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Iodine in PDB 7dn6: Crystal Structure of Bovine Lactoperoxidase with Hydrogen Peroxide Trapped Between Heme Iron and HIS109 at 1.69 A Resolution

Enzymatic activity of Crystal Structure of Bovine Lactoperoxidase with Hydrogen Peroxide Trapped Between Heme Iron and HIS109 at 1.69 A Resolution

All present enzymatic activity of Crystal Structure of Bovine Lactoperoxidase with Hydrogen Peroxide Trapped Between Heme Iron and HIS109 at 1.69 A Resolution:
1.11.1.7;

Protein crystallography data

The structure of Crystal Structure of Bovine Lactoperoxidase with Hydrogen Peroxide Trapped Between Heme Iron and HIS109 at 1.69 A Resolution, PDB code: 7dn6 was solved by P.K.Singh, A.K.Singh, 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) 39.41 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.913, 79.69, 76.965, 90, 102.23, 90
R / Rfree (%) 19.7 / 23.5

Other elements in 7dn6:

The structure of Crystal Structure of Bovine Lactoperoxidase with Hydrogen Peroxide Trapped Between Heme Iron and HIS109 at 1.69 A Resolution also contains other interesting chemical elements:

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

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 19;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of Bovine Lactoperoxidase with Hydrogen Peroxide Trapped Between Heme Iron and HIS109 at 1.69 A Resolution (pdb code 7dn6). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 19 binding sites of Iodine where determined in the Crystal Structure of Bovine Lactoperoxidase with Hydrogen Peroxide Trapped Between Heme Iron and HIS109 at 1.69 A Resolution, PDB code: 7dn6:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 19 in 7dn6

Go back to Iodine Binding Sites List in 7dn6
Iodine binding site 1 out of 19 in the Crystal Structure of Bovine Lactoperoxidase with Hydrogen Peroxide Trapped Between Heme Iron and HIS109 at 1.69 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 Hydrogen Peroxide Trapped Between Heme Iron and HIS109 at 1.69 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I604

b:19.6
occ:0.82
 O A:HOH963 3.4 22.9 1.0
N A:TRP46 3.4 20.6 1.0
N A:VAL342 3.5 16.4 1.0
CH2 A:TRP452 3.8 19.1 1.0
CA A:ARG45 3.8 20.7 1.0
CB A:ASN341 3.9 21.1 1.0
CZ2 A:TRP452 3.9 18.2 1.0
O A:ALA44 3.9 21.8 1.0
CB A:VAL342 3.9 17.2 1.0
CG1 A:VAL342 4.0 18.0 1.0
N A:ASN341 4.0 18.3 1.0
C A:ARG45 4.1 20.6 1.0
N A:LEU47 4.1 19.4 1.0
CE A:MET446 4.2 23.0 1.0
CB A:TRP46 4.2 20.8 1.0
O A:LEU47 4.2 21.1 1.0
CA A:ASN341 4.3 18.5 1.0
CA A:VAL342 4.3 17.2 1.0
CA A:TRP46 4.3 20.2 1.0
C A:ASN341 4.3 20.8 1.0
CD A:ARG45 4.3 21.2 1.0
CB A:SER340 4.6 19.4 1.0
CB A:ARG45 4.7 22.5 1.0
C A:TRP46 4.7 20.5 1.0
C A:ALA44 4.7 21.6 1.0
N A:ARG45 4.8 20.6 1.0
CG A:TRP46 4.8 22.2 1.0
NH1 A:ARG45 4.8 22.2 1.0
C A:SER340 4.9 16.7 1.0
SD A:MET446 4.9 21.7 1.0
CZ3 A:TRP452 5.0 17.6 1.0

Iodine binding site 2 out of 19 in 7dn6

Go back to Iodine Binding Sites List in 7dn6
Iodine binding site 2 out of 19 in the Crystal Structure of Bovine Lactoperoxidase with Hydrogen Peroxide Trapped Between Heme Iron and HIS109 at 1.69 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 Hydrogen Peroxide Trapped Between Heme Iron and HIS109 at 1.69 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I605

