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Iodine in PDB 4y55: Crystal Structure of Buffalo Lactoperoxidase with Rhodanide at 2.09 Angstrom Resolution

Enzymatic activity of Crystal Structure of Buffalo Lactoperoxidase with Rhodanide at 2.09 Angstrom Resolution

All present enzymatic activity of Crystal Structure of Buffalo Lactoperoxidase with Rhodanide at 2.09 Angstrom Resolution:
1.11.1.7;

Protein crystallography data

The structure of Crystal Structure of Buffalo Lactoperoxidase with Rhodanide at 2.09 Angstrom Resolution, PDB code: 4y55 was solved by A.Gupta, T.K.Tyagi, 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) 35.33 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.012, 80.047, 76.800, 90.00, 102.64, 90.00
R / Rfree (%) 23.6 / 29.8

Other elements in 4y55:

The structure of Crystal Structure of Buffalo Lactoperoxidase with Rhodanide at 2.09 Angstrom 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 Buffalo Lactoperoxidase with Rhodanide at 2.09 Angstrom Resolution (pdb code 4y55). 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 Buffalo Lactoperoxidase with Rhodanide at 2.09 Angstrom Resolution, PDB code: 4y55:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6;

Iodine binding site 1 out of 6 in 4y55

Go back to Iodine Binding Sites List in 4y55
Iodine binding site 1 out of 6 in the Crystal Structure of Buffalo Lactoperoxidase with Rhodanide at 2.09 Angstrom 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 Buffalo Lactoperoxidase with Rhodanide at 2.09 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I612

b:1.0
occ:1.00
 N A:PHE229 3.6 51.7 1.0
OD1 A:ASN216 3.7 53.5 1.0
CG A:ASN216 3.9 58.5 1.0
CD2 A:PHE229 3.9 73.5 1.0
N A:GLN217 4.0 57.0 1.0
ND2 A:ASN216 4.0 57.2 1.0
CA A:PRO228 4.1 52.1 1.0
CA A:ASN216 4.1 60.7 1.0
CB A:PHE229 4.2 58.6 1.0
CG A:PHE229 4.4 68.5 1.0
C A:PRO228 4.4 53.0 1.0
CA A:PHE229 4.5 50.9 1.0
CB A:PRO228 4.5 52.9 1.0
OE1 A:GLU218 4.5 78.2 1.0
N A:GLU218 4.5 67.3 1.0
CG A:GLU218 4.6 75.7 1.0
CD A:GLU218 4.6 77.0 1.0
CB A:ASN216 4.6 57.8 1.0
C A:ASN216 4.6 55.6 1.0
CB A:GLU218 4.7 68.0 1.0
CE2 A:PHE229 4.8 72.4 1.0
O A:PHE229 4.9 50.3 1.0
O A:HOH862 4.9 52.3 1.0
O A:HOH833 5.0 60.7 1.0
O A:VAL215 5.0 56.0 1.0

Iodine binding site 2 out of 6 in 4y55

Go back to Iodine Binding Sites List in 4y55
Iodine binding site 2 out of 6 in the Crystal Structure of Buffalo Lactoperoxidase with Rhodanide at 2.09 Angstrom 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 Buffalo Lactoperoxidase with Rhodanide at 2.09 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I613

b:79.2
occ:1.00
 O A:PRO424 2.7 78.4 1.0
CA A:PRO236 3.6 49.1 1.0
CB A:PRO236 3.7 53.5 1.0
C A:PRO424 3.8 65.7 1.0
N A:PRO236 3.9 53.8 1.0
CB A:PHE239 4.0 55.9 1.0
O A:SER235 4.1 52.2 1.0
C A:SER235 4.2 57.9 1.0
CG A:PHE239 4.3 57.8 1.0
CA A:PRO424 4.5 62.6 1.0
N A:THR425 4.6 65.8 1.0
CB A:PRO234 4.6 86.2 1.0
CG A:PRO236 4.6 55.0 1.0
CD1 A:PHE239 4.7 61.1 1.0
CD A:PRO236 4.7 53.3 1.0
CA A:THR425 4.7 77.1 1.0
CZ A:PHE422 4.9 50.4 1.0
CD2 A:PHE239 4.9 56.0 1.0
C A:PRO236 5.0 45.3 1.0
C A:PRO234 5.0 74.9 1.0

Iodine binding site 3 out of 6 in 4y55

Go back to Iodine Binding Sites List in 4y55
Iodine binding site 3 out of 6 in the Crystal Structure of Buffalo Lactoperoxidase with Rhodanide at 2.09 Angstrom 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 Buffalo Lactoperoxidase with Rhodanide at 2.09 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I614

b:74.2
occ:1.00
 NZ A:LYS561 3.4 68.3 1.0
NE A:ARG397 3.6 47.6 1.0
N A:THR560 3.8 53.2 1.0
CG2 A:ILE559 3.8 59.4 1.0
NH2 A:ARG397 3.8 52.0 1.0
O A:GLU363 4.0 51.3 1.0
CA A:ILE559 4.0 58.8 1.0
N A:LYS561 4.1 50.3 1.0
CZ A:ARG397 4.2 48.1 1.0
CA A:GLU363 4.2 56.8 1.0
CB A:GLU363 4.3 69.8 1.0
OG1 A:THR560 4.3 53.5 1.0
CE2 A:TYR365 4.3 50.1 1.0
C A:ILE559 4.4 52.5 1.0
CB A:ILE559 4.4 61.5 1.0
CB A:LYS561 4.5 56.9 1.0
C A:GLU363 4.5 53.0 1.0
O A:HIS558 4.6 55.8 1.0
CD A:ARG397 4.6 50.2 1.0
CD1 A:ILE559 4.8 62.1 1.0
CA A:THR560 4.8 48.3 1.0
C A:THR560 4.8 48.5 1.0
O A:LYS561 4.8 38.5 1.0
CE A:LYS561 4.8 66.6 1.0
CA A:LYS561 4.9 51.9 1.0
OH A:TYR365 4.9 44.4 1.0

