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Iodine in PDB 2z5z: Crystal Structure of the Complex of Buffalo Lactoperoxidase with Fluoride Ion at 3.5A Resolution

Enzymatic activity of Crystal Structure of the Complex of Buffalo Lactoperoxidase with Fluoride Ion at 3.5A Resolution

All present enzymatic activity of Crystal Structure of the Complex of Buffalo Lactoperoxidase with Fluoride Ion at 3.5A Resolution:
1.11.1.7;

Protein crystallography data

The structure of Crystal Structure of the Complex of Buffalo Lactoperoxidase with Fluoride Ion at 3.5A Resolution, PDB code: 2z5z was solved by I.A.Sheikh, R.Jain, N.Singh, S.Sharma, A.Bhushan, P.Kaur, A.Srinivasan, T.P.Singh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 75.81 / 3.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.127, 80.739, 77.699, 90.00, 102.94, 90.00
R / Rfree (%) 22.1 / 23.5

Other elements in 2z5z:

The structure of Crystal Structure of the Complex of Buffalo Lactoperoxidase with Fluoride Ion at 3.5A Resolution also contains other interesting chemical elements:

Fluorine (F) 3 atoms
Iron (Fe) 1 atom
Calcium (Ca) 1 atom

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of the Complex of Buffalo Lactoperoxidase with Fluoride Ion at 3.5A Resolution (pdb code 2z5z). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 9 binding sites of Iodine where determined in the Crystal Structure of the Complex of Buffalo Lactoperoxidase with Fluoride Ion at 3.5A Resolution, PDB code: 2z5z:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iodine binding site 1 out of 9 in 2z5z

Go back to Iodine Binding Sites List in 2z5z
Iodine binding site 1 out of 9 in the Crystal Structure of the Complex of Buffalo Lactoperoxidase with Fluoride Ion at 3.5A 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 the Complex of Buffalo Lactoperoxidase with Fluoride Ion at 3.5A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I607

b:14.2
occ:0.50
 CE A:MET446 3.2 11.9 1.0
N A:VAL342 3.2 2.8 1.0
CB A:ASN341 3.3 25.5 1.0
CB A:VAL342 3.7 6.6 1.0
CZ2 A:TRP452 3.8 14.2 1.0
C A:ASN341 3.9 2.0 1.0
CH2 A:TRP452 3.9 14.1 1.0
CA A:VAL342 3.9 2.5 1.0
CA A:ASN341 3.9 2.0 1.0
SD A:MET446 4.0 11.7 1.0
N A:ASN341 4.1 2.0 1.0
CD A:ARG45 4.2 33.1 1.0
NH1 A:ARG45 4.2 36.1 1.0
CG1 A:VAL342 4.2 6.6 1.0
N A:TRP46 4.4 26.1 1.0
CG A:ASN341 4.4 26.2 1.0
O A:LEU47 4.4 21.5 1.0
O A:ALA44 4.6 17.7 1.0
CA A:ARG45 4.6 28.0 1.0
N A:LEU47 4.7 22.1 1.0
NE A:ARG45 4.8 35.0 1.0
CZ A:ARG45 4.8 35.7 1.0
CG2 A:VAL342 4.8 7.0 1.0
O A:ASN341 4.9 2.0 1.0
ND2 A:ASN341 4.9 27.0 1.0
C A:ARG45 5.0 27.9 1.0

Iodine binding site 2 out of 9 in 2z5z

Go back to Iodine Binding Sites List in 2z5z
Iodine binding site 2 out of 9 in the Crystal Structure of the Complex of Buffalo Lactoperoxidase with Fluoride Ion at 3.5A 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 the Complex of Buffalo Lactoperoxidase with Fluoride Ion at 3.5A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I608

b:40.6
occ:0.50
 ND2 A:ASN80 3.2 29.3 1.0
CG A:PRO145 3.7 10.8 1.0
CB A:ASN80 3.8 27.8 1.0
CG A:ASN80 4.0 28.4 1.0
CB A:PRO145 4.2 10.9 1.0
O A:LYS146 4.2 40.8 1.0
CG A:GLU77 4.2 39.9 1.0
CE A:LYS81 4.4 63.8 1.0
CD A:LYS81 4.4 63.0 1.0
N A:ASP148 4.8 17.9 1.0
CA A:GLU77 4.8 23.1 1.0
CD A:GLU77 4.8 41.1 1.0
CB A:GLU77 4.9 39.3 1.0
C A:ASN147 4.9 6.1 1.0
OE2 A:GLU77 4.9 41.6 1.0
CB A:ASN147 5.0 62.9 1.0
CA A:ASP148 5.0 17.4 1.0

