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Iodine in PDB 3tgy: Crystal Structure of the Complex of Bovine Lactoperoxidase with Ascorbic Acid at 2.35 A Resolution

Enzymatic activity of Crystal Structure of the Complex of Bovine Lactoperoxidase with Ascorbic Acid at 2.35 A Resolution

All present enzymatic activity of Crystal Structure of the Complex of Bovine Lactoperoxidase with Ascorbic Acid at 2.35 A Resolution:
1.11.1.7;

Protein crystallography data

The structure of Crystal Structure of the Complex of Bovine Lactoperoxidase with Ascorbic Acid at 2.35 A Resolution, PDB code: 3tgy was solved by S.Yamini, R.P.Singh, A.K.Singh, N.Pandey, M.Sinha, 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) 50.00 / 2.35
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.706, 79.614, 65.785, 90.00, 93.23, 90.00
R / Rfree (%) 22.6 / 25

Other elements in 3tgy:

The structure of Crystal Structure of the Complex of Bovine Lactoperoxidase with Ascorbic Acid at 2.35 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 the Complex of Bovine Lactoperoxidase with Ascorbic Acid at 2.35 A Resolution (pdb code 3tgy). 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 Bovine Lactoperoxidase with Ascorbic Acid at 2.35 A Resolution, PDB code: 3tgy:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iodine binding site 1 out of 9 in 3tgy

Go back to Iodine Binding Sites List in 3tgy
Iodine binding site 1 out of 9 in the Crystal Structure of the Complex of Bovine Lactoperoxidase with Ascorbic Acid at 2.35 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 the Complex of Bovine Lactoperoxidase with Ascorbic Acid at 2.35 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I707

b:39.0
occ:1.00
 O A:HOH761 3.3 33.7 1.0
N A:TRP46 3.3 33.3 1.0
N A:VAL342 3.4 27.9 1.0
CH2 A:TRP452 3.4 32.4 1.0
CB A:VAL342 3.7 27.3 1.0
CB A:ASN341 3.7 29.9 1.0
N A:ASN341 3.8 30.1 1.0
CG1 A:VAL342 3.8 27.1 1.0
CZ2 A:TRP452 3.8 32.5 1.0
O A:ALA44 4.0 33.4 1.0
CA A:ARG45 4.0 33.2 1.0
CB A:TRP46 4.1 33.4 1.0
CA A:ASN341 4.1 29.2 1.0
CE A:MET446 4.1 31.1 1.0
CA A:VAL342 4.1 27.2 1.0
C A:ARG45 4.1 33.2 1.0
N A:LEU47 4.2 33.6 1.0
CA A:TRP46 4.2 33.4 1.0
C A:ASN341 4.2 28.6 1.0
CB A:SER340 4.3 31.3 1.0
O A:LEU47 4.4 34.0 1.0
CD A:ARG45 4.4 33.0 1.0
CZ3 A:TRP452 4.6 32.6 1.0
C A:SER340 4.6 31.0 1.0
SD A:MET446 4.7 31.2 1.0
CG A:TRP46 4.7 33.3 1.0
C A:TRP46 4.7 33.6 1.0
C A:ALA44 4.9 33.4 1.0
CB A:ARG45 4.9 33.3 1.0
CA A:SER340 4.9 31.5 1.0
N A:ARG45 5.0 33.2 1.0
OG A:SER340 5.0 30.9 1.0

Iodine binding site 2 out of 9 in 3tgy

Go back to Iodine Binding Sites List in 3tgy
Iodine binding site 2 out of 9 in the Crystal Structure of the Complex of Bovine Lactoperoxidase with Ascorbic Acid at 2.35 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 the Complex of Bovine Lactoperoxidase with Ascorbic Acid at 2.35 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I708

b:68.7
occ:1.00
 ND2 A:ASN80 3.6 34.3 1.0
CB A:ASN80 3.8 34.9 1.0
CG A:PRO145 3.8 47.2 1.0
CB A:PRO145 4.2 47.1 1.0
CG A:ASN80 4.2 34.8 1.0
CE A:LYS81 4.3 36.4 1.0
CG A:GLU77 4.5 38.8 1.0
CG A:LYS81 4.6 36.3 1.0
CA A:GLU77 4.7 37.6 1.0
O A:GLU77 4.8 37.5 1.0
O A:HOH907 4.8 60.7 1.0
CD A:LYS81 4.9 36.4 1.0
CD A:GLU77 4.9 39.4 1.0
CB A:ASN147 5.0 48.6 1.0
CB A:GLU77 5.0 38.0 1.0

