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Iodine in PDB 6dp5: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 40 Mm MG2+ and 75 Mm K+ For 40 S at 21 C

Enzymatic activity of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 40 Mm MG2+ and 75 Mm K+ For 40 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 40 Mm MG2+ and 75 Mm K+ For 40 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 40 Mm MG2+ and 75 Mm K+ For 40 S at 21 C, PDB code: 6dp5 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) 20.01 / 1.43
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 81.899, 37.505, 62.254, 90.00, 96.48, 90.00
R / Rfree (%) 15.3 / 17.6

Other elements in 6dp5:

The structure of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 40 Mm MG2+ and 75 Mm K+ For 40 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 40 Mm MG2+ and 75 Mm K+ For 40 S at 21 C (pdb code 6dp5). 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 40 Mm MG2+ and 75 Mm K+ For 40 S at 21 C, PDB code: 6dp5:
Jump to Iodine binding site number: 1; 2; 3; 4;

Iodine binding site 1 out of 4 in 6dp5

Go back to Iodine Binding Sites List in 6dp5
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 40 Mm MG2+ and 75 Mm K+ For 40 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 40 Mm MG2+ and 75 Mm K+ For 40 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I205

b:18.9
occ:0.40
 HH A:TYR83 2.5 23.8 1.0
O A:HOH377 3.2 43.4 1.0
HD22 A:LEU161 3.2 27.5 1.0
OH A:TYR83 3.3 19.8 1.0
HD22 A:LEU111 3.3 18.1 1.0
HE2 A:TYR83 3.3 20.2 1.0
HD13 A:LEU161 3.3 29.2 1.0
HB3 A:LEU161 3.4 21.0 1.0
HD13 A:LEU111 3.4 21.1 1.0
HB3 A:LEU111 3.4 19.1 1.0
HD3 A:ARG97 3.5 28.7 1.0
O A:HOH346 3.5 19.7 1.0
O A:HOH364 3.5 22.2 1.0
HH11 A:ARG97 3.9 35.0 1.0
CE2 A:TYR83 4.0 16.8 1.0
CD2 A:LEU161 4.1 22.9 1.0
CZ A:TYR83 4.1 19.4 1.0
CD2 A:LEU111 4.2 15.1 1.0
CD1 A:LEU161 4.2 24.3 1.0
O A:HOH314 4.3 31.0 1.0
CB A:LEU161 4.3 17.5 1.0
CD1 A:LEU111 4.3 17.6 1.0
CB A:LEU111 4.3 15.9 1.0
NH1 A:ARG97 4.4 29.1 1.0
CG A:LEU161 4.4 19.1 1.0
CD A:ARG97 4.4 23.9 1.0
CG A:LEU111 4.5 15.7 1.0
O A:HOH349 4.5 38.4 1.0
HG2 A:ARG97 4.5 22.1 1.0
HD21 A:LEU161 4.6 27.5 1.0
HD23 A:LEU161 4.7 27.5 1.0
HB2 A:HIS115 4.7 19.6 1.0
HD11 A:LEU161 4.7 29.2 1.0
HH12 A:ARG97 4.7 35.0 1.0
HD21 A:LEU111 4.7 18.1 1.0
HB2 A:LEU161 4.8 21.0 1.0
HD11 A:LEU111 4.8 21.1 1.0
HD23 A:LEU111 4.8 18.1 1.0
HB2 A:LEU111 4.8 19.1 1.0
HD11 A:ILE100 4.8 29.6 1.0
HD12 A:LEU161 4.8 29.2 1.0
O A:HOH366 4.8 24.8 1.0
HD12 A:LEU111 4.9 21.1 1.0
O A:HOH339 4.9 26.2 1.0
HD2 A:ARG97 5.0 28.7 1.0

Iodine binding site 2 out of 4 in 6dp5

Go back to Iodine Binding Sites List in 6dp5
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 40 Mm MG2+ and 75 Mm K+ For 40 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 40 Mm MG2+ and 75 Mm K+ For 40 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I206