b:32.6
occ:0.84
 O A:HOH1033 3.3 38.6 1.0
O A:HOH1291 3.4 49.9 1.0
ND2 A:ASN80 3.5 27.1 1.0
O A:HOH1038 3.6 62.2 1.0
CG A:PRO145 3.7 28.2 1.0
CB A:ASN80 3.9 23.1 1.0
CE A:LYS81 4.2 36.2 1.0
CG A:ASN80 4.2 25.2 1.0
CG A:GLU77 4.2 28.1 1.0
CB A:PRO145 4.3 27.9 1.0
CG A:LYS81 4.5 29.6 1.0
CA A:GLU77 4.6 24.9 1.0
CB A:ASN147 4.6 42.9 1.0
O A:HOH1195 4.6 62.9 1.0
CB A:GLU77 4.8 25.6 1.0
O A:GLU77 4.9 24.4 1.0
CD A:GLU77 4.9 31.2 1.0
CD A:LYS81 4.9 32.0 1.0
N A:ASP148 4.9 31.8 1.0
C A:ASN147 4.9 37.6 1.0

Iodine binding site 3 out of 19 in 7dn6

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Iodine binding site 3 out of 19 in the Crystal Structure of Bovine Lactoperoxidase with Hydrogen Peroxide Trapped Between Heme Iron and HIS109 at 1.69 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 Hydrogen Peroxide Trapped Between Heme Iron and HIS109 at 1.69 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I606

b:47.8
occ:0.47
 O A:HOH1344 3.3 45.0 1.0
NH1 A:ARG96 3.6 31.6 1.0
NH2 A:ARG96 3.7 25.2 1.0
O A:HOH1229 3.7 42.1 1.0
CZ A:ARG96 4.1 26.2 1.0
CA A:ARG504 4.1 32.4 1.0
NH1 A:ARG506 4.1 26.2 1.0
NH2 A:ARG506 4.2 30.1 1.0
O A:HOH840 4.2 42.4 1.0
O A:ARG504 4.3 30.6 1.0
C A:ARG504 4.4 29.3 1.0
CZ A:ARG506 4.5 27.6 1.0
CB A:ARG504 4.8 42.3 1.0
CB A:ASN95 4.9 34.7 1.0

Iodine binding site 4 out of 19 in 7dn6

Go back to Iodine Binding Sites List in 7dn6
Iodine binding site 4 out of 19 in the Crystal Structure of Bovine Lactoperoxidase with Hydrogen Peroxide Trapped Between Heme Iron and HIS109 at 1.69 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 Hydrogen Peroxide Trapped Between Heme Iron and HIS109 at 1.69 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I607

b:44.6
occ:0.74
 O A:HOH744 3.6 43.2 1.0
N A:PHE229 3.7 33.1 1.0
O A:HOH875 3.8 54.0 1.0
N A:GLN217 3.9 38.8 1.0
OD1 A:ASN216 3.9 38.9 1.0
CG A:ASN216 4.0 39.1 1.0
ND2 A:ASN216 4.0 36.8 1.0
CA A:ASN216 4.1 35.3 1.0
CA A:PRO228 4.2 35.0 1.0
CD2 A:PHE229 4.3 34.5 1.0
CB A:PHE229 4.4 33.4 1.0
C A:PRO228 4.4 34.9 1.0
CB A:PRO228 4.5 37.3 1.0
OD1 A:ASN231 4.5 70.5 1.0
C A:ASN216 4.5 33.8 1.0
CA A:PHE229 4.5 33.4 1.0
CG A:GLU218 4.6 58.8 1.0
CG A:PHE229 4.7 34.1 1.0
CD A:GLU218 4.7 69.0 1.0
CB A:ASN216 4.7 34.5 1.0
O A:PHE229 4.8 40.5 1.0
N A:GLU218 4.8 42.4 1.0
OE1 A:GLU218 4.8 76.8 1.0
CA A:GLN217 4.9 44.0 1.0
CB A:GLN217 4.9 45.6 1.0
O A:VAL215 4.9 35.4 1.0

Iodine binding site 5 out of 19 in 7dn6

Go back to Iodine Binding Sites List in 7dn6
Iodine binding site 5 out of 19 in the Crystal Structure of Bovine Lactoperoxidase with Hydrogen Peroxide Trapped Between Heme Iron and HIS109 at 1.69 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 Hydrogen Peroxide Trapped Between Heme Iron and HIS109 at 1.69 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I608