Iodine binding site 3 out of 9 in 3tgy

Go back to Iodine Binding Sites List in 3tgy
Iodine binding site 3 out of 9 in the Crystal Structure of the Complex of Bovine Lactoperoxidase with Ascorbic Acid at 2.35 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 the Complex of Bovine Lactoperoxidase with Ascorbic Acid at 2.35 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I709

b:96.5
occ:1.00
 ND2 A:ASN95 3.4 43.6 1.0
NH1 A:ARG506 3.7 35.1 1.0
NH1 A:ARG96 3.7 41.3 1.0
O5 A:NAG596 3.8 67.2 1.0
NH2 A:ARG506 3.9 34.9 1.0
NH2 A:ARG96 4.0 40.7 1.0
C1 A:NAG596 4.0 64.8 1.0
CZ A:ARG506 4.2 35.1 1.0
CB A:ASN95 4.2 43.6 1.0
CZ A:ARG96 4.3 41.3 1.0
CG A:ASN95 4.3 43.9 1.0
C2 A:NAG596 4.5 67.9 1.0
CA A:ARG504 4.7 46.3 1.0
CG A:ARG504 5.0 49.5 1.0

Iodine binding site 4 out of 9 in 3tgy

Go back to Iodine Binding Sites List in 3tgy
Iodine binding site 4 out of 9 in the Crystal Structure of the Complex of Bovine Lactoperoxidase with Ascorbic Acid at 2.35 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 the Complex of Bovine Lactoperoxidase with Ascorbic Acid at 2.35 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I710

b:76.4
occ:1.00
 CB A:PHE309 3.8 44.9 1.0
NE1 A:TRP530 3.8 59.4 1.0
CZ2 A:TRP530 3.9 59.8 1.0
CZ2 A:TRP529 4.0 52.5 1.0
CE2 A:TRP530 4.2 59.6 1.0
CA A:ILE306 4.3 46.5 1.0
CB A:ARG310 4.4 46.4 1.0
N A:ARG310 4.4 45.9 1.0
C A:PHE309 4.5 45.7 1.0
O A:ILE306 4.6 46.4 1.0
OE1 A:GLU531 4.6 60.2 1.0
CH2 A:TRP529 4.7 52.1 1.0
CA A:PHE309 4.7 45.6 1.0
O A:GLN305 4.8 46.5 1.0
CA A:ARG310 4.8 45.9 1.0
CG A:PHE309 4.9 44.5 1.0
CG2 A:ILE306 4.9 46.7 1.0
O A:PHE309 5.0 45.7 1.0
C A:ILE306 5.0 46.6 1.0

Iodine binding site 5 out of 9 in 3tgy

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Iodine binding site 5 out of 9 in the Crystal Structure of the Complex of Bovine Lactoperoxidase with Ascorbic Acid at 2.35 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 the Complex of Bovine Lactoperoxidase with Ascorbic Acid at 2.35 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I711

b:94.9
occ:1.00
 CG2 A:ILE559 3.3 65.6 1.0
N A:THR560 3.4 66.0 1.0
OG1 A:THR560 3.5 65.7 1.0
CA A:ILE559 3.7 65.9 1.0
NE A:ARG397 3.8 46.0 1.0
O A:GLU363 3.8 60.3 1.0
C A:ILE559 3.9 65.9 1.0
CB A:ILE559 4.0 65.9 1.0
CA A:GLU363 4.1 60.2 1.0
N A:LYS561 4.1 65.4 1.0
CG A:GLU363 4.3 61.4 1.0
CA A:THR560 4.3 65.8 1.0
CB A:GLU363 4.4 60.7 1.0
CB A:THR560 4.4 65.8 1.0
CG1 A:ILE559 4.4 66.0 1.0
C A:GLU363 4.4 60.4 1.0
NH2 A:ARG397 4.4 46.1 1.0
CE2 A:TYR365 4.6 59.8 1.0
CZ A:ARG397 4.6 46.0 1.0
CD A:ARG397 4.7 45.9 1.0
O A:HIS558 4.7 66.0 1.0
O A:HOH762 4.7 39.5 1.0
C A:THR560 4.8 65.6 1.0
CG2 A:THR560 4.9 65.9 1.0
OH A:TYR365 4.9 59.4 1.0
N A:ILE559 4.9 65.8 1.0
CB A:LYS561 4.9 65.2 1.0

Iodine binding site 6 out of 9 in 3tgy

Go back to Iodine Binding Sites List in 3tgy
Iodine binding site 6 out of 9 in the Crystal Structure of the Complex of Bovine Lactoperoxidase with Ascorbic Acid at 2.35 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 the Complex of Bovine Lactoperoxidase with Ascorbic Acid at 2.35 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I715

b:78.6
occ:1.00
 N A:LYS462 3.3 42.2 1.0
OG1 A:THR463 3.5 42.0 1.0
N A:THR463 3.9 42.8 1.0
CA A:GLY466 4.0 40.8 1.0
CA A:PRO461 4.0 42.0 1.0
C A:PRO461 4.2 42.0 1.0
CA A:LYS462 4.2 42.4 1.0
CB A:LYS462 4.3 42.3 1.0
CG2 A:THR463 4.4 42.5 1.0
CB A:THR463 4.4 42.4 1.0
C A:LYS462 4.5 42.5 1.0
N A:GLY466 4.5 41.3 1.0
O A:GLN460 4.6 41.9 1.0
CA A:THR463 4.7 42.7 1.0
CB A:PRO461 4.9 42.2 1.0

