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Iodine in PDB 6s42: The Double Mutant(ILE44LEU+GLN102HIS) of Haloalkane Dehalogenase Dbea From Bradyrhizobium Elkanii USDA94 with An Eliminated Halide-Binding Site

Enzymatic activity of The Double Mutant(ILE44LEU+GLN102HIS) of Haloalkane Dehalogenase Dbea From Bradyrhizobium Elkanii USDA94 with An Eliminated Halide-Binding Site

All present enzymatic activity of The Double Mutant(ILE44LEU+GLN102HIS) of Haloalkane Dehalogenase Dbea From Bradyrhizobium Elkanii USDA94 with An Eliminated Halide-Binding Site:
3.8.1.5;

Protein crystallography data

The structure of The Double Mutant(ILE44LEU+GLN102HIS) of Haloalkane Dehalogenase Dbea From Bradyrhizobium Elkanii USDA94 with An Eliminated Halide-Binding Site, PDB code: 6s42 was solved by T.Pudnikova, J.R.Mesters, I.Kuta Smatanova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.96 / 1.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 128.945, 63.950, 46.053, 90.00, 106.27, 90.00
R / Rfree (%) 14 / 15.2

Other elements in 6s42:

The structure of The Double Mutant(ILE44LEU+GLN102HIS) of Haloalkane Dehalogenase Dbea From Bradyrhizobium Elkanii USDA94 with An Eliminated Halide-Binding Site also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the The Double Mutant(ILE44LEU+GLN102HIS) of Haloalkane Dehalogenase Dbea From Bradyrhizobium Elkanii USDA94 with An Eliminated Halide-Binding Site (pdb code 6s42). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 8 binding sites of Iodine where determined in the The Double Mutant(ILE44LEU+GLN102HIS) of Haloalkane Dehalogenase Dbea From Bradyrhizobium Elkanii USDA94 with An Eliminated Halide-Binding Site, PDB code: 6s42:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iodine binding site 1 out of 8 in 6s42

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Iodine binding site 1 out of 8 in the The Double Mutant(ILE44LEU+GLN102HIS) of Haloalkane Dehalogenase Dbea From Bradyrhizobium Elkanii USDA94 with An Eliminated Halide-Binding Site


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of The Double Mutant(ILE44LEU+GLN102HIS) of Haloalkane Dehalogenase Dbea From Bradyrhizobium Elkanii USDA94 with An Eliminated Halide-Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I402

b:9.9
occ:1.00
 O1 A:HEZ401 3.4 27.3 1.0
NE1 A:TRP104 3.5 8.9 1.0
N A:PRO205 3.6 9.3 1.0
CZ A:PHE167 3.7 9.7 1.0
ND2 A:ASN38 3.7 9.4 1.0
C1 A:HEZ401 3.7 26.9 1.0
CA A:PRO205 3.7 9.4 1.0
CD A:PRO205 3.8 10.0 1.0
C A:LEU204 3.9 9.8 1.0
CE2 A:PHE167 3.9 9.6 1.0
CD1 A:TRP104 3.9 9.9 1.0
CB A:PRO205 4.1 10.7 1.0
CE2 A:PHE148 4.1 10.8 1.0
O A:LEU204 4.1 10.1 1.0
CB A:LEU204 4.1 9.5 1.0
CB A:ASN38 4.2 9.2 1.0
C2 A:HEZ401 4.2 27.0 1.0
CD1 A:LEU208 4.3 11.7 1.0
CG A:ASN38 4.4 8.4 1.0
CG A:LEU208 4.5 8.7 1.0
CG A:PRO205 4.5 11.2 1.0
CD2 A:LEU208 4.5 10.9 1.0
CA A:LEU204 4.6 9.6 1.0
CE1 A:PHE167 4.7 9.4 1.0
CE2 A:TRP104 4.8 8.2 1.0
OD2 A:ASP103 4.8 11.3 1.0
CZ A:PHE148 4.9 10.8 1.0
C3 A:HEZ401 5.0 26.4 1.0
CD2 A:PHE148 5.0 9.8 1.0

Iodine binding site 2 out of 8 in 6s42

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Iodine binding site 2 out of 8 in the The Double Mutant(ILE44LEU+GLN102HIS) of Haloalkane Dehalogenase Dbea From Bradyrhizobium Elkanii USDA94 with An Eliminated Halide-Binding Site


