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Iodine in PDB 6a4y: Crystal Structure of Bovine Lactoperoxidase with Partial Occupancies of Iodide and Scn- Ions at the Substrate Binding Site on the Distal Heme Side at 1.92 A Resolution

Enzymatic activity of Crystal Structure of Bovine Lactoperoxidase with Partial Occupancies of Iodide and Scn- Ions at the Substrate Binding Site on the Distal Heme Side at 1.92 A Resolution

All present enzymatic activity of Crystal Structure of Bovine Lactoperoxidase with Partial Occupancies of Iodide and Scn- Ions at the Substrate Binding Site on the Distal Heme Side at 1.92 A Resolution:
1.11.1.7;

Protein crystallography data

The structure of Crystal Structure of Bovine Lactoperoxidase with Partial Occupancies of Iodide and Scn- Ions at the Substrate Binding Site on the Distal Heme Side at 1.92 A Resolution, PDB code: 6a4y was solved by P.K.Singh, H.V.Sirohi, P.Kaur, S.Sharma, T.P.Singh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.52 / 1.92
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.740, 79.800, 65.180, 90.00, 91.43, 90.00
R / Rfree (%) 22.2 / 27.9

Other elements in 6a4y:

The structure of Crystal Structure of Bovine Lactoperoxidase with Partial Occupancies of Iodide and Scn- Ions at the Substrate Binding Site on the Distal Heme Side at 1.92 A Resolution also contains other interesting chemical elements:

Iron (Fe) 1 atom
Calcium (Ca) 1 atom

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of Bovine Lactoperoxidase with Partial Occupancies of Iodide and Scn- Ions at the Substrate Binding Site on the Distal Heme Side at 1.92 A Resolution (pdb code 6a4y). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 6 binding sites of Iodine where determined in the Crystal Structure of Bovine Lactoperoxidase with Partial Occupancies of Iodide and Scn- Ions at the Substrate Binding Site on the Distal Heme Side at 1.92 A Resolution, PDB code: 6a4y:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6;

Iodine binding site 1 out of 6 in 6a4y

Go back to Iodine Binding Sites List in 6a4y
Iodine binding site 1 out of 6 in the Crystal Structure of Bovine Lactoperoxidase with Partial Occupancies of Iodide and Scn- Ions at the Substrate Binding Site on the Distal Heme Side at 1.92 A Resolution


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 Bovine Lactoperoxidase with Partial Occupancies of Iodide and Scn- Ions at the Substrate Binding Site on the Distal Heme Side at 1.92 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I607

b:70.1
occ:0.30
 S A:SCN619 0.6 39.4 0.7
C A:SCN619 1.3 45.3 0.7
N A:SCN619 2.4 52.8 0.7
O A:HOH757 3.2 48.0 1.0
CD A:ARG255 3.5 55.4 1.0
C4A A:HEM601 3.6 32.4 1.0
O A:HOH786 3.6 35.5 1.0
C3A A:HEM601 3.6 33.0 1.0
CB A:ARG255 3.8 53.0 1.0
CG A:ARG255 3.8 55.8 1.0
C2A A:HEM601 3.8 33.0 1.0
NA A:HEM601 3.8 27.5 1.0
C1A A:HEM601 3.9 31.7 1.0
NE2 A:HIS109 4.0 40.5 1.0
CG A:GLU258 4.0 53.9 1.0
CE1 A:HIS109 4.0 40.6 1.0
O A:HOH785 4.0 45.6 1.0
CHB A:HEM601 4.1 30.8 1.0
CMA A:HEM601 4.2 32.5 1.0
CB A:GLU258 4.4 49.0 1.0
CD A:GLU258 4.4 59.3 1.0
OE1 A:GLU258 4.5 49.8 1.0
CAA A:HEM601 4.6 36.3 1.0
CHA A:HEM601 4.6 27.9 1.0
C1B A:HEM601 4.7 28.5 1.0
NE A:ARG255 4.8 53.3 1.0
NE2 A:GLN105 4.9 33.8 1.0