Iodine binding site 3 out of 9 in 2z5z

Go back to Iodine Binding Sites List in 2z5z
Iodine binding site 3 out of 9 in the Crystal Structure of the Complex of Buffalo Lactoperoxidase with Fluoride Ion at 3.5A 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 the Complex of Buffalo Lactoperoxidase with Fluoride Ion at 3.5A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I609

b:57.9
occ:0.50
 O A:HOH705 2.9 5.6 1.0
NH1 A:ARG506 3.2 31.2 1.0
NH2 A:ARG506 3.4 29.1 1.0
CZ A:ARG506 3.8 30.1 1.0
NH2 A:ARG96 4.0 3.8 1.0
NH1 A:ARG96 4.2 4.2 1.0
NE A:ARG504 4.2 73.1 1.0
CA A:ARG504 4.2 12.7 1.0
NH2 A:ARG504 4.3 73.1 1.0
CZ A:ARG96 4.6 3.9 1.0
O A:ARG504 4.6 12.6 1.0
C A:ARG504 4.6 12.5 1.0
CZ A:ARG504 4.7 73.1 1.0
N A:ARG504 5.0 12.3 1.0
ND2 A:ASN95 5.0 58.0 1.0

Iodine binding site 4 out of 9 in 2z5z

Go back to Iodine Binding Sites List in 2z5z
Iodine binding site 4 out of 9 in the Crystal Structure of the Complex of Buffalo Lactoperoxidase with Fluoride Ion at 3.5A 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 the Complex of Buffalo Lactoperoxidase with Fluoride Ion at 3.5A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I610

b:42.8
occ:0.50
 NE A:ARG202 3.4 40.9 1.0
CZ A:ARG202 3.7 41.5 1.0
CD A:ARG202 3.8 39.3 1.0
NH2 A:ARG202 4.0 41.3 1.0
NH1 A:ARG202 4.3 41.8 1.0
CA A:LEU199 4.4 22.5 1.0
CD1 A:LEU199 4.6 2.0 1.0
CB A:ARG202 4.6 37.4 1.0
CB A:LEU199 4.7 2.0 1.0
CG A:ARG202 4.7 38.0 1.0
N A:LEU199 4.8 22.5 1.0
O A:SEP198 5.0 56.8 1.0

Iodine binding site 5 out of 9 in 2z5z

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Iodine binding site 5 out of 9 in the Crystal Structure of the Complex of Buffalo Lactoperoxidase with Fluoride Ion at 3.5A 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 the Complex of Buffalo Lactoperoxidase with Fluoride Ion at 3.5A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I611

b:25.7
occ:0.50
 CG A:ASN216 3.1 27.7 1.0
OD1 A:ASN216 3.2 27.1 1.0
CA A:ASN216 3.2 52.5 1.0
N A:GLN217 3.2 33.5 1.0
OE1 A:GLU218 3.3 73.5 1.0
ND2 A:ASN216 3.4 27.9 1.0
CB A:ASN216 3.7 27.9 1.0
N A:PHE229 3.7 17.0 1.0
C A:ASN216 3.7 52.6 1.0
CA A:PRO228 4.1 14.1 1.0
N A:GLU218 4.2 16.9 1.0
CD2 A:PHE229 4.3 17.2 1.0
N A:ASN216 4.4 52.4 1.0
CA A:GLN217 4.4 33.6 1.0
C A:PRO228 4.4 14.1 1.0
CB A:PHE229 4.5 18.2 1.0
CD A:GLU218 4.5 73.8 1.0
CG A:PHE229 4.5 17.6 1.0
O A:VAL215 4.6 50.8 1.0
CB A:PRO228 4.7 2.0 1.0
CA A:PHE229 4.7 17.3 1.0
CB A:GLN217 4.7 77.4 1.0
CB A:GLU218 4.8 72.7 1.0
C A:GLN217 4.8 33.7 1.0
C A:VAL215 4.9 50.7 1.0
O A:ASN216 4.9 52.6 1.0
CE2 A:PHE229 5.0 17.1 1.0

Iodine binding site 6 out of 9 in 2z5z

Go back to Iodine Binding Sites List in 2z5z
Iodine binding site 6 out of 9 in the Crystal Structure of the Complex of Buffalo Lactoperoxidase with Fluoride Ion at 3.5A 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 the Complex of Buffalo Lactoperoxidase with Fluoride Ion at 3.5A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I612

b:37.6
occ:0.50
 O A:PRO424 3.1 55.2 1.0
O A:THR425 3.2 25.5 1.0
C A:THR425 4.0 25.7 1.0
C A:PRO424 4.1 55.1 1.0
CA A:THR425 4.3 25.6 1.0
CG A:PRO236 4.6 2.0 1.0
N A:THR425 4.7 25.6 1.0
O A:HIS426 4.7 68.2 1.0
CA A:PRO236 4.8 37.3 1.0
CB A:PRO236 4.8 2.0 1.0
N A:PRO236 4.9 37.4 1.0