b:38.1
occ:0.35
 HG3 A:GLN134 3.2 37.1 1.0
HD3 A:LYS180 3.2 29.0 1.0
O A:HOH419 3.2 45.6 1.0
O A:HOH350 3.3 26.5 1.0
HB2 A:LYS180 3.3 25.4 1.0
HA A:GLN134 3.3 24.3 1.0
O A:HOH347 3.6 38.8 1.0
HD12 A:ILE137 3.7 24.8 1.0
HG2 A:LYS180 3.8 29.0 1.0
CD A:LYS180 4.0 24.2 1.0
CG A:GLN134 4.0 30.9 1.0
HB2 A:GLN134 4.1 29.8 1.0
O A:HOH417 4.1 49.4 1.0
CB A:LYS180 4.1 21.2 1.0
HD13 A:ILE137 4.1 24.8 1.0
CA A:GLN134 4.2 20.2 1.0
HG21 A:ILE137 4.2 26.2 1.0
CG A:LYS180 4.2 24.2 1.0
HB A:ILE137 4.3 21.4 1.0
CB A:GLN134 4.3 24.8 1.0
HE3 A:LYS180 4.4 28.5 1.0
CD1 A:ILE137 4.4 20.6 1.0
HB3 A:LYS180 4.5 25.4 1.0
HG2 A:GLN134 4.5 37.1 1.0
HE21 A:GLN134 4.6 52.3 1.0
O A:HOH415 4.6 39.4 1.0
CE A:LYS180 4.6 23.7 1.0
HD2 A:LYS180 4.7 29.0 1.0
HE2 A:LYS180 4.7 28.5 1.0
CG2 A:ILE137 4.9 21.9 1.0
O A:GLN134 4.9 21.0 1.0
HG22 A:ILE137 4.9 26.2 1.0
CB A:ILE137 4.9 17.9 1.0

Iodine binding site 3 out of 4 in 6dp5

Go back to Iodine Binding Sites List in 6dp5
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 40 Mm MG2+ and 75 Mm K+ For 40 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 40 Mm MG2+ and 75 Mm K+ For 40 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I207

b:40.0
occ:0.30
 O A:HOH421 2.8 35.5 1.0
HD13 A:ILE64 3.0 54.0 1.0
HG2 A:PRO177 3.0 25.7 1.0
HG3 A:PRO128 3.1 26.3 1.0
HD11 A:LEU179 3.2 25.4 1.0
HB3 A:PRO128 3.5 23.1 1.0
HD12 A:ILE64 3.5 54.0 1.0
CD1 A:ILE64 3.6 45.0 1.0
HB2 A:PRO177 3.6 24.3 1.0
HD11 A:ILE64 3.6 54.0 1.0
HD21 A:LEU179 3.7 28.7 1.0
CG A:PRO177 3.8 21.4 1.0
HB3 A:PRO177 3.9 24.3 1.0
CB A:PRO177 3.9 20.2 1.0
CG A:PRO128 4.0 21.9 1.0
CD1 A:LEU179 4.1 21.2 1.0
CB A:PRO128 4.2 19.2 1.0
HG3 A:PRO177 4.3 25.7 1.0
HG21 A:ILE64 4.4 32.7 1.0
HD13 A:LEU179 4.5 25.4 1.0
HD3 A:PRO128 4.5 21.1 1.0
CD2 A:LEU179 4.5 23.9 1.0
HB2 A:PRO128 4.6 23.1 1.0
HG2 A:PRO128 4.6 26.3 1.0
HD12 A:LEU179 4.7 25.4 1.0
CG A:LEU179 4.8 20.1 1.0
HG A:LEU179 4.8 24.1 1.0
HD22 A:LEU179 4.8 28.7 1.0
HD2 A:PRO177 4.8 25.2 1.0
CD A:PRO128 4.9 17.6 1.0
O A:HOH418 4.9 47.9 1.0
CD A:PRO177 5.0 21.0 1.0
CG1 A:ILE64 5.0 34.7 1.0

Iodine binding site 4 out of 4 in 6dp5

Go back to Iodine Binding Sites List in 6dp5
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 40 Mm MG2+ and 75 Mm K+ For 40 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 40 Mm MG2+ and 75 Mm K+ For 40 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I208

b:61.8
occ:0.35
 HD2 A:HIS172 3.0 24.6 1.0
HE3 A:LYS121 3.4 37.9 1.0
HE2 A:LYS121 3.6 37.9 1.0
CD2 A:HIS172 3.7 20.5 1.0
O A:HOH367 3.7 39.6 1.0
O A:HOH409 3.8 51.5 1.0
CE A:LYS121 4.0 31.5 1.0
NE2 A:HIS172 4.1 22.9 1.0
O A:HOH379 4.4 35.3 1.0
HD3 A:LYS121 4.6 30.9 1.0
HZ1 A:LYS121 4.8 37.1 1.0
CD A:LYS121 4.9 25.8 1.0
CG A:HIS172 5.0 16.8 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 Aug 11 23:00:40 2024

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