b:32.9
occ:1.00
 O A:HOH1098 3.2 48.1 1.0
NE1 A:TRP530 3.7 28.4 1.0
O A:HOH740 3.7 34.2 1.0
O A:HOH1272 3.8 48.5 1.0
O A:HOH993 3.8 37.6 1.0
CB A:PHE309 3.9 24.2 1.0
CZ2 A:TRP530 4.1 30.3 1.0
CE2 A:TRP530 4.3 33.0 1.0
N A:ARG310 4.3 26.9 1.0
CB A:ARG310 4.4 30.1 1.0
CA A:ILE306 4.4 22.4 1.0
CZ2 A:TRP529 4.6 28.9 1.0
C A:PHE309 4.6 23.2 1.0
O A:HOH1210 4.7 52.2 1.0
CG1 A:ILE306 4.7 30.2 1.0
CA A:ARG310 4.7 27.9 1.0
O A:ILE306 4.7 26.1 1.0
O A:GLN305 4.8 20.3 1.0
CA A:PHE309 4.8 24.2 1.0
CD1 A:TRP530 4.9 31.3 1.0
CB A:ILE306 5.0 24.0 1.0
CG A:PHE309 5.0 22.7 1.0

Iodine binding site 6 out of 19 in 7dn6

Go back to Iodine Binding Sites List in 7dn6
Iodine binding site 6 out of 19 in the Crystal Structure of Bovine Lactoperoxidase with Hydrogen Peroxide Trapped Between Heme Iron and HIS109 at 1.69 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 Hydrogen Peroxide Trapped Between Heme Iron and HIS109 at 1.69 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I609

b:41.0
occ:0.48
 O A:HOH792 3.2 35.9 1.0
N A:PHE567 3.5 26.6 1.0
C A:HIS565 3.7 28.3 1.0
N A:ALA566 3.7 29.2 1.0
CA A:HIS565 3.7 32.5 1.0
CB A:PHE567 3.8 28.6 1.0
CD2 A:PHE567 3.8 33.1 1.0
CG A:PHE567 4.0 28.5 1.0
O A:HOH726 4.1 40.3 1.0
CB A:HIS565 4.1 36.4 1.0
CB A:ASP311 4.1 28.4 1.0
O A:HOH956 4.2 34.9 1.0
CA A:PHE567 4.2 29.1 1.0
O A:HOH1071 4.2 73.0 1.0
CG A:ASP311 4.3 30.7 1.0
O A:HIS565 4.3 32.9 1.0
O A:HOH989 4.4 34.1 1.0
C A:ALA566 4.5 24.6 1.0
CA A:ALA566 4.6 24.1 1.0
OD2 A:ASP311 4.7 30.2 1.0
OD1 A:ASP311 4.7 31.1 1.0
CE2 A:PHE567 4.7 34.1 1.0
N A:GLN568 4.7 29.4 1.0
ND1 A:HIS565 4.8 42.4 1.0
O A:HOH926 4.8 32.6 1.0
C A:PHE567 4.9 30.4 1.0
CA A:ASP311 4.9 26.6 1.0
CG A:HIS565 4.9 42.7 1.0

Iodine binding site 7 out of 19 in 7dn6

Go back to Iodine Binding Sites List in 7dn6
Iodine binding site 7 out of 19 in the Crystal Structure of Bovine Lactoperoxidase with Hydrogen Peroxide Trapped Between Heme Iron and HIS109 at 1.69 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 Bovine Lactoperoxidase with Hydrogen Peroxide Trapped Between Heme Iron and HIS109 at 1.69 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I610

b:60.9
occ:0.55
 CG2 A:ILE387 3.9 48.9 1.0
CZ A:PHE229 4.0 35.6 1.0
CE2 A:PHE229 4.0 35.9 1.0
CB A:ALA219 4.5 40.5 1.0
O A:GLU218 4.7 44.8 1.0
NZ A:LYS388 4.8 70.3 1.0
CG2 A:VAL246 4.8 33.5 1.0
CG1 A:VAL246 4.9 32.4 1.0
OE2 A:GLU218 4.9 77.9 1.0
O A:HOH1252 4.9 51.1 1.0
CB A:GLU218 5.0 50.3 1.0
CB A:ILE387 5.0 48.1 1.0