Iodine binding site 2 out of 6 in 6a4y

Go back to Iodine Binding Sites List in 6a4y
Iodine binding site 2 out of 6 in the Crystal Structure of Bovine Lactoperoxidase with Partial Occupancies of Iodide and Scn- Ions at the Substrate Binding Site on the Distal Heme Side at 1.92 A Resolution


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 Bovine Lactoperoxidase with Partial Occupancies of Iodide and Scn- Ions at the Substrate Binding Site on the Distal Heme Side at 1.92 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I608

b:53.7
occ:0.50
 ND2 A:ASN80 3.3 39.8 1.0
CG A:PRO145 3.7 39.8 1.0
CB A:ASN80 3.7 35.2 1.0
CG A:ASN80 4.0 36.8 1.0
CE A:LYS81 4.3 64.4 1.0
CB A:PRO145 4.3 43.0 1.0
CG A:GLU77 4.5 48.6 1.0
CA A:GLU77 4.6 37.9 1.0
O A:LYS146 4.7 65.7 1.0
CG A:LYS81 4.7 51.7 1.0
CB A:GLU77 4.8 43.6 1.0
CB A:ASN147 4.9 70.8 1.0
CD A:GLU77 4.9 55.9 1.0
O A:GLU77 4.9 33.0 1.0
NZ A:LYS81 5.0 69.4 1.0

Iodine binding site 3 out of 6 in 6a4y

Go back to Iodine Binding Sites List in 6a4y
Iodine binding site 3 out of 6 in the Crystal Structure of Bovine Lactoperoxidase with Partial Occupancies of Iodide and Scn- Ions at the Substrate Binding Site on the Distal Heme Side at 1.92 A Resolution


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 Bovine Lactoperoxidase with Partial Occupancies of Iodide and Scn- Ions at the Substrate Binding Site on the Distal Heme Side at 1.92 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I609

b:55.7
occ:0.50
 C A:SCN616 0.7 23.4 0.5
S A:SCN616 1.5 30.3 0.5
N A:SCN616 1.6 21.6 0.5
NE1 A:TRP530 3.7 62.0 1.0
CZ2 A:TRP530 3.9 68.0 1.0
CB A:PHE309 4.0 45.7 1.0
CE2 A:TRP530 4.2 64.0 1.0
CB A:ARG310 4.3 47.3 1.0
N A:ARG310 4.4 47.7 1.0
CZ2 A:TRP529 4.5 65.1 1.0
C A:PHE309 4.6 44.5 1.0
CA A:ILE306 4.6 57.8 1.0
CA A:ARG310 4.7 51.2 1.0
O A:ILE306 4.7 50.7 1.0
O A:GLN305 4.7 43.2 1.0
CG1 A:ILE306 4.8 61.3 1.0
CA A:PHE309 4.9 41.5 1.0
OE1 A:GLU531 4.9 63.9 1.0
CD1 A:TRP530 5.0 64.2 1.0
O A:PHE309 5.0 43.5 1.0

Iodine binding site 4 out of 6 in 6a4y

Go back to Iodine Binding Sites List in 6a4y
Iodine binding site 4 out of 6 in the Crystal Structure of Bovine Lactoperoxidase with Partial Occupancies of Iodide and Scn- Ions at the Substrate Binding Site on the Distal Heme Side at 1.92 A Resolution


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 Bovine Lactoperoxidase with Partial Occupancies of Iodide and Scn- Ions at the Substrate Binding Site on the Distal Heme Side at 1.92 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I610