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of The Double Mutant(ILE44LEU+GLN102HIS) of Haloalkane Dehalogenase Dbea From Bradyrhizobium Elkanii USDA94 with An Eliminated Halide-Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I403

b:15.3
occ:1.00
 O A:HOH835 3.5 18.0 1.0
ND2 A:ASN164 3.7 18.7 1.0
NH1 A:ARG170 3.8 27.5 1.0
CG A:MET160 4.1 10.6 1.0
CB A:MET160 4.2 11.1 1.0
CA A:MET160 4.3 11.1 1.0
CB A:ASN164 4.4 12.8 1.0
CB A:ALA166 4.4 11.5 1.0
CD A:ARG170 4.4 23.9 1.0
CE A:MET160 4.4 15.5 1.0
CG A:ASN164 4.5 15.9 1.0
O A:MET160 4.7 11.6 1.0
CZ A:ARG170 4.8 27.6 1.0

Iodine binding site 3 out of 8 in 6s42

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Iodine binding site 3 out of 8 in the The Double Mutant(ILE44LEU+GLN102HIS) of Haloalkane Dehalogenase Dbea From Bradyrhizobium Elkanii USDA94 with An Eliminated Halide-Binding Site


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of The Double Mutant(ILE44LEU+GLN102HIS) of Haloalkane Dehalogenase Dbea From Bradyrhizobium Elkanii USDA94 with An Eliminated Halide-Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I404

b:19.0
occ:0.95
 O A:HOH774 3.3 40.6 1.0
O A:HOH911 3.5 18.6 1.0
CB A:ALA223 4.2 14.7 1.0
CB A:ALA114 4.5 11.4 1.0
O A:ALA114 4.8 15.7 1.0
O A:ALA223 4.8 11.3 1.0
C A:ALA223 5.0 10.1 1.0

Iodine binding site 4 out of 8 in 6s42

Go back to Iodine Binding Sites List in 6s42
Iodine binding site 4 out of 8 in the The Double Mutant(ILE44LEU+GLN102HIS) of Haloalkane Dehalogenase Dbea From Bradyrhizobium Elkanii USDA94 with An Eliminated Halide-Binding Site


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of The Double Mutant(ILE44LEU+GLN102HIS) of Haloalkane Dehalogenase Dbea From Bradyrhizobium Elkanii USDA94 with An Eliminated Halide-Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I405

b:20.1
occ:0.75
 O A:HOH853 2.9 17.9 1.0
O A:HOH613 3.4 16.8 1.0
O A:HOH604 3.5 48.8 1.0
O A:HOH674 3.6 24.1 1.0
O A:HOH786 3.7 28.0 1.0
CB A:ALA144 4.0 18.8 1.0
CA A:ALA144 4.1 16.6 1.0
O6 A:HEZ401 4.1 25.3 1.0
CE1 A:PHE148 4.2 10.3 1.0
CG1 A:VAL171 4.4 12.1 1.0
CG2 A:VAL171 4.4 13.9 1.0
C6 A:HEZ401 4.6 24.6 1.0
CD1 A:PHE148 4.8 10.2 1.0
NE2 A:HIS139 4.8 15.2 1.0
CB A:THR147 4.8 11.3 1.0
CG2 A:THR147 4.8 15.4 1.0
CB A:VAL171 4.8 8.8 1.0
CA A:VAL171 4.8 10.3 1.0
O A:HOH708 4.9 41.2 1.0
N A:ALA144 5.0 15.8 1.0
OG1 A:THR147 5.0 12.8 1.0

Iodine binding site 5 out of 8 in 6s42

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Iodine binding site 5 out of 8 in the The Double Mutant(ILE44LEU+GLN102HIS) of Haloalkane Dehalogenase Dbea From Bradyrhizobium Elkanii USDA94 with An Eliminated Halide-Binding Site


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of The Double Mutant(ILE44LEU+GLN102HIS) of Haloalkane Dehalogenase Dbea From Bradyrhizobium Elkanii USDA94 with An Eliminated Halide-Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I406

b:25.8
occ:0.68
 NH1 A:ARG22 3.4 18.5 0.5
O A:HOH845 3.4 39.2 1.0
NE A:ARG22 3.5 19.9 0.5
O A:HOH751 3.7 40.2 1.0
CZ A:ARG22 3.9 16.9 0.5
NH1 A:ARG22 3.9 22.1 0.5
CG2 A:THR24 4.0 19.5 1.0
CB A:THR24 4.1 16.4 1.0
CB A:MET49 4.2 18.4 1.0
SD A:MET49 4.3 20.7 1.0
CE A:MET49 4.5 21.0 1.0
CD A:ARG22 4.5 18.1 0.5
OG1 A:THR24 4.7 23.0 1.0
O A:HOH552 4.7 30.1 1.0
CD A:PRO50 4.7 15.8 1.0
CG A:PRO50 4.7 16.4 1.0
CB A:ARG22 4.7 15.9 0.5
CB A:ARG22 4.7 15.9 0.5
CD A:ARG22 4.7 16.3 0.5
O A:HOH601 4.8 27.2 1.0
O A:HOH913 4.8 34.7 1.0
CG A:MET49 4.9 13.8 1.0
O A:GLU23 4.9 18.9 1.0

