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Iodine in PDB 6dmv: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Soaked For 40 S in 2 Mm MG2+ and 200 Mm K+ at 21 C

Enzymatic activity of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Soaked For 40 S in 2 Mm MG2+ and 200 Mm K+ at 21 C

All present enzymatic activity of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Soaked For 40 S in 2 Mm MG2+ and 200 Mm K+ 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: Soaked For 40 S in 2 Mm MG2+ and 200 Mm K+ at 21 C, PDB code: 6dmv 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) 19.88 / 1.52
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 81.422, 37.803, 61.986, 90.00, 96.31, 90.00
R / Rfree (%) 16.1 / 18.2

Other elements in 6dmv:

The structure of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Soaked For 40 S in 2 Mm MG2+ and 200 Mm K+ 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 in Complex with An Rna/Dna Hybrid: Soaked For 40 S in 2 Mm MG2+ and 200 Mm K+ at 21 C (pdb code 6dmv). 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: Soaked For 40 S in 2 Mm MG2+ and 200 Mm K+ at 21 C, PDB code: 6dmv:
Jump to Iodine binding site number: 1; 2; 3; 4;

Iodine binding site 1 out of 4 in 6dmv

Go back to Iodine Binding Sites List in 6dmv
Iodine binding site 1 out of 4 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Soaked For 40 S in 2 Mm MG2+ and 200 Mm K+ 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: Soaked For 40 S in 2 Mm MG2+ and 200 Mm K+ at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I204

b:22.3
occ:0.50
 HH A:TYR83 2.5 35.0 1.0
HD22 A:LEU161 3.1 36.3 1.0
HD13 A:LEU161 3.3 34.6 1.0
OH A:TYR83 3.3 29.1 1.0
HB3 A:LEU161 3.4 26.0 1.0
HD22 A:LEU111 3.4 21.1 1.0
HD13 A:LEU111 3.4 22.5 1.0
HD3 A:ARG97 3.4 36.1 1.0
HE2 A:TYR83 3.5 26.4 1.0
HB3 A:LEU111 3.5 20.5 1.0
O A:HOH378 3.5 24.6 1.0
O A:HOH352 3.7 23.4 1.0
HH11 A:ARG97 3.8 45.4 1.0
C1 A:GOL209 3.9 33.8 0.8
CD2 A:LEU161 4.0 30.3 1.0
CD1 A:LEU161 4.1 28.9 1.0
CE2 A:TYR83 4.2 22.0 1.0
CZ A:TYR83 4.2 22.2 1.0
CB A:LEU161 4.3 21.7 1.0
CD2 A:LEU111 4.3 17.6 1.0
CD1 A:LEU111 4.3 18.8 1.0
NH1 A:ARG97 4.3 37.8 1.0
CG A:LEU161 4.4 25.5 1.0
CD A:ARG97 4.4 30.1 1.0
CB A:LEU111 4.4 17.1 1.0
O1 A:GOL209 4.4 30.4 0.8
HG2 A:ARG97 4.5 28.6 1.0
HD21 A:LEU161 4.5 36.3 1.0
O A:HOH417 4.5 48.8 1.0
CG A:LEU111 4.6 17.4 1.0
HD23 A:LEU161 4.6 36.3 1.0
HD11 A:LEU161 4.6 34.6 1.0
HB2 A:HIS115 4.6 20.0 1.0
HH12 A:ARG97 4.7 45.4 1.0
HD11 A:ILE100 4.7 28.4 1.0
HB2 A:LEU161 4.8 26.0 1.0
HD12 A:LEU161 4.8 34.6 1.0
HD11 A:LEU111 4.8 22.5 1.0
HD21 A:LEU111 4.8 21.1 1.0
O A:HOH398 4.8 25.6 1.0
HD23 A:LEU111 4.9 21.1 1.0
HD12 A:LEU111 4.9 22.5 1.0
HB2 A:LEU111 4.9 20.5 1.0
HD2 A:ARG97 4.9 36.1 1.0
CZ A:ARG97 5.0 32.5 1.0
NE A:ARG97 5.0 29.1 1.0
CG A:ARG97 5.0 23.8 1.0

