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Iodine in PDB 6dpj: Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 4 Mm MN2+ and 200 Mm K+ For 80 S at 21 C

Enzymatic activity of Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 4 Mm MN2+ and 200 Mm K+ For 80 S at 21 C

All present enzymatic activity of Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 4 Mm MN2+ and 200 Mm K+ For 80 S at 21 C:
3.1.26.4;

Protein crystallography data

The structure of Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 4 Mm MN2+ and 200 Mm K+ For 80 S at 21 C, PDB code: 6dpj 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) 19.41 / 1.55
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 81.884, 37.549, 62.400, 90.00, 97.23, 90.00
R / Rfree (%) 17 / 21.1

Other elements in 6dpj:

The structure of Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 4 Mm MN2+ and 200 Mm K+ For 80 S at 21 C also contains other interesting chemical elements:

Potassium (K) 2 atoms
Manganese (Mn) 2 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 4 Mm MN2+ and 200 Mm K+ For 80 S at 21 C (pdb code 6dpj). 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 K196A in Complex with An Rna/Dna Hybrid: Reaction in 4 Mm MN2+ and 200 Mm K+ For 80 S at 21 C, PDB code: 6dpj:
Jump to Iodine binding site number: 1; 2; 3; 4;

Iodine binding site 1 out of 4 in 6dpj

Go back to Iodine Binding Sites List in 6dpj
Iodine binding site 1 out of 4 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 4 Mm MN2+ and 200 Mm K+ For 80 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 K196A in Complex with An Rna/Dna Hybrid: Reaction in 4 Mm MN2+ and 200 Mm K+ For 80 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I204

b:29.6
occ:0.60
 HH A:TYR83 2.6 42.0 1.0
HD22 A:LEU161 3.2 40.5 1.0
HD13 A:LEU161 3.2 42.5 1.0
HD22 A:LEU111 3.3 30.6 1.0
HB3 A:LEU161 3.4 35.2 1.0
OH A:TYR83 3.4 35.0 1.0
HD3 A:ARG97 3.4 34.2 1.0
HD13 A:LEU111 3.4 28.7 1.0
HE2 A:TYR83 3.4 35.7 1.0
HB3 A:LEU111 3.5 26.7 1.0
O A:HOH360 3.6 32.5 1.0
O A:HOH331 3.6 29.6 1.0
HH11 A:ARG97 3.9 48.1 1.0
CD2 A:LEU161 4.1 33.8 1.0
CD1 A:LEU161 4.1 35.4 1.0
CE2 A:TYR83 4.1 29.7 1.0
CB A:LEU161 4.2 29.3 1.0
CD2 A:LEU111 4.2 25.5 1.0
CZ A:TYR83 4.2 27.4 1.0
CG A:LEU161 4.3 30.1 1.0
CD1 A:LEU111 4.3 23.9 1.0
O A:HOH328 4.3 36.9 1.0
CB A:LEU111 4.4 22.2 1.0
NH1 A:ARG97 4.4 40.1 1.0
CD A:ARG97 4.4 28.5 1.0
HG2 A:ARG97 4.5 30.6 1.0
HD11 A:LEU161 4.5 42.5 1.0
HD21 A:LEU161 4.5 40.5 1.0
CG A:LEU111 4.5 23.4 1.0
O A:HOH376 4.6 30.1 1.0
HD23 A:LEU161 4.7 40.5 1.0
HB2 A:HIS115 4.7 30.7 1.0
HD12 A:LEU161 4.7 42.5 1.0
HH12 A:ARG97 4.7 48.1 1.0
HB2 A:LEU161 4.7 35.2 1.0
HD21 A:LEU111 4.7 30.6 1.0
HD23 A:LEU111 4.8 30.6 1.0
HD11 A:LEU111 4.8 28.7 1.0
HB2 A:LEU111 4.9 26.7 1.0
HD2 A:ARG97 4.9 34.2 1.0
HD12 A:LEU111 4.9 28.7 1.0
HD11 A:ILE100 4.9 34.2 1.0
CG A:ARG97 5.0 25.5 1.0
O A:HOH316 5.0 33.2 1.0
HB2 A:ARG97 5.0 30.2 1.0
CZ A:ARG97 5.0 38.7 1.0
NE A:ARG97 5.0 31.5 1.0

