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Iodine in PDB 6dpn: Crystal Structure of Bacillus Halodurans Ribonuclease H1 E188A in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 200 Mm K+ For 200 S at 21 C

Enzymatic activity of Crystal Structure of Bacillus Halodurans Ribonuclease H1 E188A in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 200 Mm K+ For 200 S at 21 C

All present enzymatic activity of Crystal Structure of Bacillus Halodurans Ribonuclease H1 E188A in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 200 Mm K+ For 200 S at 21 C:
3.1.26.4;

Protein crystallography data

The structure of Crystal Structure of Bacillus Halodurans Ribonuclease H1 E188A in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 200 Mm K+ For 200 S at 21 C, PDB code: 6dpn 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) 19.89 / 1.49
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 81.501, 37.581, 61.951, 90.00, 96.24, 90.00
R / Rfree (%) 15.9 / 17.9

Other elements in 6dpn:

The structure of Crystal Structure of Bacillus Halodurans Ribonuclease H1 E188A in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 200 Mm K+ For 200 S at 21 C also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Potassium (K) 2 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 E188A in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 200 Mm K+ For 200 S at 21 C (pdb code 6dpn). 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 E188A in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 200 Mm K+ For 200 S at 21 C, PDB code: 6dpn:
Jump to Iodine binding site number: 1; 2; 3; 4;

Iodine binding site 1 out of 4 in 6dpn

Go back to Iodine Binding Sites List in 6dpn
Iodine binding site 1 out of 4 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 E188A in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 200 Mm K+ For 200 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 E188A in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 200 Mm K+ For 200 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I204

b:24.8
occ:0.50
HH A:TYR83 2.5 39.6 1.0
HD22 A:LEU161 3.1 36.1 1.0
HD13 A:LEU161 3.2 34.6 1.0
OH A:TYR83 3.3 33.0 1.0
HD22 A:LEU111 3.3 23.0 1.0
HB3 A:LEU161 3.4 27.9 1.0
HD3 A:ARG97 3.4 34.9 1.0
HE2 A:TYR83 3.4 24.6 1.0
HD13 A:LEU111 3.4 24.7 1.0
O A:HOH386 3.5 28.4 1.0
HB3 A:LEU111 3.5 22.2 1.0
O A:HOH342 3.8 23.1 1.0
HH11 A:ARG97 3.8 44.0 1.0
C1 A:GOL209 3.9 53.1 1.0
CD2 A:LEU161 4.0 30.1 1.0
CD1 A:LEU161 4.1 28.8 1.0
CE2 A:TYR83 4.1 20.5 1.0
CZ A:TYR83 4.2 21.5 1.0
CB A:LEU161 4.2 23.3 1.0
CD2 A:LEU111 4.2 19.2 1.0
O1 A:GOL209 4.3 34.2 1.0
NH1 A:ARG97 4.3 36.7 1.0
CD1 A:LEU111 4.3 20.6 1.0
CG A:LEU161 4.3 26.9 1.0
CD A:ARG97 4.3 29.1 1.0
CB A:LEU111 4.4 18.5 1.0
HG2 A:ARG97 4.4 24.7 1.0
HD21 A:LEU161 4.5 36.1 1.0
CG A:LEU111 4.5 17.8 1.0
O A:HOH303 4.5 53.3 1.0
HD23 A:LEU161 4.6 36.1 1.0
HD11 A:LEU161 4.6 34.6 1.0
HH12 A:ARG97 4.6 44.0 1.0
HB2 A:HIS115 4.7 20.6 1.0
HD11 A:ILE100 4.7 33.3 1.0
HB2 A:LEU161 4.7 27.9 1.0
HD12 A:LEU161 4.7 34.6 1.0
HD21 A:LEU111 4.7 23.0 1.0
HD11 A:LEU111 4.8 24.7 1.0
HD23 A:LEU111 4.8 23.0 1.0
O A:HOH405 4.8 26.6 1.0
HB2 A:LEU111 4.9 22.2 1.0
HD2 A:ARG97 4.9 34.9 1.0
CG A:ARG97 4.9 20.6 1.0
HD12 A:LEU111 4.9 24.7 1.0
CZ A:ARG97 4.9 31.1 1.0
NE A:ARG97 4.9 29.5 1.0

