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Iodine in PDB 2qpk: Crystal Structure of the Complex of Bovine Lactoperoxidase with Salicylhydroxamic Acid at 2.34 A Resolution

Enzymatic activity of Crystal Structure of the Complex of Bovine Lactoperoxidase with Salicylhydroxamic Acid at 2.34 A Resolution

All present enzymatic activity of Crystal Structure of the Complex of Bovine Lactoperoxidase with Salicylhydroxamic Acid at 2.34 A Resolution:
1.11.1.7;

Protein crystallography data

The structure of Crystal Structure of the Complex of Bovine Lactoperoxidase with Salicylhydroxamic Acid at 2.34 A Resolution, PDB code: 2qpk was solved by A.K.Singh, N.Singh, S.Sharma, P.Kaur, T.P.Singh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.34
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.618, 80.553, 77.803, 90.00, 102.56, 90.00
R / Rfree (%) 17.2 / 22

Other elements in 2qpk:

The structure of Crystal Structure of the Complex of Bovine Lactoperoxidase with Salicylhydroxamic Acid at 2.34 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 Salicylhydroxamic Acid at 2.34 A Resolution (pdb code 2qpk). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 8 binding sites of Iodine where determined in the Crystal Structure of the Complex of Bovine Lactoperoxidase with Salicylhydroxamic Acid at 2.34 A Resolution, PDB code: 2qpk:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iodine binding site 1 out of 8 in 2qpk

Go back to Iodine Binding Sites List in 2qpk
Iodine binding site 1 out of 8 in the Crystal Structure of the Complex of Bovine Lactoperoxidase with Salicylhydroxamic Acid at 2.34 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 Salicylhydroxamic Acid at 2.34 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I607

b:24.6
occ:1.00
 O A:HOH736 3.4 22.7 1.0
N A:TRP46 3.5 22.5 1.0
N A:VAL342 3.5 20.4 1.0
CH2 A:TRP452 3.7 18.9 1.0
CB A:ASN341 3.8 21.5 1.0
CB A:VAL342 3.9 20.7 1.0
CA A:ARG45 3.9 21.8 1.0
CG1 A:VAL342 3.9 19.1 1.0
CZ2 A:TRP452 4.0 19.2 1.0
N A:ASN341 4.0 20.0 1.0
O A:ALA44 4.1 20.6 1.0
CE A:MET446 4.1 16.9 1.0
C A:ARG45 4.2 22.4 1.0
N A:LEU47 4.2 20.5 1.0
CD A:ARG45 4.2 21.9 1.0
CA A:ASN341 4.3 21.2 1.0
CA A:VAL342 4.3 19.9 1.0
CB A:TRP46 4.3 20.9 1.0
C A:ASN341 4.3 20.8 1.0
O A:LEU47 4.4 22.6 1.0
CA A:TRP46 4.4 20.8 1.0
CB A:SER340 4.6 17.6 1.0
CB A:ARG45 4.7 21.7 1.0
SD A:MET446 4.8 24.5 1.0
C A:TRP46 4.8 21.3 1.0
N A:ARG45 4.9 21.1 1.0
C A:SER340 4.9 19.6 1.0
C A:ALA44 4.9 20.6 1.0
OG A:SER340 4.9 15.2 1.0
CG A:TRP46 4.9 19.9 1.0
CG A:ARG45 4.9 22.3 1.0
CZ3 A:TRP452 4.9 18.8 1.0
NH1 A:ARG45 5.0 21.7 1.0

Iodine binding site 2 out of 8 in 2qpk

Go back to Iodine Binding Sites List in 2qpk
Iodine binding site 2 out of 8 in the Crystal Structure of the Complex of Bovine Lactoperoxidase with Salicylhydroxamic Acid at 2.34 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 Salicylhydroxamic Acid at 2.34 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I608

b:78.7
occ:1.00
 ND2 A:ASN80 3.4 18.4 1.0
O A:HOH896 3.8 50.4 1.0
CB A:PRO145 3.9 32.7 1.0
CB A:ASN80 3.9 23.9 1.0
CG A:PRO145 4.2 31.1 1.0
O A:LYS146 4.2 44.6 1.0
CG A:ASN80 4.2 25.8 1.0
CG A:GLU77 4.2 33.0 1.0
CE A:LYS81 4.6 39.2 1.0
CG A:LYS81 4.8 30.2 1.0
CA A:GLU77 4.9 26.4 1.0
NZ A:LYS81 4.9 41.3 1.0