Iodine binding site 2 out of 4 in 6dmv

Go back to Iodine Binding Sites List in 6dmv
Iodine binding site 2 out of 4 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Soaked For 40 S in 2 Mm MG2+ and 200 Mm K+ 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: Soaked For 40 S in 2 Mm MG2+ and 200 Mm K+ at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I205

b:39.4
occ:0.40
 HG3 A:GLN134 3.2 34.8 1.0
O A:HOH351 3.2 27.2 1.0
HB2 A:LYS180 3.3 25.9 1.0
O A:HOH441 3.3 39.0 1.0
HD3 A:LYS180 3.3 28.9 1.0
HA A:GLN134 3.3 26.1 1.0
O A:HOH324 3.7 35.0 1.0
HD12 A:ILE137 3.7 27.6 1.0
HG2 A:LYS180 3.8 29.1 1.0
O A:HOH442 4.0 51.8 1.0
HG21 A:ILE137 4.0 26.1 1.0
CG A:GLN134 4.1 29.0 1.0
HD13 A:ILE137 4.1 27.6 1.0
CB A:LYS180 4.1 21.6 1.0
CD A:LYS180 4.1 24.1 1.0
HB A:ILE137 4.1 23.1 1.0
CG A:LYS180 4.2 24.2 1.0
CA A:GLN134 4.2 21.7 1.0
CD1 A:ILE137 4.4 23.0 1.0
HB2 A:GLN134 4.4 28.6 1.0
O A:HOH436 4.4 37.8 1.0
HG2 A:GLN134 4.4 34.8 1.0
CB A:GLN134 4.4 23.9 1.0
HB3 A:LYS180 4.5 25.9 1.0
HE3 A:LYS180 4.5 28.9 1.0
HE21 A:GLN134 4.6 39.1 1.0
CG2 A:ILE137 4.7 21.8 1.0
HG22 A:ILE137 4.8 26.1 1.0
CE A:LYS180 4.8 24.1 1.0
CB A:ILE137 4.8 19.2 1.0
O A:GLN134 4.8 23.8 1.0
HD2 A:LYS180 4.8 28.9 1.0
HE2 A:LYS180 4.9 28.9 1.0

Iodine binding site 3 out of 4 in 6dmv

Go back to Iodine Binding Sites List in 6dmv
Iodine binding site 3 out of 4 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Soaked For 40 S in 2 Mm MG2+ and 200 Mm K+ 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: Soaked For 40 S in 2 Mm MG2+ and 200 Mm K+ at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I206

b:33.5
occ:0.25
 O A:HOH445 2.9 41.1 1.0
HG2 A:PRO177 3.1 23.8 1.0
HD11 A:LEU179 3.1 25.5 1.0
HG3 A:PRO128 3.2 28.2 1.0
HB3 A:PRO128 3.5 28.0 1.0
CD1 A:ILE64 3.5 33.7 1.0
HB2 A:PRO177 3.6 24.7 1.0
HD21 A:LEU179 3.7 29.2 1.0
CG A:PRO177 3.9 19.9 1.0
CB A:PRO177 4.0 20.6 1.0
HB3 A:PRO177 4.0 24.7 1.0
CG A:PRO128 4.1 23.5 1.0
CD1 A:LEU179 4.1 21.2 1.0
CB A:PRO128 4.1 23.3 1.0
O A:HOH444 4.3 43.4 0.8
HG3 A:PRO177 4.3 23.8 1.0
HD13 A:LEU179 4.4 25.5 1.0
HD3 A:PRO128 4.4 24.6 1.0
HB2 A:PRO128 4.5 28.0 1.0
CD2 A:LEU179 4.6 24.3 1.0
HD12 A:LEU179 4.6 25.5 1.0
HG2 A:PRO128 4.7 28.2 1.0
CG A:LEU179 4.8 21.9 1.0
HG A:LEU179 4.8 26.3 1.0
CD A:PRO128 4.8 20.5 1.0
HD2 A:PRO177 4.8 21.9 1.0
HD22 A:LEU179 4.9 29.2 1.0
CG1 A:ILE64 4.9 30.7 1.0
O A:HOH431 5.0 37.4 1.0
CD A:PRO177 5.0 18.3 1.0

Iodine binding site 4 out of 4 in 6dmv

Go back to Iodine Binding Sites List in 6dmv
Iodine binding site 4 out of 4 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Soaked For 40 S in 2 Mm MG2+ and 200 Mm K+ 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: Soaked For 40 S in 2 Mm MG2+ and 200 Mm K+ at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I207

b:53.4
occ:0.35
 O A:HOH434 3.0 47.0 1.0
HD2 A:HIS172 3.0 32.0 1.0
HE3 A:LYS121 3.7 34.0 1.0
CD2 A:HIS172 3.8 26.7 1.0
O A:HOH323 3.8 45.0 1.0
O A:HOH423 3.8 49.1 1.0
HE2 A:LYS121 3.9 34.0 1.0
O A:HOH386 4.1 33.8 1.0
O A:HOH379 4.1 38.2 1.0
NE2 A:HIS172 4.1 27.9 1.0
CE A:LYS121 4.2 28.3 1.0
HD3 A:LYS121 4.6 30.9 1.0
CD A:LYS121 5.0 25.7 1.0
HG2 A:LYS121 5.0 29.0 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: Fri Aug 8 21:10:17 2025

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