A:LEU111 4.8 16.5 1.0
HD21 A:LEU111 4.8 19.2 1.0
HB2 A:LEU161 4.8 20.1 1.0
O A:HOH403 4.9 19.1 1.0
HD23 A:LEU111 4.9 19.2 1.0
HD12 A:LEU161 4.9 33.0 1.0
HD12 A:LEU111 4.9 16.5 1.0
HD2 A:ARG97 5.0 25.4 1.0
CZ A:ARG97 5.0 24.1 1.0
HB2 A:LEU111 5.0 13.5 1.0

Iodine binding site 2 out of 4 in 6doa

Go back to Iodine Binding Sites List in 6doa
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 K+ For 480 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 K+ For 480 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I205

b:29.9
occ:0.40
HD3 A:LYS180 3.2 27.9 1.0
O A:HOH450 3.2 30.5 1.0
O A:HOH366 3.2 21.9 1.0
HB2 A:LYS180 3.2 18.8 1.0
HG3 A:GLN134 3.3 26.3 1.0
HA A:GLN134 3.3 17.6 1.0
O4 A:PGE215 3.6 30.4 1.0
HD12 A:ILE137 3.7 18.1 1.0
C6 A:PGE215 3.7 58.1 1.0
HG2 A:LYS180 4.0 20.7 1.0
O A:HOH452 4.0 62.2 1.0
HG21 A:ILE137 4.0 19.0 1.0
CD A:LYS180 4.0 23.3 1.0
CB A:LYS180 4.1 15.7 1.0
HD13 A:ILE137 4.1 18.1 1.0
HB A:ILE137 4.2 15.0 1.0
CG A:GLN134 4.2 21.9 1.0
CA A:GLN134 4.2 14.7 1.0
CG A:LYS180 4.2 17.2 1.0
HB2 A:GLN134 4.3 23.3 1.0
CD1 A:ILE137 4.4 15.1 1.0
CB A:GLN134 4.4 19.4 1.0
HE21 A:GLN134 4.5 32.7 1.0
HB3 A:LYS180 4.5 18.8 1.0
HE3 A:LYS180 4.5 26.8 1.0
O A:HOH448 4.6 35.4 1.0
HD2 A:LYS180 4.7 27.9 1.0
CG2 A:ILE137 4.7 15.8 1.0
CE A:LYS180 4.7 22.3 1.0
HG2 A:GLN134 4.7 26.3 1.0
HE2 A:LYS180 4.8 26.8 1.0
HG22 A:ILE137 4.8 19.0 1.0
CB A:ILE137 4.8 12.5 1.0
O A:GLN134 4.9 16.9 1.0

Iodine binding site 3 out of 4 in 6doa

Go back to Iodine Binding Sites List in 6doa
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 K+ For 480 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 K+ For 480 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I206

b:28.0
occ:0.30
O A:HOH455 2.8 32.7 1.0
HD13 A:ILE64 2.9 38.6 1.0
HG2 A:PRO177 3.1 17.6 1.0
HD11 A:LEU179 3.1 21.5 1.0
HG3 A:PRO128 3.2 20.5 1.0
HB3 A:PRO128 3.5 16.6 1.0
HB2 A:PRO177 3.6 15.6 1.0
CD1 A:ILE64 3.6 32.2 1.0
HD11 A:ILE64 3.7 38.6 1.0
HD12 A:ILE64 3.7 38.6 1.0
HD21 A:LEU179 3.8 21.2 1.0
CG A:PRO177 3.9 14.7 1.0
CB A:PRO177 4.0 13.0 1.0
HB3 A:PRO177 4.0 15.6 1.0
CG A:PRO128 4.0 17.1 1.0
CD1 A:LEU179 4.1 17.9 1.0
CB A:PRO128 4.1 13.8 1.0
HG21 A:ILE64 4.2 27.1 1.0
HG3 A:PRO177 4.4 17.6 1.0
HD13 A:LEU179 4.4 21.5 1.0
HD3 A:PRO128 4.5 14.6 1.0
HB2 A:PRO128 4.5 16.6 1.0
CD2 A:LEU179 4.6 17.7 1.0
HD12 A:LEU179 4.6 21.5 1.0
HG2 A:PRO128 4.7 20.5 1.0
HD2 A:PRO177 4.8 16.8 1.0
CG A:LEU179 4.8 15.4 1.0
CD A:PRO128 4.8 12.2 1.0
HG A:LEU179 4.8 18.5 1.0
HD22 A:LEU179 4.9 21.2 1.0
CG1 A:ILE64 5.0 25.4 1.0
CD A:PRO177 5.0 14.0 1.0

Iodine binding site 4 out of 4 in 6doa

Go back to Iodine Binding Sites List in 6doa
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 K+ For 480 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 K+ For 480 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I207

b:43.1
occ:0.35
HD2 A:HIS172 3.0 23.3 1.0
HE3 A:LYS121 3.5 35.2 1.0
O A:HOH377 3.6 42.2 1.0
CD2 A:HIS172 3.7 19.4 1.0
HE2 A:LYS121 3.8 35.2 1.0
O A:HOH434 4.0 42.9 1.0
O A:HOH417 4.1 27.7 1.0
NE2 A:HIS172 4.1 21.2 1.0
CE A:LYS121 4.1 29.3 1.0
O A:HOH410 4.3 30.3 1.0
HD3 A:LYS121 4.6 23.6 1.0
CD A:LYS121 4.9 19.6 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 19:43:09 2020

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