Iodine binding site 4 out of 6 in 4y55

Go back to Iodine Binding Sites List in 4y55
Iodine binding site 4 out of 6 in the Crystal Structure of Buffalo Lactoperoxidase with Rhodanide at 2.09 Angstrom 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 Buffalo Lactoperoxidase with Rhodanide at 2.09 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I615

b:33.9
occ:1.00
 O A:HOH778 3.3 32.2 1.0
N A:TRP46 3.3 30.0 1.0
N A:VAL342 3.4 28.4 1.0
CH2 A:TRP452 3.7 36.7 1.0
CB A:ASN341 3.9 27.9 1.0
CA A:ARG45 3.9 34.5 1.0
N A:ASN341 3.9 33.1 1.0
CB A:VAL342 3.9 29.0 1.0
O A:ALA44 3.9 36.8 1.0
CZ2 A:TRP452 3.9 33.9 1.0
C A:ARG45 4.1 34.8 1.0
N A:LEU47 4.1 35.1 1.0
CG1 A:VAL342 4.1 26.2 1.0
CE A:MET446 4.2 27.2 1.0
CA A:VAL342 4.2 27.7 1.0
C A:ASN341 4.2 31.1 1.0
CA A:ASN341 4.2 30.6 1.0
O A:LEU47 4.3 37.0 1.0
CA A:TRP46 4.3 32.8 1.0
CB A:TRP46 4.3 32.3 1.0
CD A:ARG45 4.4 32.6 1.0
CB A:SER340 4.6 30.4 1.0
NH1 A:ARG45 4.7 36.3 1.0
C A:TRP46 4.7 35.2 1.0
CB A:ARG45 4.8 33.1 1.0
C A:ALA44 4.8 42.0 1.0
N A:ARG45 4.8 35.9 1.0
C A:SER340 4.8 33.8 1.0
CG A:TRP46 4.9 34.1 1.0
SD A:MET446 4.9 31.1 1.0
OG A:SER340 5.0 31.9 1.0
CZ3 A:TRP452 5.0 29.7 1.0

Iodine binding site 5 out of 6 in 4y55

Go back to Iodine Binding Sites List in 4y55
Iodine binding site 5 out of 6 in the Crystal Structure of Buffalo Lactoperoxidase with Rhodanide at 2.09 Angstrom 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 Buffalo Lactoperoxidase with Rhodanide at 2.09 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I616

b:88.3
occ:1.00
 OG1 A:THR463 3.2 42.6 1.0
N A:LYS462 3.4 41.8 1.0
N A:THR463 3.7 44.7 1.0
CA A:GLY466 4.0 45.5 1.0
CB A:THR463 4.1 45.9 1.0
CA A:PRO461 4.2 49.0 1.0
CG2 A:THR463 4.2 49.2 1.0
CA A:LYS462 4.3 46.1 1.0
C A:PRO461 4.3 41.1 1.0
O A:THR463 4.4 39.8 1.0
CB A:LYS462 4.4 44.7 1.0
CA A:THR463 4.4 44.5 1.0
C A:LYS462 4.5 44.1 1.0
N A:GLY466 4.5 43.4 1.0
CG A:LYS462 4.8 51.4 1.0
CB A:PRO461 4.8 50.4 1.0
C A:THR463 4.9 40.5 1.0
C A:GLY466 5.0 40.2 1.0

Iodine binding site 6 out of 6 in 4y55

Go back to Iodine Binding Sites List in 4y55
Iodine binding site 6 out of 6 in the Crystal Structure of Buffalo Lactoperoxidase with Rhodanide at 2.09 Angstrom 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 Buffalo Lactoperoxidase with Rhodanide at 2.09 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I626

b:56.8
occ:1.00
 NE1 A:TRP530 3.7 36.8 1.0
CB A:PHE309 3.9 39.0 1.0
CZ2 A:TRP530 4.0 36.0 1.0
CE2 A:TRP530 4.2 37.7 1.0
N A:ARG310 4.4 39.7 1.0
CA A:ILE306 4.6 35.4 1.0
CB A:ARG310 4.6 42.3 1.0
OE1 A:GLU531 4.6 63.9 1.0
C A:PHE309 4.6 37.5 1.0
CZ2 A:TRP529 4.7 49.5 1.0
CG1 A:ILE306 4.8 43.3 1.0
O A:ILE306 4.8 40.6 1.0
CA A:PHE309 4.8 36.0 1.0
CD1 A:TRP530 4.9 40.4 1.0
CA A:ARG310 4.9 41.6 1.0
O A:GLN305 4.9 28.9 1.0
CG A:PHE309 4.9 37.1 1.0

Reference:

A.Gupta, T.K.Tyagi, P.Kaur, S.Sharma, T.P.Singh. Crystal Structure of Buffalo Lactoperoxidase with Rhodanide at 2.09 Angstrom Resolution To Be Published.
Page generated: Sun Dec 13 19:38:00 2020

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