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Iodine in PDB 6dop: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 200 Mm K+ For 120 S at 21 C (Dataset 1)

Enzymatic activity of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 200 Mm K+ For 120 S at 21 C (Dataset 1)

All present enzymatic activity of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 200 Mm K+ For 120 S at 21 C (Dataset 1):
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 2 Mm MG2+ and 200 Mm K+ For 120 S at 21 C (Dataset 1), PDB code: 6dop 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) 19.87 / 1.25
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 81.535, 37.625, 61.837, 90.00, 95.84, 90.00
R / Rfree (%) 16.2 / 17.8

Other elements in 6dop:

The structure of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 200 Mm K+ For 120 S at 21 C (Dataset 1) 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: Reaction in 2 Mm MG2+ and 200 Mm K+ For 120 S at 21 C (Dataset 1) (pdb code 6dop). 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 2 Mm MG2+ and 200 Mm K+ For 120 S at 21 C (Dataset 1), PDB code: 6dop:
Jump to Iodine binding site number: 1; 2; 3; 4;

Iodine binding site 1 out of 4 in 6dop

Go back to Iodine Binding Sites List in 6dop
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 2 Mm MG2+ and 200 Mm K+ For 120 S at 21 C (Dataset 1)


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 2 Mm MG2+ and 200 Mm K+ For 120 S at 21 C (Dataset 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I203

b:16.1
occ:0.70
HH A:TYR83 2.6 21.6 1.0
HD3 A:ARG97 3.3 23.4 1.0
HD22 A:LEU161 3.3 26.2 1.0
HD22 A:LEU111 3.4 16.6 1.0
HE2 A:TYR83 3.4 17.4 1.0
OH A:TYR83 3.4 18.0 1.0
HB3 A:LEU111 3.4 15.8 1.0
HB3 A:LEU161 3.4 20.6 1.0
HD13 A:LEU161 3.4 27.8 1.0
HD13 A:LEU111 3.4 18.4 1.0
O A:HOH368 3.5 18.1 1.0
O A:HOH352 3.6 16.9 1.0
HH11 A:ARG97 3.7 32.5 1.0
C1 A:GOL213 3.8 42.5 1.0
CE2 A:TYR83 4.1 14.5 1.0
NH1 A:ARG97 4.2 27.1 1.0
CZ A:TYR83 4.2 14.8 1.0
CD2 A:LEU161 4.2 21.8 1.0
CD2 A:LEU111 4.3 13.8 1.0
O1 A:GOL213 4.3 28.9 1.0
CD A:ARG97 4.3 19.5 1.0
CB A:LEU161 4.3 17.2 1.0
CD1 A:LEU161 4.3 23.2 1.0
CB A:LEU111 4.3 13.2 1.0
CD1 A:LEU111 4.3 15.3 1.0
HG2 A:ARG97 4.4 18.7 1.0
CG A:LEU161 4.5 19.6 1.0
HH12 A:ARG97 4.5 32.5 1.0
CG A:LEU111 4.5 13.7 1.0
HB2 A:HIS115 4.6 16.0 1.0
HD11 A:ILE100 4.7 24.6 1.0
HD21 A:LEU161 4.7 26.2 1.0
HD23 A:LEU161 4.8 26.2 1.0
O A:HOH305 4.8 43.8 1.0
HD2 A:ARG97 4.8 23.4 1.0
HD21 A:LEU111 4.8 16.6 1.0
HD23 A:LEU111 4.8 16.6 1.0
HD11 A:LEU161 4.8 27.8 1.0
HB2 A:LEU111 4.8 15.8 1.0
HB2 A:LEU161 4.8 20.6 1.0
O A:HOH379 4.8 20.3 1.0
HD11 A:LEU111 4.8 18.4 1.0
CZ A:ARG97 4.9 21.4 1.0
CG A:ARG97 4.9 15.6 1.0
NE A:ARG97 4.9 20.4 1.0
HD12 A:LEU111 4.9 18.4 1.0
HD12 A:LEU161 4.9 27.8 1.0

Iodine binding site 2 out of 4 in 6dop

Go back to Iodine Binding Sites List in 6dop
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 2 Mm MG2+ and 200 Mm K+ For 120 S at 21 C (Dataset 1)