Iodine binding site 7 out of 9 in 2z5z

Go back to Iodine Binding Sites List in 2z5z
Iodine binding site 7 out of 9 in the Crystal Structure of the Complex of Buffalo Lactoperoxidase with Fluoride Ion at 3.5A Resolution


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Structure of the Complex of Buffalo Lactoperoxidase with Fluoride Ion at 3.5A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I613

b:21.0
occ:0.50
 CB A:PHE309 3.4 10.8 1.0
N A:ARG310 3.5 4.5 1.0
C A:PHE309 3.6 4.8 1.0
CB A:ARG310 3.7 23.7 1.0
CA A:ARG310 3.8 4.7 1.0
O A:PHE309 4.0 4.8 1.0
CA A:PHE309 4.1 4.8 1.0
O A:ILE306 4.2 37.3 1.0
NE1 A:TRP530 4.5 29.1 1.0
CA A:ILE306 4.6 37.5 1.0
CG A:PHE309 4.7 10.5 1.0
CZ2 A:TRP529 4.8 11.3 1.0
O A:GLN305 4.8 14.7 1.0
CG A:ARG310 4.8 24.2 1.0
N A:PHE309 4.9 4.8 1.0
C A:ILE306 4.9 37.3 1.0
CZ2 A:TRP530 4.9 29.2 1.0

Iodine binding site 8 out of 9 in 2z5z

Go back to Iodine Binding Sites List in 2z5z
Iodine binding site 8 out of 9 in the Crystal Structure of the Complex of Buffalo Lactoperoxidase with Fluoride Ion at 3.5A Resolution


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Crystal Structure of the Complex of Buffalo Lactoperoxidase with Fluoride Ion at 3.5A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I614

b:41.9
occ:0.50
 O A:GLU363 3.0 33.8 1.0
NE A:ARG397 3.1 30.0 1.0
NH2 A:ARG397 3.4 30.8 1.0
CZ A:ARG397 3.7 30.3 1.0
C A:GLU363 3.7 33.7 1.0
CA A:GLU363 3.7 33.5 1.0
CE2 A:TYR365 3.8 8.2 1.0
NZ A:LYS561 3.8 31.7 1.0
CG2 A:ILE559 4.0 3.0 1.0
CD A:ARG397 4.2 29.7 1.0
CB A:GLU363 4.2 68.1 1.0
N A:THR560 4.3 24.3 1.0
CD2 A:TYR365 4.4 8.9 1.0
CA A:ILE559 4.4 21.5 1.0
CZ A:TYR365 4.5 7.7 1.0
OH A:TYR365 4.6 7.2 1.0
OG1 A:THR560 4.7 49.4 1.0
CG A:GLU363 4.7 69.1 1.0
CG A:ARG397 4.8 29.5 1.0
CD1 A:ILE559 4.8 3.0 1.0
N A:LYS561 4.8 53.2 1.0
CB A:ILE559 4.8 3.0 1.0
O A:ASP362 4.8 11.3 1.0
N A:GLU363 4.9 32.8 1.0
C A:ILE559 4.9 21.6 1.0
N A:ASN364 5.0 19.4 1.0
CE A:LYS561 5.0 31.1 1.0

Iodine binding site 9 out of 9 in 2z5z

Go back to Iodine Binding Sites List in 2z5z
Iodine binding site 9 out of 9 in the Crystal Structure of the Complex of Buffalo Lactoperoxidase with Fluoride Ion at 3.5A Resolution


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Crystal Structure of the Complex of Buffalo Lactoperoxidase with Fluoride Ion at 3.5A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I615

b:35.9
occ:0.50
 O A:HOH724 2.5 2.1 1.0
OG1 A:THR463 2.7 10.4 1.0
N A:LYS462 2.8 22.8 1.0
N A:THR463 2.9 2.0 1.0
CA A:LYS462 3.4 23.1 1.0
C A:LYS462 3.5 23.2 1.0
CB A:LYS462 3.6 18.2 1.0
CB A:THR463 3.7 10.2 1.0
CA A:THR463 3.8 2.0 1.0
C A:PRO461 3.8 12.3 1.0
CA A:GLY466 3.9 8.5 1.0
CA A:PRO461 4.0 12.3 1.0
CG2 A:THR463 4.0 10.2 1.0
O A:THR463 4.1 2.0 1.0
N A:GLY466 4.3 8.5 1.0
C A:THR463 4.4 2.0 1.0
CG A:LYS462 4.5 18.5 1.0
O A:LYS462 4.6 23.3 1.0
CB A:PRO461 4.7 2.0 1.0
O A:PRO461 4.9 12.2 1.0

Reference:

I.A.Sheikh, R.Jain, N.Singh, S.Sharma, A.Bhushan, P.Kaur, A.Srinivasan, T.P.Singh. Crystal Structure of the Complex of Buffalo Lactoperoxidase with Fluoride Ion at 3.5A Resolution To Be Published.
Page generated: Sun Aug 11 14:39:36 2024

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