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Iodine in PDB 1arx: Crystal Structures of Cyanide-and Triiodide-Bound Forms of Arthromyces Ramosus Peroxidase at Different pH Values. Perturbations of Active Site Residues and Their Implication in Enzyme Catalysis

Enzymatic activity of Crystal Structures of Cyanide-and Triiodide-Bound Forms of Arthromyces Ramosus Peroxidase at Different pH Values. Perturbations of Active Site Residues and Their Implication in Enzyme Catalysis

All present enzymatic activity of Crystal Structures of Cyanide-and Triiodide-Bound Forms of Arthromyces Ramosus Peroxidase at Different pH Values. Perturbations of Active Site Residues and Their Implication in Enzyme Catalysis:
1.11.1.7;

Protein crystallography data

The structure of Crystal Structures of Cyanide-and Triiodide-Bound Forms of Arthromyces Ramosus Peroxidase at Different pH Values. Perturbations of Active Site Residues and Their Implication in Enzyme Catalysis, PDB code: 1arx was solved by K.Fukuyama, N.Kunishima, F.Amada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 7.00 / 1.90
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 74.570, 74.570, 117.470, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / n/a

Other elements in 1arx:

The structure of Crystal Structures of Cyanide-and Triiodide-Bound Forms of Arthromyces Ramosus Peroxidase at Different pH Values. Perturbations of Active Site Residues and Their Implication in Enzyme Catalysis also contains other interesting chemical elements:

Potassium (K) 1 atom
Iron (Fe) 1 atom
Calcium (Ca) 2 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structures of Cyanide-and Triiodide-Bound Forms of Arthromyces Ramosus Peroxidase at Different pH Values. Perturbations of Active Site Residues and Their Implication in Enzyme Catalysis (pdb code 1arx). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 7 binding sites of Iodine where determined in the Crystal Structures of Cyanide-and Triiodide-Bound Forms of Arthromyces Ramosus Peroxidase at Different pH Values. Perturbations of Active Site Residues and Their Implication in Enzyme Catalysis, PDB code: 1arx:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7;

Iodine binding site 1 out of 7 in 1arx

Go back to Iodine Binding Sites List in 1arx
Iodine binding site 1 out of 7 in the Crystal Structures of Cyanide-and Triiodide-Bound Forms of Arthromyces Ramosus Peroxidase at Different pH Values. Perturbations of Active Site Residues and Their Implication in Enzyme Catalysis


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structures of Cyanide-and Triiodide-Bound Forms of Arthromyces Ramosus Peroxidase at Different pH Values. Perturbations of Active Site Residues and Their Implication in Enzyme Catalysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I675

b:40.2
occ:1.00
 I A:IOD676 3.0 35.2 1.0
O A:HOH733 3.0 23.3 1.0
O A:HOH827 3.2 30.2 1.0
I A:IOD679 3.3 37.7 1.0
CMA A:HEM345 3.7 8.3 1.0
CA A:ALA92 3.9 13.0 1.0
O A:ALA92 4.1 13.3 1.0
I A:IOD680 4.2 28.4 1.0
CB A:ALA92 4.3 12.6 1.0
CD A:PRO156 4.3 18.1 1.0
C3A A:HEM345 4.3 10.7 1.0
C A:ALA92 4.4 11.9 1.0
CD1 A:LEU192 4.5 20.5 1.0
NH2 A:ARG52 4.5 12.3 1.0
O A:PRO91 4.5 15.1 1.0
CBA A:HEM345 4.6 12.9 1.0
CG A:PRO156 4.7 16.1 1.0
C2A A:HEM345 4.9 10.8 1.0
N A:ALA92 4.9 15.4 1.0

Iodine binding site 2 out of 7 in 1arx

Go back to Iodine Binding Sites List in 1arx
Iodine binding site 2 out of 7 in the Crystal Structures of Cyanide-and Triiodide-Bound Forms of Arthromyces Ramosus Peroxidase at Different pH Values. Perturbations of Active Site Residues and Their Implication in Enzyme Catalysis


