Iodine in PDB 6kmk: Crystal Structure of Hydrogen Peroxide Bound Bovine Lactoperoxidase at 2.3 A Resolution

Enzymatic activity of Crystal Structure of Hydrogen Peroxide Bound Bovine Lactoperoxidase at 2.3 A Resolution

All present enzymatic activity of Crystal Structure of Hydrogen Peroxide Bound Bovine Lactoperoxidase at 2.3 A Resolution:
1.11.1.7;

Protein crystallography data

The structure of Crystal Structure of Hydrogen Peroxide Bound Bovine Lactoperoxidase at 2.3 A Resolution, PDB code: 6kmk was solved by P.K.Singh, H.V.Sirohi, A.Bhusan, 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) 54.46 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.828, 80.420, 75.823, 90.00, 102.58, 90.00
R / Rfree (%) 24.5 / 29.5

Other elements in 6kmk:

The structure of Crystal Structure of Hydrogen Peroxide Bound Bovine Lactoperoxidase at 2.3 A Resolution also contains other interesting chemical elements:

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

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of Hydrogen Peroxide Bound Bovine Lactoperoxidase at 2.3 A Resolution (pdb code 6kmk). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 15 binding sites of Iodine where determined in the Crystal Structure of Hydrogen Peroxide Bound Bovine Lactoperoxidase at 2.3 A Resolution, PDB code: 6kmk:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 15 in 6kmk

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Iodine binding site 1 out of 15 in the Crystal Structure of Hydrogen Peroxide Bound Bovine Lactoperoxidase at 2.3 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 Hydrogen Peroxide Bound Bovine Lactoperoxidase at 2.3 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I607

b:55.1
occ:1.00
 N A:THR425 3.4 50.0 1.0
CA A:PRO236 3.7 37.9 1.0
CB A:PRO236 3.8 37.2 1.0
N A:PRO236 4.0 41.8 1.0
CA A:THR425 4.1 50.1 1.0
CA A:PRO424 4.1 43.9 1.0
CB A:PHE239 4.2 44.8 1.0
C A:PRO424 4.2 46.3 1.0
O A:PRO234 4.3 64.0 1.0
CG A:PHE239 4.4 49.0 1.0
CD A:PRO236 4.4 38.0 1.0
CD2 A:PHE239 4.4 51.8 1.0
C A:SER235 4.5 47.4 1.0
CB A:PRO424 4.5 43.9 1.0
CB A:PRO234 4.5 67.3 1.0
CG A:PRO236 4.6 36.9 1.0
O A:SER235 4.6 48.3 1.0
CZ A:PHE422 4.6 39.4 1.0
CG A:PRO234 4.7 68.5 1.0
C A:PRO234 4.7 62.8 1.0
CE1 A:PHE422 4.9 37.5 1.0
CG2 A:THR425 5.0 48.1 1.0

Iodine binding site 2 out of 15 in 6kmk

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Iodine binding site 2 out of 15 in the Crystal Structure of Hydrogen Peroxide Bound Bovine Lactoperoxidase at 2.3 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 Hydrogen Peroxide Bound Bovine Lactoperoxidase at 2.3 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I608

b:36.3
occ:0.80
 O A:HOH818 3.0 29.4 1.0
N A:TRP46 3.3 26.0 1.0
N A:VAL342 3.5 20.6 1.0
CH2 A:TRP452 3.6 24.4 1.0
CA A:ARG45 3.7 30.3 1.0
CZ2 A:TRP452 3.8 24.4 1.0
CG1 A:VAL342 3.9 22.0 1.0
O A:ALA44 3.9 27.2 1.0
CB A:ASN341 3.9 23.8 1.0
CB A:VAL342 3.9 21.1 1.0
C A:ARG45 4.0 27.5 1.0
N A:ASN341 4.0 22.6 1.0
N A:LEU47 4.1 25.8 1.0
CD A:ARG45 4.2 27.0 1.0
O A:LEU47 4.2 28.5 1.0
CB A:TRP46 4.2 29.1 1.0
CA A:ASN341 4.3 23.4 1.0
CA A:VAL342 4.3 21.8 1.0
CA A:TRP46 4.3 27.6 1.0
CE A:MET446 4.3 29.5 1.0
C A:ASN341 4.3 23.2 1.0
CB A:SER340 4.4 22.4 1.0
CB A:ARG45 4.7 31.8 1.0
C A:ALA44 4.7 29.1 1.0
N A:ARG45 4.7 29.8 1.0
NH1 A:ARG45 4.7 24.8 1.0
OG A:SER340 4.7 20.4 1.0
C A:TRP46 4.7 27.5 1.0
CG A:TRP46 4.8 29.3 1.0
C A:SER340 4.8 22.3 1.0
CZ3 A:TRP452 4.8 24.9 1.0
CG A:ARG45 5.0 29.7 1.0
SD A:MET446 5.0 31.1 1.0