Iodine binding site 2 out of 4 in 6dpj

Go back to Iodine Binding Sites List in 6dpj
Iodine binding site 2 out of 4 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 4 Mm MN2+ and 200 Mm K+ For 80 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 K196A in Complex with An Rna/Dna Hybrid: Reaction in 4 Mm MN2+ and 200 Mm K+ For 80 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I205

b:42.3
occ:0.40
 O A:HOH400 3.2 49.1 1.0
HG3 A:GLN134 3.2 54.4 1.0
HD3 A:LYS180 3.3 52.5 1.0
HB2 A:LYS180 3.3 35.3 1.0
HA A:GLN134 3.3 32.4 1.0
O A:HOH338 3.4 34.2 1.0
O A:HOH326 3.5 34.7 1.0
HD12 A:ILE137 3.6 33.5 1.0
HG2 A:LYS180 3.8 45.0 1.0
HG21 A:ILE137 4.0 29.9 1.0
HD13 A:ILE137 4.0 33.5 1.0
CD A:LYS180 4.1 43.7 1.0
CB A:LYS180 4.1 29.4 1.0
CG A:GLN134 4.1 45.3 1.0
HB A:ILE137 4.2 27.6 1.0
CG A:LYS180 4.2 37.5 1.0
CA A:GLN134 4.2 27.0 1.0
CD1 A:ILE137 4.3 27.9 1.0
HB2 A:GLN134 4.3 40.4 1.0
HE3 A:LYS180 4.4 55.3 1.0
CB A:GLN134 4.4 33.7 1.0
HE21 A:GLN134 4.4 38.5 1.0
O A:HOH397 4.5 41.3 1.0
HB3 A:LYS180 4.5 35.3 1.0
HG2 A:GLN134 4.6 54.4 1.0
CE A:LYS180 4.7 46.1 1.0
CG2 A:ILE137 4.7 24.9 1.0
HE2 A:LYS180 4.7 55.3 1.0
HG22 A:ILE137 4.8 29.9 1.0
CB A:ILE137 4.8 23.0 1.0
O A:GLN134 4.8 24.5 1.0
HD2 A:LYS180 4.8 52.5 1.0
HD11 A:ILE137 5.0 33.5 1.0

Iodine binding site 3 out of 4 in 6dpj

Go back to Iodine Binding Sites List in 6dpj
Iodine binding site 3 out of 4 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 4 Mm MN2+ and 200 Mm K+ For 80 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 K196A in Complex with An Rna/Dna Hybrid: Reaction in 4 Mm MN2+ and 200 Mm K+ For 80 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I206

b:40.1
occ:0.25
 O A:HOH404 2.8 43.0 1.0
HD13 A:ILE64 3.0 60.1 1.0
HD11 A:LEU179 3.0 39.2 1.0
HG2 A:PRO177 3.1 37.8 1.0
HG3 A:PRO128 3.2 34.5 1.0
HB3 A:PRO128 3.4 32.0 1.0
HB2 A:PRO177 3.5 44.8 1.0
CD1 A:ILE64 3.7 50.1 1.0
HD21 A:LEU179 3.8 39.0 1.0
HD11 A:ILE64 3.8 60.1 1.0
HD12 A:ILE64 3.9 60.1 1.0
CG A:PRO177 3.9 31.5 1.0
HB3 A:PRO177 3.9 44.8 1.0
CB A:PRO177 3.9 37.4 1.0
CD1 A:LEU179 4.0 32.6 1.0
CG A:PRO128 4.0 28.8 1.0
CB A:PRO128 4.1 26.6 1.0
HG21 A:ILE64 4.2 42.3 1.0
HD3 A:PRO128 4.3 29.9 1.0
HD13 A:LEU179 4.3 39.2 1.0
HG3 A:PRO177 4.4 37.8 1.0
HB2 A:PRO128 4.5 32.0 1.0
HD12 A:LEU179 4.5 39.2 1.0
CD2 A:LEU179 4.6 32.5 1.0
HG2 A:PRO128 4.7 34.5 1.0
CG A:LEU179 4.7 31.1 1.0
CD A:PRO128 4.7 24.9 1.0
HG A:LEU179 4.7 37.4 1.0
HD2 A:PRO177 4.8 35.3 1.0
HD22 A:LEU179 4.9 39.0 1.0
O A:HOH403 4.9 47.0 1.0
CD A:PRO177 5.0 29.4 1.0

Iodine binding site 4 out of 4 in 6dpj

Go back to Iodine Binding Sites List in 6dpj
Iodine binding site 4 out of 4 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with An Rna/Dna Hybrid: Reaction in 4 Mm MN2+ and 200 Mm K+ For 80 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 K196A in Complex with An Rna/Dna Hybrid: Reaction in 4 Mm MN2+ and 200 Mm K+ For 80 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I207

b:61.0
occ:0.35
 HD2 A:HIS172 2.9 40.7 1.0
CD2 A:HIS172 3.7 33.9 1.0
HE3 A:LYS121 3.7 55.0 1.0
HE2 A:LYS121 4.0 55.0 1.0
NE2 A:HIS172 4.1 31.8 1.0
O A:HOH382 4.1 43.1 1.0
CE A:LYS121 4.3 45.9 1.0
O A:HOH346 4.3 46.1 1.0
HD3 A:LYS121 4.6 37.4 1.0
CG A:HIS172 5.0 27.8 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 23:04:06 2024

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