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Iodine in PDB 6dpk: 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 240 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 240 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 240 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 240 S at 21 C, PDB code: 6dpk 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) 19.92 / 1.39
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 81.492, 37.598, 61.734, 90.00, 96.79, 90.00
R / Rfree (%) 14.3 / 16.9

Other elements in 6dpk:

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 240 S at 21 C also contains other interesting chemical elements:

Potassium (K) 2 atoms
Manganese (Mn) 4 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 240 S at 21 C (pdb code 6dpk). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 3 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 240 S at 21 C, PDB code: 6dpk:
Jump to Iodine binding site number: 1; 2; 3;

Iodine binding site 1 out of 3 in 6dpk

Go back to Iodine Binding Sites List in 6dpk
Iodine binding site 1 out of 3 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 240 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 240 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I202

b:17.2
occ:0.50
HH A:TYR83 2.5 25.2 1.0
HD22 A:LEU161 3.2 27.7 1.0
HD13 A:LEU161 3.3 27.3 1.0
OH A:TYR83 3.3 21.0 1.0
HD22 A:LEU111 3.3 20.4 1.0
HD13 A:LEU111 3.4 20.6 1.0
HE2 A:TYR83 3.4 22.7 1.0
HD3 A:ARG97 3.4 27.9 1.0
HB3 A:LEU161 3.4 21.0 1.0
HB3 A:LEU111 3.5 18.1 1.0
O A:HOH379 3.5 29.0 1.0
O A:HOH361 3.6 20.0 1.0
C1 A:GOL207 3.8 77.0 1.0
HH11 A:ARG97 3.8 34.4 1.0
CE2 A:TYR83 4.1 18.9 1.0
CD2 A:LEU161 4.1 23.1 1.0
CZ A:TYR83 4.2 17.6 1.0
CD1 A:LEU161 4.2 22.7 1.0
CD2 A:LEU111 4.3 17.0 1.0
CD1 A:LEU111 4.3 17.1 1.0
CB A:LEU161 4.3 17.5 1.0
NH1 A:ARG97 4.3 28.7 1.0
CD A:ARG97 4.3 23.3 1.0
CB A:LEU111 4.4 15.0 1.0
CG A:LEU161 4.4 21.0 1.0
O1 A:GOL207 4.4 74.5 1.0
HG2 A:ARG97 4.5 23.4 1.0
CG A:LEU111 4.5 14.9 1.0
HD21 A:LEU161 4.6 27.7 1.0
O A:HOH347 4.6 78.1 1.0
HH12 A:ARG97 4.6 34.4 1.0
HD11 A:LEU161 4.6 27.3 1.0
HD23 A:LEU161 4.7 27.7 1.0
HB2 A:HIS115 4.7 18.8 1.0
HD21 A:LEU111 4.8 20.4 1.0
HD11 A:ILE100 4.8 25.4 1.0
HD11 A:LEU111 4.8 20.6 1.0
HB2 A:LEU161 4.8 21.0 1.0
HD12 A:LEU161 4.8 27.3 1.0
HD23 A:LEU111 4.8 20.4 1.0
O A:HOH392 4.8 22.3 1.0
HB2 A:LEU111 4.9 18.1 1.0
HD12 A:LEU111 4.9 20.6 1.0
HD2 A:ARG97 4.9 27.9 1.0
C2 A:GOL207 4.9 79.9 1.0
CG A:ARG97 4.9 19.5 1.0
HB2 A:ARG97 5.0 23.3 1.0
CZ A:ARG97 5.0 24.0 1.0
NE A:ARG97 5.0 22.1 1.0
O A:HOH331 5.0 23.6 1.0

