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Iodine in PDB 6dpb: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 8 Mm MN2+ and 200 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 8 Mm MN2+ and 200 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 8 Mm MN2+ and 200 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 8 Mm MN2+ and 200 Mm K+ For 40 S at 21 C, PDB code: 6dpb 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) 33.89 / 1.32
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 81.546, 37.318, 62.154, 90.00, 96.85, 90.00
R / Rfree (%) 14.8 / 17.2

Other elements in 6dpb:

The structure of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 8 Mm MN2+ and 200 Mm K+ For 40 S at 21 C also contains other interesting chemical elements:

Potassium (K) 3 atoms
Manganese (Mn) 4 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 8 Mm MN2+ and 200 Mm K+ For 40 S at 21 C (pdb code 6dpb). 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 8 Mm MN2+ and 200 Mm K+ For 40 S at 21 C, PDB code: 6dpb:
Jump to Iodine binding site number: 1; 2; 3; 4;

Iodine binding site 1 out of 4 in 6dpb

Go back to Iodine Binding Sites List in 6dpb
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 8 Mm MN2+ and 200 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 8 Mm MN2+ and 200 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:0.75
 HH A:TYR83 2.6 22.6 1.0
HD22 A:LEU161 3.2 27.4 1.0
HD22 A:LEU111 3.3 21.1 1.0
HE2 A:TYR83 3.3 19.5 1.0
HD13 A:LEU111 3.4 21.8 1.0
HD3 A:ARG97 3.4 24.7 1.0
HD13 A:LEU161 3.4 27.7 1.0
OH A:TYR83 3.4 18.8 1.0
HB3 A:LEU161 3.4 20.6 1.0
O A:HOH391 3.5 20.4 1.0
HB3 A:LEU111 3.5 19.2 1.0
O A:HOH362 3.6 18.7 1.0
HH11 A:ARG97 3.8 32.5 1.0
CE2 A:TYR83 4.1 16.3 1.0
CD2 A:LEU161 4.2 22.9 1.0
CZ A:TYR83 4.2 17.8 1.0
C1 A:GOL211 4.2 55.0 1.0
CD2 A:LEU111 4.2 17.6 1.0
NH1 A:ARG97 4.3 27.1 1.0
CD1 A:LEU161 4.3 23.1 1.0
CD1 A:LEU111 4.3 18.1 1.0
O1 A:GOL211 4.3 51.2 1.0
CB A:LEU161 4.3 17.2 1.0
CD A:ARG97 4.4 20.6 1.0
CB A:LEU111 4.4 16.0 1.0
CG A:LEU161 4.5 19.9 1.0
HG2 A:ARG97 4.5 21.1 1.0
CG A:LEU111 4.5 16.3 1.0
HH12 A:ARG97 4.6 32.5 1.0
HB2 A:HIS115 4.7 18.4 1.0
HD21 A:LEU161 4.7 27.4 1.0
HD23 A:LEU161 4.7 27.4 1.0
HD21 A:LEU111 4.7 21.1 1.0
HD11 A:LEU161 4.7 27.7 1.0
HD11 A:LEU111 4.7 21.8 1.0
HD11 A:ILE100 4.8 28.3 1.0
HD23 A:LEU111 4.8 21.1 1.0
O A:HOH398 4.8 22.9 1.0
HB2 A:LEU161 4.9 20.6 1.0
HD12 A:LEU111 4.9 21.8 1.0
HD2 A:ARG97 4.9 24.7 1.0
HD12 A:LEU161 4.9 27.7 1.0
CZ A:ARG97 4.9 22.2 1.0
HB2 A:LEU111 4.9 19.2 1.0
O A:HOH365 4.9 23.0 1.0
NE A:ARG97 4.9 21.4 1.0
CG A:ARG97 5.0 17.6 1.0