b:64.3
occ:0.40
 C A:SCN618 0.9 45.5 0.6
S A:SCN618 0.9 42.4 0.6
N A:SCN618 2.0 50.4 0.6
O A:PRO424 2.7 70.9 1.0
C A:PRO424 3.9 70.2 1.0
CA A:PRO236 3.9 49.8 1.0
CB A:PRO236 4.1 50.8 1.0
CB A:PHE239 4.1 58.5 1.0
CG A:PHE239 4.2 58.7 1.0
N A:PRO236 4.2 51.9 1.0
CD2 A:PHE239 4.2 54.1 1.0
CA A:PRO424 4.4 68.5 1.0
C A:SER235 4.5 63.1 1.0
CB A:PRO234 4.7 84.8 1.0
O A:SER235 4.7 59.1 1.0
CZ A:PHE422 4.8 54.8 1.0
CD A:PRO236 4.8 50.4 1.0
O A:PRO234 4.8 74.3 1.0
CG A:PRO234 4.9 83.9 1.0
C A:PRO234 4.9 77.1 1.0
CD1 A:PHE239 4.9 52.1 1.0
CE2 A:PHE239 4.9 55.9 1.0
N A:THR425 4.9 70.0 1.0
CG A:PRO236 5.0 51.5 1.0
CB A:PRO424 5.0 66.0 1.0

Iodine binding site 5 out of 6 in 6a4y

Go back to Iodine Binding Sites List in 6a4y
Iodine binding site 5 out of 6 in the Crystal Structure of Bovine Lactoperoxidase with Partial Occupancies of Iodide and Scn- Ions at the Substrate Binding Site on the Distal Heme Side at 1.92 A Resolution


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure of Bovine Lactoperoxidase with Partial Occupancies of Iodide and Scn- Ions at the Substrate Binding Site on the Distal Heme Side at 1.92 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I620

b:52.9
occ:0.50
 N A:ASP87 3.3 41.7 1.0
N A:LEU86 3.4 40.3 1.0
CB A:ASP87 3.8 48.2 1.0
CE A:LYS411 4.0 47.5 1.0
CB A:LEU86 4.0 44.9 1.0
CA A:LEU86 4.1 45.4 1.0
CA A:ASP87 4.1 43.8 1.0
CB A:TYR85 4.1 33.2 1.0
C A:LEU86 4.2 40.8 1.0
C A:TYR85 4.4 42.8 1.0
CA A:TYR85 4.5 35.1 1.0
O A:ASP87 4.6 43.4 1.0
NZ A:LYS411 4.7 53.2 1.0
CG A:LEU86 4.7 52.5 1.0
CD2 A:TYR85 4.8 34.0 1.0
C A:ASP87 4.9 39.4 1.0
CG A:TYR85 5.0 33.5 1.0
CD A:LYS411 5.0 41.8 1.0

Iodine binding site 6 out of 6 in 6a4y

Go back to Iodine Binding Sites List in 6a4y
Iodine binding site 6 out of 6 in the Crystal Structure of Bovine Lactoperoxidase with Partial Occupancies of Iodide and Scn- Ions at the Substrate Binding Site on the Distal Heme Side at 1.92 A Resolution


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structure of Bovine Lactoperoxidase with Partial Occupancies of Iodide and Scn- Ions at the Substrate Binding Site on the Distal Heme Side at 1.92 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I621

b:62.1
occ:0.50
 N A:LYS462 3.5 43.2 1.0
OG1 A:THR463 3.6 48.5 1.0
N A:THR463 3.9 45.8 1.0
CA A:GLY466 4.0 40.2 1.0
CA A:PRO461 4.1 42.3 1.0
CG2 A:THR463 4.2 49.4 1.0
C A:PRO461 4.3 44.3 1.0
CA A:LYS462 4.3 48.5 1.0
CB A:THR463 4.4 44.1 1.0
CB A:LYS462 4.4 53.7 1.0
N A:GLY466 4.5 42.8 1.0
C A:LYS462 4.6 45.2 1.0
CB A:PRO461 4.6 45.3 1.0
CA A:THR463 4.8 44.4 1.0

Reference:

P.K.Singh, H.V.Sirohi, P.Kaur, S.Sharma, T.P.Singh. Crystal Structure of Bovine Lactoperoxidase with Partial Occupancies of Iodide and Scn- Ions at the Substrate Binding Site on the Distal Heme Side at 1.92 A Resolution To Be Published.
Page generated: Sun Aug 11 22:28:41 2024

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