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 2 Mm MG2+ and 200 Mm K+ For 120 S at 21 C (Dataset 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I204

b:38.5
occ:0.40
HB2 A:LYS180 3.2 23.4 1.0
HD3 A:LYS180 3.2 26.8 1.0
O A:HOH366 3.2 22.0 1.0
O A:HOH433 3.2 38.0 1.0
HA A:GLN134 3.3 23.4 1.0
HG3 A:GLN134 3.3 31.0 1.0
O A:HOH317 3.6 35.4 1.0
HD12 A:ILE137 3.7 21.9 1.0
HG2 A:LYS180 3.8 24.2 1.0
HG21 A:ILE137 4.0 21.5 1.0
CD A:LYS180 4.0 22.3 1.0
CB A:LYS180 4.0 19.5 1.0
HD13 A:ILE137 4.0 21.9 1.0
HB A:ILE137 4.1 19.8 1.0
CG A:LYS180 4.1 20.2 1.0
CA A:GLN134 4.2 19.5 1.0
CG A:GLN134 4.2 25.8 1.0
HB2 A:GLN134 4.3 25.4 1.0
CD1 A:ILE137 4.3 18.3 1.0
HB3 A:LYS180 4.4 23.4 1.0
HE3 A:LYS180 4.4 26.8 1.0
CB A:GLN134 4.5 21.1 1.0
O A:HOH427 4.5 33.5 1.0
HE21 A:GLN134 4.6 31.7 1.0
CG2 A:ILE137 4.6 17.9 1.0
HD2 A:LYS180 4.7 26.8 1.0
CE A:LYS180 4.7 22.4 1.0
HG22 A:ILE137 4.7 21.5 1.0
HG2 A:GLN134 4.7 31.0 1.0
CB A:ILE137 4.8 16.5 1.0
HE2 A:LYS180 4.9 26.8 1.0
O A:GLN134 4.9 19.0 1.0

Iodine binding site 3 out of 4 in 6dop

Go back to Iodine Binding Sites List in 6dop
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 2 Mm MG2+ and 200 Mm K+ For 120 S at 21 C (Dataset 1)


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 2 Mm MG2+ and 200 Mm K+ For 120 S at 21 C (Dataset 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I205

b:31.5
occ:0.30
O A:HOH439 2.9 39.5 1.0
O A:HOH436 3.0 37.6 1.0
HD11 A:LEU179 3.1 23.3 1.0
HG2 A:PRO177 3.1 22.3 1.0
HG3 A:PRO128 3.2 23.7 1.0
CD1 A:ILE64 3.5 40.2 1.0
HB3 A:PRO128 3.5 19.7 1.0
HB2 A:PRO177 3.6 21.7 1.0
HD21 A:LEU179 3.8 25.5 1.0
CG A:PRO177 3.9 18.6 1.0
CB A:PRO177 4.0 18.1 1.0
HB3 A:PRO177 4.0 21.7 1.0
CG A:PRO128 4.0 19.8 1.0
CD1 A:LEU179 4.0 19.4 1.0
HG21 A:ILE64 4.1 29.3 1.0
CB A:PRO128 4.2 16.4 1.0
O A:HOH440 4.3 51.7 1.0
HD13 A:LEU179 4.3 23.3 1.0
HD3 A:PRO128 4.4 17.1 1.0
HG3 A:PRO177 4.5 22.3 1.0
HB2 A:PRO128 4.6 19.7 1.0
HD12 A:LEU179 4.6 23.3 1.0
CD2 A:LEU179 4.6 21.3 1.0
HG2 A:PRO128 4.7 23.7 1.0
CG1 A:ILE64 4.8 32.6 1.0
CG A:LEU179 4.8 18.0 1.0
HD2 A:PRO177 4.8 20.1 1.0
CD A:PRO128 4.8 14.3 1.0
HG A:LEU179 4.8 21.6 1.0
HD22 A:LEU179 4.9 25.5 1.0
HG12 A:ILE64 4.9 39.2 1.0
O A:HOH434 4.9 34.9 1.0
CD A:PRO177 5.0 16.7 1.0

Iodine binding site 4 out of 4 in 6dop

Go back to Iodine Binding Sites List in 6dop
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 2 Mm MG2+ and 200 Mm K+ For 120 S at 21 C (Dataset 1)


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 2 Mm MG2+ and 200 Mm K+ For 120 S at 21 C (Dataset 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I206

b:38.3
occ:0.35
HD2 A:HIS172 3.0 22.8 1.0
HE3 A:LYS121 3.4 58.3 1.0
O A:HOH421 3.7 38.9 1.0
HE2 A:LYS121 3.7 58.3 1.0
CD2 A:HIS172 3.7 19.0 1.0
O A:HOH395 3.9 35.2 1.0
CE A:LYS121 4.0 48.6 1.0
O A:HOH385 4.0 37.6 1.0
NE2 A:HIS172 4.1 20.1 1.0
HD3 A:LYS121 4.4 29.2 1.0
CD A:LYS121 4.8 24.4 1.0
CG A:HIS172 5.0 16.1 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 22:57:30 2024

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