Iodine binding site 3 out of 15 in 6kmk

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Iodine binding site 3 out of 15 in the Crystal Structure of Hydrogen Peroxide Bound Bovine Lactoperoxidase at 2.3 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 Hydrogen Peroxide Bound Bovine Lactoperoxidase at 2.3 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I609

b:45.0
occ:1.00
 NE1 A:TRP530 3.6 37.4 1.0
CB A:PHE309 3.8 32.4 1.0
CZ2 A:TRP530 4.0 42.2 1.0
N A:ARG310 4.1 37.3 1.0
CE2 A:TRP530 4.1 39.1 1.0
CB A:ARG310 4.3 41.5 1.0
CA A:ILE306 4.4 31.7 1.0
CZ2 A:TRP529 4.4 38.4 1.0
C A:PHE309 4.5 36.1 1.0
CG1 A:ILE306 4.5 32.9 1.0
CA A:ARG310 4.6 38.0 1.0
CA A:PHE309 4.7 35.9 1.0
O A:GLN305 4.7 28.7 1.0
O A:ILE306 4.8 28.7 1.0
CD1 A:TRP530 4.8 37.9 1.0
CB A:ILE306 4.8 31.5 1.0
CG2 A:ILE306 4.9 30.0 1.0
CG A:PHE309 5.0 32.7 1.0

Iodine binding site 4 out of 15 in 6kmk

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Iodine binding site 4 out of 15 in the Crystal Structure of Hydrogen Peroxide Bound Bovine Lactoperoxidase at 2.3 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 Hydrogen Peroxide Bound Bovine Lactoperoxidase at 2.3 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I610

b:51.5
occ:1.00
 ND2 A:ASN80 3.5 31.7 1.0
CG A:PRO145 3.6 37.0 1.0
CB A:ASN80 3.9 31.4 1.0
O A:LYS146 4.2 51.5 1.0
CG A:ASN80 4.2 30.5 1.0
CB A:PRO145 4.2 37.3 1.0
CE A:LYS81 4.5 37.7 1.0
CG A:GLU77 4.5 36.7 1.0
CA A:GLU77 4.5 33.0 1.0
CG A:LYS81 4.6 37.7 1.0
OE2 A:GLU77 4.7 43.9 1.0
CB A:GLU77 4.8 35.4 1.0
CD A:GLU77 4.8 40.3 1.0
CD A:LYS81 4.8 39.3 1.0
O A:GLU77 4.8 35.4 1.0
CD A:PRO145 5.0 37.5 1.0

Iodine binding site 5 out of 15 in 6kmk

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Iodine binding site 5 out of 15 in the Crystal Structure of Hydrogen Peroxide Bound Bovine Lactoperoxidase at 2.3 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 Hydrogen Peroxide Bound Bovine Lactoperoxidase at 2.3 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I611

b:43.0
occ:0.80
 NE A:ARG397 3.4 37.0 1.0
CE A:LYS561 3.6 58.4 1.0
N A:THR560 3.7 41.9 1.0
CG A:GLU363 3.9 58.6 1.0
CA A:GLU363 3.9 49.5 1.0
NH2 A:ARG397 4.0 38.4 1.0
CG2 A:ILE559 4.0 44.0 1.0
N A:LYS561 4.0 40.9 1.0
O A:GLU363 4.0 41.0 1.0
CA A:ILE559 4.0 44.8 1.0
OG1 A:THR560 4.1 44.2 1.0
CZ A:ARG397 4.1 36.2 1.0
CB A:GLU363 4.2 51.9 1.0
CD A:ARG397 4.2 37.6 1.0
CE1 A:TYR365 4.2 37.4 1.0
C A:ILE559 4.4 43.9 1.0
NZ A:LYS561 4.4 61.0 1.0
CB A:ILE559 4.5 44.5 1.0
C A:GLU363 4.5 42.9 1.0
CB A:LYS561 4.5 46.8 1.0
O A:LYS561 4.6 40.0 1.0
CA A:THR560 4.6 41.8 1.0
CD A:LYS561 4.6 52.7 1.0
C A:THR560 4.7 40.5 1.0
CG1 A:ILE559 4.8 44.6 1.0
O A:HIS558 4.8 39.5 1.0
CA A:LYS561 4.8 42.1 1.0
CB A:THR560 4.9 43.7 1.0
CG A:LYS561 4.9 48.8 1.0
CD1 A:TYR365 4.9 37.8 1.0
OH A:TYR365 5.0 34.9 1.0
CZ A:TYR365 5.0 39.6 1.0