Iodine binding site 2 out of 3 in 6dpk

Go back to Iodine Binding Sites List in 6dpk
Iodine binding site 2 out of 3 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 240 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 240 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I203

b:33.3
occ:0.40
O A:HOH441 3.2 41.1 1.0
O A:HOH365 3.2 23.0 1.0
HB2 A:LYS180 3.2 24.0 1.0
HD3 A:LYS180 3.3 30.2 1.0
HG3 A:GLN134 3.3 29.8 1.0
HA A:GLN134 3.4 23.0 1.0
O A:HOH344 3.7 28.2 1.0
HD12 A:ILE137 3.7 21.8 1.0
HG2 A:LYS180 3.9 26.4 1.0
HG21 A:ILE137 4.0 20.7 1.0
HD13 A:ILE137 4.0 21.8 1.0
CD A:LYS180 4.1 25.2 1.0
CB A:LYS180 4.1 20.0 1.0
CG A:GLN134 4.2 24.8 1.0
HB A:ILE137 4.2 19.7 1.0
CG A:LYS180 4.3 22.0 1.0
CA A:GLN134 4.3 19.2 1.0
CD1 A:ILE137 4.3 18.1 1.0
HB2 A:GLN134 4.4 25.0 1.0
HE21 A:GLN134 4.4 31.9 1.0
CB A:GLN134 4.5 20.8 1.0
HB3 A:LYS180 4.5 24.0 1.0
HE3 A:LYS180 4.6 34.3 1.0
O A:HOH436 4.6 37.5 1.0
HG2 A:GLN134 4.7 29.8 1.0
CG2 A:ILE137 4.7 17.2 1.0
HG22 A:ILE137 4.8 20.7 1.0
CE A:LYS180 4.8 28.6 1.0
HD2 A:LYS180 4.8 30.2 1.0
HE2 A:LYS180 4.8 34.3 1.0
CB A:ILE137 4.9 16.4 1.0
O A:GLN134 4.9 17.9 1.0
HD11 A:ILE137 5.0 21.8 1.0

Iodine binding site 3 out of 3 in 6dpk

Go back to Iodine Binding Sites List in 6dpk
Iodine binding site 3 out of 3 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 240 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 240 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I204

b:29.9
occ:0.25
O A:HOH445 2.9 30.8 1.0
O A:HOH447 2.9 42.0 1.0
HD13 A:ILE64 3.0 46.2 1.0
HG2 A:PRO177 3.1 22.9 1.0
HD11 A:LEU179 3.1 24.2 1.0
HG3 A:PRO128 3.2 25.4 1.0
HB3 A:PRO128 3.4 21.0 1.0
HB2 A:PRO177 3.6 21.1 1.0
CD1 A:ILE64 3.7 38.5 1.0
HD11 A:ILE64 3.7 46.2 1.0
HD21 A:LEU179 3.7 25.5 1.0
HD12 A:ILE64 3.8 46.2 1.0
CG A:PRO177 3.9 19.1 1.0
CB A:PRO177 4.0 17.6 1.0
HB3 A:PRO177 4.0 21.1 1.0
CG A:PRO128 4.0 21.2 1.0
CD1 A:LEU179 4.0 20.1 1.0
O A:HOH448 4.1 36.8 1.0
CB A:PRO128 4.1 17.5 1.0
HG21 A:ILE64 4.2 28.3 1.0
HD3 A:PRO128 4.3 19.5 1.0
HG3 A:PRO177 4.3 22.9 1.0
HD13 A:LEU179 4.4 24.2 1.0
HB2 A:PRO128 4.5 21.0 1.0
HD12 A:LEU179 4.5 24.2 1.0
CD2 A:LEU179 4.6 21.2 1.0
HG2 A:PRO128 4.7 25.4 1.0
CD A:PRO128 4.8 16.2 1.0
CG A:LEU179 4.8 19.1 1.0
HG A:LEU179 4.8 22.9 1.0
HD2 A:PRO177 4.8 19.8 1.0
HD22 A:LEU179 4.8 25.5 1.0
CD A:PRO177 5.0 16.5 1.0
O A:HOH444 5.0 41.1 1.0
CG1 A:ILE64 5.0 28.3 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 19:43:42 2020

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