Iodine binding site 8 out of 19 in 7dn6

Go back to Iodine Binding Sites List in 7dn6
Iodine binding site 8 out of 19 in the Crystal Structure of Bovine Lactoperoxidase with Hydrogen Peroxide Trapped Between Heme Iron and HIS109 at 1.69 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 Bovine Lactoperoxidase with Hydrogen Peroxide Trapped Between Heme Iron and HIS109 at 1.69 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I611

b:48.1
occ:0.46
 O A:HOH959 2.9 39.2 1.0
O A:HOH1172 3.3 46.0 1.0
N A:ALA225 3.4 38.1 1.0
O A:HOH990 3.5 52.9 1.0
CB A:ALA225 3.8 35.8 1.0
CA A:LEU224 4.0 39.4 1.0
CG A:ARG271 4.1 30.8 1.0
O A:HOH821 4.1 32.2 1.0
CD2 A:LEU224 4.1 39.7 1.0
CD A:ARG271 4.2 28.8 1.0
CA A:ALA225 4.2 34.5 1.0
C A:LEU224 4.2 38.1 1.0
CB A:LEU224 4.3 38.9 1.0
CB A:ARG271 4.5 30.6 1.0
NH2 A:ARG278 4.5 46.2 1.0
NE A:ARG271 4.6 30.2 1.0
CG A:LEU224 4.8 43.7 1.0
CA A:ARG271 4.8 31.1 1.0
O A:HOH1301 4.9 63.9 1.0
O A:HOH869 5.0 56.0 1.0

Iodine binding site 9 out of 19 in 7dn6

Go back to Iodine Binding Sites List in 7dn6
Iodine binding site 9 out of 19 in the Crystal Structure of Bovine Lactoperoxidase with Hydrogen Peroxide Trapped Between Heme Iron and HIS109 at 1.69 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 Bovine Lactoperoxidase with Hydrogen Peroxide Trapped Between Heme Iron and HIS109 at 1.69 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I612

b:46.1
occ:0.43
 O A:HOH1220 3.0 50.6 1.0
OG A:SER359 3.1 28.9 1.0
CB A:SER359 3.6 26.4 1.0
CD2 A:LEU361 3.9 35.5 1.0
CG A:PRO367 3.9 41.6 1.0
NZ A:LYS402 4.1 33.8 1.0
CB A:PRO367 4.1 41.6 1.0
CB A:ALA372 4.2 37.2 1.0
CB A:GLU373 4.2 32.0 1.0
CA A:PRO367 4.3 39.6 1.0
CE A:LYS402 4.4 31.0 1.0
N A:GLU373 4.4 34.8 1.0
O A:ARG360 4.6 32.3 1.0
CA A:GLU373 4.7 28.9 1.0
O A:HOH925 4.7 45.6 1.0
OE1 A:GLU373 4.7 45.1 1.0
C A:ALA372 4.7 31.2 1.0
CA A:SER359 4.7 26.6 1.0
CD A:PRO367 4.8 39.1 1.0
N A:PRO367 4.8 38.2 1.0
CD A:GLU373 4.9 36.8 1.0
CG A:GLU373 5.0 33.8 1.0

Iodine binding site 10 out of 19 in 7dn6

Go back to Iodine Binding Sites List in 7dn6
Iodine binding site 10 out of 19 in the Crystal Structure of Bovine Lactoperoxidase with Hydrogen Peroxide Trapped Between Heme Iron and HIS109 at 1.69 A Resolution


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Crystal Structure of Bovine Lactoperoxidase with Hydrogen Peroxide Trapped Between Heme Iron and HIS109 at 1.69 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I613

b:42.9
occ:0.38
 C A:OSM619 0.9 36.3 0.4
S A:OSM619 1.3 30.0 0.4
N A:OSM619 1.8 37.3 0.4
O A:OSM619 2.6 32.7 0.4
O A:HOH902 3.1 43.3 1.0
O A:HOH1197 3.6 42.2 1.0
ND2 A:ASN333 3.9 42.4 1.0
CD A:ARG31 3.9 44.4 1.0
O A:HOH884 4.0 49.5 1.0
NH1 A:ARG31 4.0 54.5 1.0
CE2 A:TYR331 4.0 31.5 1.0
CG A:ARG31 4.3 39.4 1.0
CD A:ARG527 4.4 29.7 1.0
CB A:ARG31 4.5 35.7 1.0
O A:HOH950 4.6 46.7 1.0
CD2 A:TYR331 4.7 29.4 1.0
NE A:ARG31 4.8 47.7 1.0
CG A:ASN333 4.8 38.3 1.0
CZ A:ARG31 4.8 52.9 1.0
CB A:ASN333 4.8 35.5 1.0
OH A:TYR331 4.9 29.1 1.0
CZ A:TYR331 5.0 26.6 1.0

Reference:

P.K.Singh, P.Kaur, S.Sharma, T.P.Singh. Crystal Structure of Bovine Lactoperoxidase with Hydrogen Peroxide Trapped Between Heme Iron and HIS109 at 1.69 A Resolution To Be Published.
Page generated: Mon Aug 12 00:58:51 2024

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