Iodine binding site 2 out of 4 in 6dpb

Go back to Iodine Binding Sites List in 6dpb
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 8 Mm MN2+ and 200 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 8 Mm MN2+ and 200 Mm K+ For 40 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I206

b:31.9
occ:0.40
 HD3 A:LYS180 3.2 27.9 1.0
HB2 A:LYS180 3.2 25.1 1.0
HG3 A:GLN134 3.2 34.0 1.0
O A:HOH349 3.2 24.6 1.0
HA A:GLN134 3.3 23.5 1.0
O A:HOH468 3.3 36.5 1.0
O A:HOH373 3.6 29.3 1.0
HD12 A:ILE137 3.7 21.9 1.0
HG2 A:LYS180 4.0 28.9 1.0
HG21 A:ILE137 4.0 23.1 1.0
HD13 A:ILE137 4.1 21.9 1.0
CD A:LYS180 4.1 23.2 1.0
CB A:LYS180 4.1 20.9 1.0
CG A:GLN134 4.1 28.3 1.0
CA A:GLN134 4.2 19.6 1.0
HB A:ILE137 4.2 22.7 1.0
CG A:LYS180 4.2 24.0 1.0
HB2 A:GLN134 4.3 28.4 1.0
CD1 A:ILE137 4.3 18.2 1.0
CB A:GLN134 4.4 23.7 1.0
HB3 A:LYS180 4.5 25.1 1.0
O A:HOH470 4.5 60.3 1.0
HE21 A:GLN134 4.5 37.1 1.0
O A:HOH455 4.5 39.9 1.0
HE3 A:LYS180 4.6 27.6 1.0
HG2 A:GLN134 4.6 34.0 1.0
CG2 A:ILE137 4.7 19.3 1.0
HD2 A:LYS180 4.7 27.9 1.0
CE A:LYS180 4.8 23.0 1.0
HG22 A:ILE137 4.8 23.1 1.0
HE2 A:LYS180 4.8 27.6 1.0
O A:HOH460 4.8 58.7 1.0
CB A:ILE137 4.8 18.9 1.0
O A:GLN134 4.9 19.5 1.0

Iodine binding site 3 out of 4 in 6dpb

Go back to Iodine Binding Sites List in 6dpb
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 8 Mm MN2+ and 200 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 8 Mm MN2+ and 200 Mm K+ For 40 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I207

b:30.0
occ:0.25
 O A:HOH476 2.8 31.8 1.0
O A:HOH474 2.9 26.6 1.0
HG2 A:PRO177 3.0 27.1 1.0
HD11 A:LEU179 3.1 26.0 1.0
HB2 A:PRO177 3.5 26.9 1.0
HD21 A:LEU179 3.6 26.3 1.0
CD1 A:ILE64 3.7 44.1 1.0
CG A:PRO177 3.8 22.6 1.0
HB3 A:PRO177 3.9 26.9 1.0
CB A:PRO177 3.9 22.5 1.0
CD1 A:LEU179 4.1 21.7 1.0
CB A:PRO128 4.1 18.6 1.0
O A:HOH479 4.1 50.0 1.0
CG A:PRO128 4.2 19.6 1.0
HG3 A:PRO177 4.3 27.1 1.0
HD13 A:LEU179 4.4 26.0 1.0
CD2 A:LEU179 4.5 21.9 1.0
HD12 A:LEU179 4.6 26.0 1.0
HD22 A:LEU179 4.7 26.3 1.0
HD2 A:PRO177 4.7 23.3 1.0
CG A:LEU179 4.7 20.3 1.0
HG A:LEU179 4.8 24.4 1.0
CD A:PRO128 4.8 18.5 1.0
CD A:PRO177 4.9 19.4 1.0
O A:HOH473 5.0 37.3 1.0

Iodine binding site 4 out of 4 in 6dpb

Go back to Iodine Binding Sites List in 6dpb
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 8 Mm MN2+ and 200 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 8 Mm MN2+ and 200 Mm K+ For 40 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I208

b:57.2
occ:0.35
 HD2 A:HIS172 3.0 23.5 1.0
HE3 A:LYS121 3.6 30.4 1.0
O A:HOH340 3.7 47.8 1.0
HE2 A:LYS121 3.8 30.4 1.0
CD2 A:HIS172 3.8 19.6 1.0
O A:HOH447 3.9 42.3 1.0
CE A:LYS121 4.2 25.4 1.0
NE2 A:HIS172 4.2 23.6 1.0
O A:HOH408 4.2 33.0 1.0
O A:HOH407 4.5 30.8 1.0
HD3 A:LYS121 4.9 25.0 1.0
HZ1 A:LYS121 4.9 33.6 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 Aug 11 23:01:23 2024

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