Iodine binding site 6 out of 15 in 6kmk

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Iodine binding site 6 out of 15 in the Crystal Structure of Hydrogen Peroxide Bound Bovine Lactoperoxidase at 2.3 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 Hydrogen Peroxide Bound Bovine Lactoperoxidase at 2.3 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I612

b:43.7
occ:0.50
 N A:LYS462 3.6 44.9 1.0
OG1 A:THR463 3.8 39.8 1.0
CA A:GLY466 3.9 37.4 1.0
CG2 A:THR463 4.0 40.4 1.0
O A:HOH913 4.0 32.6 1.0
N A:THR463 4.0 37.6 1.0
CA A:PRO461 4.1 41.1 1.0
C A:PRO461 4.3 41.7 1.0
CB A:THR463 4.4 37.7 1.0
CA A:LYS462 4.5 46.2 1.0
CB A:LYS462 4.6 47.8 1.0
N A:GLY466 4.6 37.8 1.0
C A:LYS462 4.7 42.2 1.0
CG A:LYS462 4.8 52.2 1.0
CA A:THR463 4.8 36.6 1.0
CB A:PRO461 4.9 42.1 1.0
O A:GLN460 5.0 39.4 1.0

Iodine binding site 7 out of 15 in 6kmk

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Iodine binding site 7 out of 15 in the Crystal Structure of Hydrogen Peroxide Bound Bovine Lactoperoxidase at 2.3 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 Hydrogen Peroxide Bound Bovine Lactoperoxidase at 2.3 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I613

b:61.1
occ:1.00
 O A:HOH880 3.2 39.5 1.0
ND1 A:HIS429 3.5 44.2 1.0
CE1 A:HIS429 3.6 48.4 1.0
CD2 A:HIS377 3.7 31.3 1.0
NE2 A:HIS377 3.8 30.9 1.0
CG A:HIS429 3.9 40.0 1.0
NE2 A:HIS429 4.1 43.3 1.0
CD2 A:HIS429 4.2 43.6 1.0
CG2 A:THR378 4.2 32.1 1.0
CB A:HIS429 4.6 40.6 1.0
CA A:THR378 4.7 31.3 1.0
CB A:THR378 4.9 30.0 1.0
CG A:HIS377 4.9 31.7 1.0

Iodine binding site 8 out of 15 in 6kmk

Go back to Iodine Binding Sites List in 6kmk
Iodine binding site 8 out of 15 in the Crystal Structure of Hydrogen Peroxide Bound Bovine Lactoperoxidase at 2.3 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 Hydrogen Peroxide Bound Bovine Lactoperoxidase at 2.3 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I614

b:57.1
occ:1.00
 N A:PHE229 3.7 44.5 1.0
N A:GLN217 3.7 46.8 1.0
OD1 A:ASN216 3.9 47.6 1.0
CD2 A:PHE229 4.0 54.7 1.0
CG A:GLU218 4.0 61.6 1.0
CA A:ASN216 4.1 45.7 1.0
CG A:ASN216 4.1 49.9 1.0
CA A:PRO228 4.2 44.1 1.0
CB A:PRO228 4.3 46.5 1.0
ND2 A:ASN216 4.3 49.4 1.0
CB A:PHE229 4.3 44.8 1.0
C A:ASN216 4.4 42.7 1.0
C A:PRO228 4.4 44.5 1.0
CG A:PHE229 4.6 52.5 1.0
N A:GLU218 4.6 49.9 1.0
CA A:PHE229 4.6 43.4 1.0
CB A:GLN217 4.6 50.8 1.0
CA A:GLN217 4.7 50.2 1.0
CB A:ASN216 4.7 47.5 1.0
O A:VAL215 4.7 48.5 1.0
O A:PHE229 4.7 47.3 1.0
OE2 A:GLU218 4.8 66.6 1.0
CD A:GLU218 4.8 64.1 1.0
CE2 A:PHE229 4.9 56.9 1.0
ND2 A:ASN231 4.9 56.6 1.0
CB A:GLU218 4.9 58.5 1.0
CG A:GLN217 5.0 46.8 1.0