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structures of Cyanide-and Triiodide-Bound Forms of Arthromyces Ramosus Peroxidase at Different pH Values. Perturbations of Active Site Residues and Their Implication in Enzyme Catalysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I676

b:35.2
occ:1.00
 I A:IOD677 3.0 35.2 1.0
I A:IOD675 3.0 40.2 1.0
O A:HOH884 3.3 20.4 1.0
C3A A:HEM345 3.4 10.7 1.0
C4A A:HEM345 3.4 10.0 1.0
CE1 A:HIS56 3.5 17.1 1.0
NE A:ARG52 3.7 13.5 1.0
NH2 A:ARG52 3.7 12.3 1.0
CHB A:HEM345 3.8 10.6 1.0
C2A A:HEM345 3.8 10.8 1.0
NE2 A:HIS56 3.8 15.9 1.0
O A:ALA92 3.9 13.3 1.0
NA A:HEM345 3.9 11.3 1.0
CMA A:HEM345 3.9 8.3 1.0
CZ A:ARG52 4.1 13.9 1.0
C1A A:HEM345 4.1 11.3 1.0
CBA A:HEM345 4.2 12.9 1.0
C1B A:HEM345 4.5 12.5 1.0
CAA A:HEM345 4.6 13.4 1.0
CB A:ALA92 4.7 12.6 1.0
ND1 A:HIS56 4.7 14.4 1.0
CD A:ARG52 4.8 14.9 1.0
C A:ALA92 4.8 11.9 1.0
CA A:ALA92 4.9 13.0 1.0
CHA A:HEM345 5.0 10.5 1.0
NB A:HEM345 5.0 10.9 1.0

Iodine binding site 3 out of 7 in 1arx

Go back to Iodine Binding Sites List in 1arx
Iodine binding site 3 out of 7 in the Crystal Structures of Cyanide-and Triiodide-Bound Forms of Arthromyces Ramosus Peroxidase at Different pH Values. Perturbations of Active Site Residues and Their Implication in Enzyme Catalysis


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structures of Cyanide-and Triiodide-Bound Forms of Arthromyces Ramosus Peroxidase at Different pH Values. Perturbations of Active Site Residues and Their Implication in Enzyme Catalysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I677

b:35.2
occ:1.00
 I A:IOD676 3.0 35.2 1.0
NE2 A:HIS56 3.1 15.9 1.0
FE A:HEM345 3.2 10.7 1.0
O A:HOH884 3.4 20.4 1.0
NA A:HEM345 3.4 11.3 1.0
CE1 A:HIS56 3.5 17.1 1.0
CG A:ARG52 3.6 12.1 1.0
NB A:HEM345 3.7 10.9 1.0
ND A:HEM345 3.7 10.4 1.0
NE A:ARG52 3.7 13.5 1.0
NC A:HEM345 3.8 11.3 1.0
C4A A:HEM345 3.9 10.0 1.0
CD2 A:PHE55 4.0 13.7 1.0
CD2 A:HIS56 4.0 14.0 1.0
C1A A:HEM345 4.0 11.3 1.0
CB A:ARG52 4.1 11.2 1.0
C1B A:HEM345 4.1 12.5 1.0
CD A:ARG52 4.1 14.9 1.0
CHB A:HEM345 4.2 10.6 1.0
C4C A:HEM345 4.3 11.0 1.0
C4D A:HEM345 4.3 11.2 1.0
CA A:ARG52 4.3 9.5 1.0
CHA A:HEM345 4.4 10.5 1.0
C1D A:HEM345 4.4 12.0 1.0
CE2 A:PHE55 4.4 11.9 1.0
C1C A:HEM345 4.5 12.1 1.0
C4B A:HEM345 4.5 12.6 1.0
ND1 A:HIS56 4.5 14.4 1.0
CHD A:HEM345 4.6 11.0 1.0
C3A A:HEM345 4.7 10.7 1.0
C2A A:HEM345 4.7 10.8 1.0
CG A:HIS56 4.7 12.7 1.0
O A:ARG52 4.8 10.2 1.0
CHC A:HEM345 4.8 11.8 1.0
CZ A:ARG52 4.9 13.9 1.0

Iodine binding site 4 out of 7 in 1arx

Go back to Iodine Binding Sites List in 1arx
Iodine binding site 4 out of 7 in the Crystal Structures of Cyanide-and Triiodide-Bound Forms of Arthromyces Ramosus Peroxidase at Different pH Values. Perturbations of Active Site Residues and Their Implication in Enzyme Catalysis


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structures of Cyanide-and Triiodide-Bound Forms of Arthromyces Ramosus Peroxidase at Different pH Values. Perturbations of Active Site Residues and Their Implication in Enzyme Catalysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I678

b:34.4
occ:0.54
 I A:IOD679 2.9 37.7 1.0
O A:HOH735 3.1 36.1 1.0
O A:HOH733 3.5 23.3 1.0
O A:HOH858 3.7 23.9 1.0
O A:GLY191 3.7 20.2 1.0
CD1 A:LEU192 3.8 20.5 1.0
O A:HOH827 4.3 30.2 1.0
C A:GLY191 4.3 18.2 1.0
CD2 A:PHE230 4.4 23.7 1.0
O A:HOH734 4.7 33.7 1.0
CA A:LEU192 4.7 19.1 1.0
N A:LEU192 4.7 18.7 1.0