Iodine binding site 2 out of 4 in 6dpn

Go back to Iodine Binding Sites List in 6dpn
Iodine binding site 2 out of 4 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 E188A in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 200 Mm K+ For 200 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 E188A in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 200 Mm K+ For 200 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I205

b:37.6
occ:0.40
HD3 A:LYS180 3.2 30.3 1.0
O A:HOH350 3.2 26.7 1.0
HG3 A:GLN134 3.2 34.6 1.0
HB2 A:LYS180 3.2 28.6 1.0
O A:HOH446 3.2 41.8 1.0
HA A:GLN134 3.3 27.0 1.0
O A:HOH348 3.6 33.5 1.0
HD12 A:ILE137 3.7 27.6 1.0
HG2 A:LYS180 3.8 30.7 1.0
O A:HOH445 3.8 61.7 1.0
CD A:LYS180 4.0 25.2 1.0
CB A:LYS180 4.0 23.8 1.0
HG21 A:ILE137 4.1 26.0 1.0
HD13 A:ILE137 4.1 27.6 1.0
CG A:GLN134 4.1 28.9 1.0
HB A:ILE137 4.1 22.4 1.0
CG A:LYS180 4.1 25.6 1.0
CA A:GLN134 4.2 22.5 1.0
CD1 A:ILE137 4.3 23.0 1.0
HB2 A:GLN134 4.4 28.9 1.0
HB3 A:LYS180 4.4 28.6 1.0
HE3 A:LYS180 4.4 31.0 1.0
CB A:GLN134 4.5 24.1 1.0
HG2 A:GLN134 4.5 34.6 1.0
HE21 A:GLN134 4.6 36.5 1.0
O A:HOH442 4.6 42.2 1.0
HD2 A:LYS180 4.7 30.3 1.0
CE A:LYS180 4.7 25.8 1.0
CG2 A:ILE137 4.7 21.7 1.0
HG22 A:ILE137 4.8 26.0 1.0
O A:GLN134 4.8 23.1 1.0
CB A:ILE137 4.8 18.7 1.0
HE2 A:LYS180 4.9 31.0 1.0

Iodine binding site 3 out of 4 in 6dpn

Go back to Iodine Binding Sites List in 6dpn
Iodine binding site 3 out of 4 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 E188A in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 200 Mm K+ For 200 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 E188A in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 200 Mm K+ For 200 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I206

b:31.1
occ:0.25
O A:HOH452 2.9 50.0 1.0
HG3 A:PRO128 3.1 30.0 1.0
HD11 A:LEU179 3.1 26.9 1.0
HG2 A:PRO177 3.1 28.5 1.0
CD1 A:ILE64 3.4 39.5 1.0
HB3 A:PRO128 3.5 25.0 1.0
HB2 A:PRO177 3.6 27.6 1.0
HD21 A:LEU179 3.8 28.2 1.0
CG A:PRO177 4.0 23.7 1.0
CG A:PRO128 4.0 25.0 1.0
HB3 A:PRO177 4.0 27.6 1.0
CB A:PRO177 4.0 23.0 1.0
CD1 A:LEU179 4.1 22.4 1.0
CB A:PRO128 4.2 20.8 1.0
O A:HOH451 4.3 49.9 0.8
HD13 A:LEU179 4.4 26.9 1.0
HD3 A:PRO128 4.4 22.6 1.0
HG3 A:PRO177 4.4 28.5 1.0
HB2 A:PRO128 4.5 25.0 1.0
HD12 A:LEU179 4.6 26.9 1.0
HG2 A:PRO128 4.6 30.0 1.0
CD2 A:LEU179 4.6 23.5 1.0
CG A:LEU179 4.8 20.8 1.0
CG1 A:ILE64 4.8 28.5 1.0
CD A:PRO128 4.8 18.9 1.0
HD2 A:PRO177 4.8 24.4 1.0
HG A:LEU179 4.8 24.9 1.0
O A:HOH447 4.9 35.4 1.0
HD22 A:LEU179 4.9 28.2 1.0
CG2 A:ILE64 4.9 24.4 1.0

Iodine binding site 4 out of 4 in 6dpn

Go back to Iodine Binding Sites List in 6dpn
Iodine binding site 4 out of 4 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 E188A in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 200 Mm K+ For 200 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 E188A in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 200 Mm K+ For 200 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I207

b:52.1
occ:0.35
HD2 A:HIS172 2.9 30.3 1.0
O A:HOH437 2.9 55.3 1.0
HE3 A:LYS121 3.6 44.9 1.0
CD2 A:HIS172 3.7 25.2 1.0
O A:HOH329 3.7 43.3 1.0
O A:HOH430 3.8 42.8 1.0
HE2 A:LYS121 3.9 44.9 1.0
NE2 A:HIS172 4.0 28.6 1.0
O A:HOH407 4.0 34.9 1.0
CE A:LYS121 4.2 37.4 1.0
O A:HOH381 4.2 42.0 1.0
HD3 A:LYS121 4.7 33.2 1.0
CG A:HIS172 4.9 21.0 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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