Iodine binding site 6 out of 8 in 6s42

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Iodine binding site 6 out of 8 in the The Double Mutant(ILE44LEU+GLN102HIS) of Haloalkane Dehalogenase Dbea From Bradyrhizobium Elkanii USDA94 with An Eliminated Halide-Binding Site


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of The Double Mutant(ILE44LEU+GLN102HIS) of Haloalkane Dehalogenase Dbea From Bradyrhizobium Elkanii USDA94 with An Eliminated Halide-Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I407

b:19.8
occ:0.62
 O A:HOH813 3.5 39.6 1.0
NZ A:LYS150 3.6 25.3 1.0
O A:HOH890 3.8 38.8 1.0
CE A:LYS150 3.9 20.9 1.0
O A:HOH699 4.6 37.1 1.0
O A:HOH900 4.7 30.0 1.0
CD A:LYS150 4.8 16.2 1.0
CG A:GLU146 4.8 29.2 1.0
O A:HOH778 4.9 22.8 1.0

Iodine binding site 7 out of 8 in 6s42

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Iodine binding site 7 out of 8 in the The Double Mutant(ILE44LEU+GLN102HIS) of Haloalkane Dehalogenase Dbea From Bradyrhizobium Elkanii USDA94 with An Eliminated Halide-Binding Site


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of The Double Mutant(ILE44LEU+GLN102HIS) of Haloalkane Dehalogenase Dbea From Bradyrhizobium Elkanii USDA94 with An Eliminated Halide-Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I408

b:21.7
occ:0.51
 O A:HOH619 3.7 23.7 1.0
CD2 A:HIS11 4.0 17.8 1.0
NE2 A:HIS11 4.3 21.3 1.0
O A:HOH582 4.6 24.2 1.0
CG A:HIS11 5.0 16.2 1.0

Iodine binding site 8 out of 8 in 6s42

Go back to Iodine Binding Sites List in 6s42
Iodine binding site 8 out of 8 in the The Double Mutant(ILE44LEU+GLN102HIS) of Haloalkane Dehalogenase Dbea From Bradyrhizobium Elkanii USDA94 with An Eliminated Halide-Binding Site


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of The Double Mutant(ILE44LEU+GLN102HIS) of Haloalkane Dehalogenase Dbea From Bradyrhizobium Elkanii USDA94 with An Eliminated Halide-Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I409

b:24.3
occ:0.67
 NE2 A:GLN265 2.9 32.1 1.0
O A:HOH830 3.5 36.9 1.0
N A:GLY267 3.6 14.2 1.0
CB A:GLN265 3.8 20.1 1.0
CB A:SER241 3.9 18.6 1.0
CA A:GLY267 4.0 16.5 1.0
N A:SER241 4.0 15.8 1.0
O A:VAL239 4.0 13.8 1.0
C A:GLY240 4.1 13.5 1.0
CD A:GLN265 4.1 24.5 1.0
O A:GLY267 4.1 16.5 1.0
CG A:PRO248 4.2 18.6 1.0
CA A:GLN265 4.3 15.7 1.0
N A:LEU266 4.3 15.4 1.0
CA A:GLY240 4.3 13.5 1.0
C A:GLY267 4.4 17.5 1.0
CG A:GLN265 4.5 25.7 1.0
CA A:SER241 4.5 16.2 1.0
O A:GLY240 4.5 15.6 1.0
CG1 A:VAL239 4.5 14.5 1.0
C A:GLN265 4.6 14.6 1.0
C A:VAL239 4.6 12.3 1.0
CB A:PRO248 4.7 19.3 1.0
C A:LEU266 4.8 14.6 1.0
N A:GLY240 4.8 11.9 1.0

Reference:

T.Prudnikova, I.Kuta Smatanova. Crystallization and Crystallographic Analysis of A Bradyrhizobium Elkanii USDA94 Haloalkane Dehalogenase Variant with An Eliminated Halide-Binding Site Crystals 2019.
ISSN: ESSN 2073-4352
DOI: 10.3390/CRYST9070375
Page generated: Mon Aug 12 00:14:11 2024

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