Iodine binding site 7 out of 9 in 3tgy

Go back to Iodine Binding Sites List in 3tgy
Iodine binding site 7 out of 9 in the Crystal Structure of the Complex of Bovine Lactoperoxidase with Ascorbic Acid at 2.35 A 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 Bovine Lactoperoxidase with Ascorbic Acid at 2.35 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I718

b:67.0
occ:1.00
 N A:GLN217 3.6 55.7 1.0
N A:PHE229 3.6 56.1 1.0
OD1 A:ASN216 3.9 54.0 1.0
OE1 A:GLU218 3.9 57.4 1.0
CA A:PRO228 4.0 54.5 1.0
OE2 A:GLU218 4.0 57.2 1.0
CG A:ASN216 4.0 54.2 1.0
CA A:ASN216 4.1 54.9 1.0
CB A:PRO228 4.1 54.4 1.0
CD2 A:PHE229 4.2 56.6 1.0
CD A:GLU218 4.2 57.3 1.0
ND2 A:ASN216 4.3 54.2 1.0
CB A:GLN217 4.3 56.0 1.0
C A:PRO228 4.3 55.1 1.0
C A:ASN216 4.4 55.2 1.0
CA A:GLN217 4.4 56.2 1.0
CB A:PHE229 4.5 56.8 1.0
N A:GLU218 4.6 57.0 1.0
CA A:PHE229 4.6 57.2 1.0
CB A:ASN216 4.7 54.5 1.0
CG A:PHE229 4.7 56.7 1.0
CG A:GLN217 4.7 56.0 1.0
O A:PHE229 4.8 58.1 1.0
OD1 A:ASN231 4.8 64.0 1.0
O A:VAL215 4.8 54.4 1.0
O A:HOH876 4.9 64.1 1.0

Iodine binding site 8 out of 9 in 3tgy

Go back to Iodine Binding Sites List in 3tgy
Iodine binding site 8 out of 9 in the Crystal Structure of the Complex of Bovine Lactoperoxidase with Ascorbic Acid at 2.35 A 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 Bovine Lactoperoxidase with Ascorbic Acid at 2.35 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I719

b:96.2
occ:1.00
 CD1 A:PHE239 4.1 58.4 1.0
CA A:PRO236 4.1 59.8 1.0
CB A:PHE239 4.2 58.5 1.0
CG A:PHE239 4.2 58.4 1.0
N A:PRO236 4.4 60.5 1.0
O A:SER235 4.5 61.3 1.0
N A:THR425 4.6 51.9 1.0
C A:SER235 4.6 61.2 1.0
CG A:PRO236 4.6 60.1 1.0
CB A:PRO234 4.7 64.7 1.0
CB A:PRO236 4.7 59.8 1.0
CE1 A:PHE239 4.8 58.5 1.0
CD A:PRO236 4.8 60.4 1.0
CG A:PRO234 4.9 64.9 1.0

Iodine binding site 9 out of 9 in 3tgy

Go back to Iodine Binding Sites List in 3tgy
Iodine binding site 9 out of 9 in the Crystal Structure of the Complex of Bovine Lactoperoxidase with Ascorbic Acid at 2.35 A 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 Bovine Lactoperoxidase with Ascorbic Acid at 2.35 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I720

b:95.8
occ:1.00
 O A:HOH747 3.5 43.7 1.0
CB A:HIS565 3.6 61.8 1.0
N A:PHE567 3.6 59.2 1.0
CA A:HIS565 3.7 61.5 1.0
CD2 A:PHE567 3.8 57.5 1.0
CB A:PHE567 3.8 58.2 1.0
N A:ALA566 3.9 60.7 1.0
O A:HOH865 3.9 71.0 1.0
C A:HIS565 4.0 61.1 1.0
ND1 A:HIS565 4.2 62.0 1.0
CG A:PHE567 4.3 57.6 1.0
CA A:PHE567 4.3 58.7 1.0
CB A:ASP311 4.4 45.0 1.0
CG A:HIS565 4.4 62.0 1.0
CG A:ASP311 4.4 45.1 1.0
OD2 A:ASP311 4.5 44.8 1.0
C A:ALA566 4.6 59.9 1.0
CA A:ALA566 4.7 60.2 1.0
O A:HIS565 4.8 61.2 1.0
O A:ASP311 4.8 44.6 1.0
N A:GLN568 4.8 58.6 1.0
O A:HOH949 4.8 47.0 1.0
CE2 A:PHE567 4.8 57.1 1.0
OD1 A:ASP311 4.9 45.5 1.0

Reference:

P.K.Singh, H.V.Sirohi, N.Iqbal, P.Tiwari, P.Kaur, S.Sharma, T.P.Singh. Structure of Bovine Lactoperoxidase with A Partially Linked Heme Moiety at 1.98 Angstrom Resolution. Biochim.Biophys.Acta V.1865 329 2017.
ISSN: ISSN 0006-3002
PubMed: 27986533
DOI: 10.1016/J.BBAPAP.2016.12.006
Page generated: Sun Aug 11 16:50:36 2024

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