Iodine binding site 9 out of 15 in 6kmk

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Iodine binding site 9 out of 15 in the Crystal Structure of Hydrogen Peroxide Bound Bovine Lactoperoxidase at 2.3 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 Hydrogen Peroxide Bound Bovine Lactoperoxidase at 2.3 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I615

b:45.4
occ:0.50
 N A:PHE567 3.5 31.3 1.0
N A:ALA566 3.6 36.6 1.0
C A:HIS565 3.6 37.3 1.0
CA A:HIS565 3.7 40.8 1.0
CD2 A:PHE567 3.7 32.5 1.0
CB A:PHE567 3.7 31.4 1.0
CB A:HIS565 3.8 42.3 1.0
CG A:PHE567 4.1 33.1 1.0
CA A:PHE567 4.2 34.2 1.0
O A:HOH889 4.2 44.6 1.0
O A:HIS565 4.2 37.7 1.0
CB A:ASP311 4.3 29.5 1.0
C A:ALA566 4.5 33.8 1.0
CG A:ASP311 4.5 29.3 1.0
N A:GLN568 4.5 34.9 1.0
O A:HOH763 4.5 32.1 1.0
CA A:ALA566 4.6 35.3 1.0
CE2 A:PHE567 4.7 32.3 1.0
CG A:GLN568 4.7 48.0 1.0
OE1 A:GLN568 4.8 60.3 1.0
CG A:HIS565 4.8 47.8 1.0
OD2 A:ASP311 4.8 33.2 1.0
C A:PHE567 4.8 33.5 1.0
OD1 A:ASP311 4.9 33.6 1.0
O A:HOH752 4.9 31.7 1.0
ND1 A:HIS565 4.9 53.1 1.0
O A:HOH712 5.0 39.7 1.0
O A:ASP311 5.0 30.0 1.0

Iodine binding site 10 out of 15 in 6kmk

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Iodine binding site 10 out of 15 in the Crystal Structure of Hydrogen Peroxide Bound Bovine Lactoperoxidase at 2.3 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 Hydrogen Peroxide Bound Bovine Lactoperoxidase at 2.3 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I616

b:55.1
occ:0.60
 O1 A:PEO622 3.5 41.6 1.0
O2 A:PEO622 3.5 36.7 1.0
CD A:ARG255 3.5 38.5 1.0
CG A:ARG255 3.5 42.0 1.0
CB A:ARG255 3.6 43.9 1.0
CG A:GLU258 3.7 28.9 1.0
C4A A:HEM601 3.8 23.5 1.0
C3A A:HEM601 3.8 23.8 1.0
NE2 A:HIS109 3.8 26.6 1.0
CE1 A:HIS109 3.8 26.1 1.0
CB A:GLU258 4.0 28.2 1.0
NA A:HEM601 4.1 22.2 1.0
CHB A:HEM601 4.1 22.1 1.0
C2A A:HEM601 4.1 25.0 1.0
CD A:GLU258 4.1 29.8 1.0
O2 A:PEO623 4.2 49.1 1.0
C1A A:HEM601 4.3 23.4 1.0
CMA A:HEM601 4.3 23.8 1.0
OE1 A:GLU258 4.3 29.4 1.0
NE2 A:GLN105 4.4 17.7 1.0
C1B A:HEM601 4.7 20.9 1.0
O A:ARG255 4.8 36.4 1.0
NE A:ARG255 4.8 34.4 1.0
O A:HOH936 4.8 28.7 1.0
CA A:ARG255 4.8 44.2 1.0
OE2 A:GLU258 4.8 27.6 1.0
CAA A:HEM601 4.9 25.7 1.0

Reference:

P.K.Singh, H.V.Sirohi, A.Bhushan, P.Kaur, S.Sharma, T.P.Singh. Crystal Structure of Hydrogen Peroxide Bound Bovine Lactoperoxidase at 2.3 A Resolution To Be Published.
Page generated: Sun Dec 13 19:44:45 2020

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