Iodine binding site 5 out of 7 in 1arx

Go back to Iodine Binding Sites List in 1arx
Iodine binding site 5 out of 7 in the Crystal Structures of Cyanide-and Triiodide-Bound Forms of Arthromyces Ramosus Peroxidase at Different pH Values. Perturbations of Active Site Residues and Their Implication in Enzyme Catalysis


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structures of Cyanide-and Triiodide-Bound Forms of Arthromyces Ramosus Peroxidase at Different pH Values. Perturbations of Active Site Residues and Their Implication in Enzyme Catalysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I679

b:37.7
occ:1.00
 I A:IOD680 2.7 28.4 1.0
I A:IOD678 2.9 34.4 0.5
I A:IOD675 3.3 40.2 1.0
O A:PRO91 3.8 15.1 1.0
O A:HOH733 3.9 23.3 1.0
CE2 A:PHE230 3.9 23.0 1.0
O A:HOH827 3.9 30.2 1.0
CD2 A:PHE230 4.0 23.7 1.0
O A:HOH735 4.0 36.1 1.0
CD1 A:LEU192 4.2 20.5 1.0
C A:PRO91 4.6 14.3 1.0
CD A:PRO156 4.7 18.1 1.0
CG A:PRO156 4.7 16.1 1.0
CA A:ALA92 4.8 13.0 1.0
N A:ALA92 5.0 15.4 1.0

Iodine binding site 6 out of 7 in 1arx

Go back to Iodine Binding Sites List in 1arx
Iodine binding site 6 out of 7 in the Crystal Structures of Cyanide-and Triiodide-Bound Forms of Arthromyces Ramosus Peroxidase at Different pH Values. Perturbations of Active Site Residues and Their Implication in Enzyme Catalysis


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structures of Cyanide-and Triiodide-Bound Forms of Arthromyces Ramosus Peroxidase at Different pH Values. Perturbations of Active Site Residues and Their Implication in Enzyme Catalysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I680

b:28.4
occ:1.00
 I A:IOD679 2.7 37.7 1.0
I A:IOD681 2.9 35.9 0.5
O A:HOH883 3.5 22.1 1.0
O A:HOH737 4.0 11.8 1.0
CD A:PRO156 4.0 18.1 1.0
N A:ALA92 4.2 15.4 1.0
I A:IOD675 4.2 40.2 1.0
C A:PRO91 4.2 14.3 1.0
CA A:ALA92 4.2 13.0 1.0
O A:PRO91 4.3 15.1 1.0
CB A:ALA92 4.3 12.6 1.0
CB A:PRO91 4.3 12.9 1.0
CE2 A:PHE230 4.4 23.0 1.0
CA A:GLY155 4.4 16.8 1.0
CG A:PRO156 4.8 16.1 1.0
CG A:PRO91 4.9 13.5 1.0
CA A:PRO91 4.9 14.5 1.0

Iodine binding site 7 out of 7 in 1arx

Go back to Iodine Binding Sites List in 1arx
Iodine binding site 7 out of 7 in the Crystal Structures of Cyanide-and Triiodide-Bound Forms of Arthromyces Ramosus Peroxidase at Different pH Values. Perturbations of Active Site Residues and Their Implication in Enzyme Catalysis


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Structures of Cyanide-and Triiodide-Bound Forms of Arthromyces Ramosus Peroxidase at Different pH Values. Perturbations of Active Site Residues and Their Implication in Enzyme Catalysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I681

b:35.9
occ:0.46
 O A:HOH883 2.6 22.1 1.0
I A:IOD680 2.9 28.4 1.0
O A:HOH737 3.8 11.8 1.0
O A:HOH756 4.0 18.8 1.0
CA A:GLY155 4.0 16.8 1.0
O A:HOH833 4.1 36.8 1.0
O A:ILE153 4.3 14.7 1.0
N A:GLY155 4.4 17.7 1.0
CG A:PRO91 4.4 13.5 1.0
CB A:ALA92 4.7 12.6 1.0
ND2 A:ASN158 4.8 21.7 1.0
CB A:PRO91 4.9 12.9 1.0
N A:ALA92 4.9 15.4 1.0
C A:PRO154 5.0 17.5 1.0

Reference:

K.Fukuyama, N.Kunishima, F.Amada, T.Kubota, H.Matsubara. Crystal Structures of Cyanide- and Triiodide-Bound Forms of Arthromyces Ramosus Peroxidase at Different pH Values. Perturbations of Active Site Residues and Their Implication in Enzyme Catalysis. J.Biol.Chem. V. 270 21884 1995.
ISSN: ISSN 0021-9258
PubMed: 7665612
DOI: 10.1074/JBC.270.37.21884
Page generated: Sun Dec 13 19:19:05 2020

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