Iodine binding site 3 out of 8 in 2qpk

Go back to Iodine Binding Sites List in 2qpk
Iodine binding site 3 out of 8 in the Crystal Structure of the Complex of Bovine Lactoperoxidase with Salicylhydroxamic Acid at 2.34 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 Salicylhydroxamic Acid at 2.34 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I609

b:58.6
occ:0.50
 NH1 A:ARG504 3.4 64.1 1.0
NH1 A:ARG96 3.7 25.5 1.0
ND2 A:ASN95 3.8 46.6 1.0
NH2 A:ARG96 3.8 26.5 1.0
CD A:ARG504 4.0 55.7 1.0
O5 A:NAG701 4.2 62.6 1.0
CZ A:ARG96 4.2 26.8 1.0
CA A:ARG504 4.4 35.9 1.0
NH1 A:ARG506 4.5 26.2 1.0
CZ A:ARG504 4.5 65.0 1.0
C1 A:NAG701 4.5 58.8 1.0
O A:ARG504 4.5 34.1 1.0
NH2 A:ARG506 4.5 31.0 1.0
C2 A:NAG701 4.6 65.1 1.0
C A:ARG504 4.7 34.3 1.0
NE A:ARG504 4.7 62.3 1.0
O7 A:NAG701 4.8 65.7 1.0
CZ A:ARG506 4.9 26.9 1.0
CG A:ASN95 4.9 38.8 1.0
O6 A:NAG701 4.9 68.9 1.0
CB A:ASN95 5.0 32.8 1.0

Iodine binding site 4 out of 8 in 2qpk

Go back to Iodine Binding Sites List in 2qpk
Iodine binding site 4 out of 8 in the Crystal Structure of the Complex of Bovine Lactoperoxidase with Salicylhydroxamic Acid at 2.34 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 Salicylhydroxamic Acid at 2.34 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I610

b:64.7
occ:1.00
 N A:PHE229 3.7 38.0 1.0
N A:GLN217 3.9 40.0 1.0
OD1 A:ASN216 4.0 41.6 1.0
O A:HOH898 4.0 39.6 1.0
CG A:ASN216 4.1 38.6 1.0
CA A:PRO228 4.1 35.8 1.0
CA A:ASN216 4.2 37.0 1.0
ND2 A:ASN216 4.2 36.4 1.0
CB A:PRO228 4.3 36.1 1.0
OE2 A:GLU218 4.3 60.2 1.0
CG A:GLU218 4.3 52.4 1.0
CD2 A:PHE229 4.4 40.7 1.0
C A:PRO228 4.4 36.4 1.0
CB A:PHE229 4.5 39.4 1.0
C A:ASN216 4.6 38.3 1.0
CA A:PHE229 4.6 40.0 1.0
CB A:ASN216 4.7 36.2 1.0
CG A:PHE229 4.8 40.2 1.0
CB A:GLN217 4.8 43.0 1.0
N A:GLU218 4.8 44.1 1.0
O A:PHE229 4.8 42.2 1.0
CD A:GLU218 4.8 58.1 1.0
O A:VAL215 4.8 34.1 1.0
CA A:GLN217 4.9 42.4 1.0

Iodine binding site 5 out of 8 in 2qpk

Go back to Iodine Binding Sites List in 2qpk
Iodine binding site 5 out of 8 in the Crystal Structure of the Complex of Bovine Lactoperoxidase with Salicylhydroxamic Acid at 2.34 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 Salicylhydroxamic Acid at 2.34 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I611

b:79.8
occ:1.00
 O A:HOH830 3.6 31.7 1.0
CB A:PHE309 3.9 23.4 1.0
NE1 A:TRP530 3.9 32.2 1.0
CZ2 A:TRP530 3.9 34.5 1.0
CE2 A:TRP530 4.3 31.3 1.0
N A:ARG310 4.3 26.1 1.0
OE1 A:GLU531 4.3 42.9 1.0
C A:PHE309 4.4 26.1 1.0
CB A:ARG310 4.5 27.9 1.0
CD A:GLU531 4.6 44.5 1.0
CZ2 A:TRP529 4.7 28.2 1.0
OE2 A:GLU531 4.7 46.0 1.0
O A:ILE306 4.7 26.4 1.0
CA A:ARG310 4.7 27.3 1.0
CA A:ILE306 4.7 24.9 1.0
CA A:PHE309 4.7 24.6 1.0
O A:PHE309 4.9 26.2 1.0
CG A:PHE309 5.0 23.9 1.0

Iodine binding site 6 out of 8 in 2qpk

Go back to Iodine Binding Sites List in 2qpk
Iodine binding site 6 out of 8 in the Crystal Structure of the Complex of Bovine Lactoperoxidase with Salicylhydroxamic Acid at 2.34 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 Salicylhydroxamic Acid at 2.34 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I612

b:62.2
occ:1.00
 O A:GLU363 3.5 48.0 1.0
NE A:ARG397 3.5 32.6 1.0
N A:THR560 3.8 38.5 1.0
NH2 A:ARG397 3.9 37.6 1.0
CG2 A:ILE559 4.0 35.2 1.0
CE2 A:TYR365 4.1 42.0 1.0
CA A:ILE559 4.2 38.1 1.0
CZ A:ARG397 4.2 33.9 1.0
CA A:GLU363 4.2 46.9 1.0
C A:GLU363 4.2 47.3 1.0
OG1 A:THR560 4.3 41.3 1.0
CG A:LYS561 4.3 43.5 1.0
N A:LYS561 4.3 39.1 1.0
CD A:ARG397 4.4 29.4 1.0
C A:ILE559 4.5 38.2 1.0
CB A:GLU363 4.5 47.4 1.0
CB A:ILE559 4.6 37.4 1.0
CD2 A:TYR365 4.7 42.3 1.0
CB A:LYS561 4.8 40.2 1.0
CA A:THR560 4.9 39.3 1.0
O A:HIS558 4.9 42.0 1.0
CG1 A:ILE559 4.9 36.9 1.0
CZ A:TYR365 4.9 42.0 1.0
OH A:TYR365 5.0 40.1 1.0

Iodine binding site 7 out of 8 in 2qpk

Go back to Iodine Binding Sites List in 2qpk
Iodine binding site 7 out of 8 in the Crystal Structure of the Complex of Bovine Lactoperoxidase with Salicylhydroxamic Acid at 2.34 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 Salicylhydroxamic Acid at 2.34 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I613

b:55.4
occ:1.00
 OG1 A:THR463 3.5 34.5 1.0
N A:LYS462 3.5 31.8 1.0
N A:THR463 3.9 33.8 1.0
O A:HOH987 3.9 51.6 1.0
CA A:GLY466 4.0 30.0 1.0
CG2 A:THR463 4.2 32.0 1.0
CB A:LYS462 4.2 34.4 1.0
CA A:PRO461 4.3 30.4 1.0
CA A:LYS462 4.3 33.4 1.0
CB A:THR463 4.4 33.4 1.0
C A:PRO461 4.4 30.7 1.0
N A:GLY466 4.5 33.4 1.0
C A:LYS462 4.6 33.2 1.0
CA A:THR463 4.7 33.5 1.0
CG A:LYS462 4.8 39.0 1.0

Iodine binding site 8 out of 8 in 2qpk

Go back to Iodine Binding Sites List in 2qpk
Iodine binding site 8 out of 8 in the Crystal Structure of the Complex of Bovine Lactoperoxidase with Salicylhydroxamic Acid at 2.34 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 Salicylhydroxamic Acid at 2.34 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I614

b:72.7
occ:0.50
 O A:HOH845 3.3 31.6 1.0
N A:PHE567 3.4 30.5 1.0
CB A:PHE567 3.5 30.8 1.0
CB A:HIS565 3.5 36.5 1.0
CD2 A:PHE567 3.6 32.2 1.0
C A:HIS565 3.6 34.6 1.0
CA A:HIS565 3.6 35.9 1.0
N A:ALA566 3.9 32.4 1.0
CA A:PHE567 3.9 31.5 1.0
O A:HIS565 4.0 34.2 1.0
CG A:PHE567 4.0 30.9 1.0
N A:GLN568 4.2 32.5 1.0
C A:ALA566 4.5 30.7 1.0
C A:PHE567 4.5 31.8 1.0
CG A:HIS565 4.6 40.9 1.0
CB A:ASP311 4.6 26.4 1.0
ND1 A:HIS565 4.6 44.7 1.0
CA A:ALA566 4.7 30.7 1.0
CE2 A:PHE567 4.7 33.4 1.0
O A:HOH716 4.7 35.7 1.0
CG A:ASP311 5.0 28.2 1.0
CG A:GLN568 5.0 38.0 1.0
O A:ASP311 5.0 27.3 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 14:20:39 2024

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