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Iodine in PDB 9it8: Crystal Structure of the Ternary Complex of Lactoperoxidase with Nitric Oxide and Nitrite Ion at 1.95 A Resolution

Enzymatic activity of Crystal Structure of the Ternary Complex of Lactoperoxidase with Nitric Oxide and Nitrite Ion at 1.95 A Resolution

All present enzymatic activity of Crystal Structure of the Ternary Complex of Lactoperoxidase with Nitric Oxide and Nitrite Ion at 1.95 A Resolution:
1.11.1.7;

Protein crystallography data

The structure of Crystal Structure of the Ternary Complex of Lactoperoxidase with Nitric Oxide and Nitrite Ion at 1.95 A Resolution, PDB code: 9it8 was solved by A.Maurya, N.Ahmad, P.Sharma, S.Sharma, T.P.Singh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 74.05 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.048, 80.503, 75.951, 90, 102.85, 90
R / Rfree (%) 18.8 / 24.7

Other elements in 9it8:

The structure of Crystal Structure of the Ternary Complex of Lactoperoxidase with Nitric Oxide and Nitrite Ion at 1.95 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 - 17;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of the Ternary Complex of Lactoperoxidase with Nitric Oxide and Nitrite Ion at 1.95 A Resolution (pdb code 9it8). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 17 binding sites of Iodine where determined in the Crystal Structure of the Ternary Complex of Lactoperoxidase with Nitric Oxide and Nitrite Ion at 1.95 A Resolution, PDB code: 9it8:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 17 in 9it8

Go back to Iodine Binding Sites List in 9it8
Iodine binding site 1 out of 17 in the Crystal Structure of the Ternary Complex of Lactoperoxidase with Nitric Oxide and Nitrite Ion at 1.95 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 Ternary Complex of Lactoperoxidase with Nitric Oxide and Nitrite Ion at 1.95 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I616

b:36.0
occ:0.20
 N A:NO2605 0.1 36.8 0.8
O1 A:NO2605 1.2 32.5 0.8
O2 A:NO2605 1.2 39.0 0.8
I A:IOD641 2.9 53.7 0.2
O A:NO604 3.1 55.1 1.0
O A:HOH714 3.3 57.5 1.0
C4A A:HEM624 3.6 36.5 1.0
O A:HOH922 3.6 47.9 1.0
C3A A:HEM624 3.6 31.6 1.0
CD A:ARG255 3.8 42.4 1.0
N A:NO604 3.8 41.6 1.0
CG A:GLU258 3.8 36.6 1.0
CG A:ARG255 3.9 46.7 1.0
C2A A:HEM624 3.9 34.7 1.0
CB A:ARG255 3.9 45.6 1.0
NA A:HEM624 3.9 33.8 1.0
CHB A:HEM624 4.0 34.9 1.0
CMA A:HEM624 4.1 33.8 1.0
C1A A:HEM624 4.1 33.4 1.0
NE2 A:HIS109 4.1 41.4 1.0
CB A:GLU258 4.2 37.9 1.0
CE1 A:HIS109 4.2 37.2 1.0
CD A:GLU258 4.2 37.1 1.0
O A:HOH992 4.4 45.0 0.8
OE2 A:GLU258 4.6 36.8 1.0
C1B A:HEM624 4.7 31.1 1.0
OE1 A:GLU258 4.7 36.5 1.0
CAA A:HEM624 4.7 34.8 1.0
NE2 A:GLN105 4.9 29.5 1.0
CHA A:HEM624 4.9 32.9 1.0
I A:IOD642 5.0 51.7 0.3

Iodine binding site 2 out of 17 in 9it8

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Iodine binding site 2 out of 17 in the Crystal Structure of the Ternary Complex of Lactoperoxidase with Nitric Oxide and Nitrite Ion at 1.95 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 Ternary Complex of Lactoperoxidase with Nitric Oxide and Nitrite Ion at 1.95 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I617

b:60.0
occ:0.90
 N A:THR425 3.6 53.6 1.0
CA A:PRO236 3.7 40.2 1.0
N A:PRO236 3.9 44.4 1.0
CB A:PRO236 4.1 40.6 1.0
CB A:PHE239 4.1 47.3 1.0
C A:SER235 4.2 54.8 1.0
CA A:PRO424 4.3 49.7 1.0
CG A:PHE239 4.3 51.1 1.0
O A:SER235 4.3 54.9 1.0
CB A:PRO234 4.4 85.1 1.0
CA A:THR425 4.4 58.5 1.0
C A:PRO424 4.4 47.0 1.0
CD2 A:PHE239 4.5 55.9 1.0
CD A:PRO236 4.5 45.3 1.0
O A:PRO234 4.6 79.1 1.0
C A:PRO234 4.6 75.8 1.0
CB A:PRO424 4.7 52.3 1.0
CZ A:PHE422 4.8 50.3 1.0
N A:SER235 4.8 66.0 1.0
CG A:PRO234 4.9 87.3 1.0
CG A:PRO236 4.9 44.9 1.0
C A:PRO236 5.0 37.7 1.0
CD1 A:PHE239 5.0 50.8 1.0

Iodine binding site 3 out of 17 in 9it8

Go back to Iodine Binding Sites List in 9it8
Iodine binding site 3 out of 17 in the Crystal Structure of the Ternary Complex of Lactoperoxidase with Nitric Oxide and Nitrite Ion at 1.95 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 Ternary Complex of Lactoperoxidase with Nitric Oxide and Nitrite Ion at 1.95 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I618

b:43.1
occ:0.70
 N A:TRP46 3.2 34.8 1.0
O A:HOH834 3.4 47.1 1.0
N A:VAL342 3.4 32.4 1.0
CH2 A:TRP452 3.7 34.7 1.0
CA A:ARG45 3.7 40.3 1.0
CB A:ASN341 3.8 38.9 1.0
CB A:VAL342 3.9 28.8 1.0
O A:ALA44 3.9 37.1 1.0
C A:ARG45 3.9 42.4 1.0
CG1 A:VAL342 3.9 34.8 1.0
CZ2 A:TRP452 3.9 36.4 1.0
N A:ASN341 4.0 31.2 1.0
N A:LEU47 4.0 37.1 1.0
CE A:MET446 4.1 37.4 1.0
O A:LEU47 4.1 37.2 1.0
CA A:TRP46 4.2 37.7 1.0
CD A:ARG45 4.2 36.4 1.0
CA A:ASN341 4.2 32.0 1.0
C A:ASN341 4.2 35.1 1.0
CB A:TRP46 4.2 38.0 1.0
CA A:VAL342 4.2 30.6 1.0
CB A:SER340 4.5 30.4 1.0
CB A:ARG45 4.7 39.9 1.0
NH1 A:ARG45 4.7 32.9 1.0
C A:TRP46 4.7 33.6 1.0
N A:ARG45 4.7 37.5 1.0
C A:ALA44 4.7 42.9 1.0
C A:SER340 4.8 30.8 1.0
CG A:TRP46 4.8 37.4 1.0
CZ3 A:TRP452 4.9 36.1 1.0
OG A:SER340 4.9 31.3 1.0
SD A:MET446 4.9 41.1 1.0

Iodine binding site 4 out of 17 in 9it8

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Iodine binding site 4 out of 17 in the Crystal Structure of the Ternary Complex of Lactoperoxidase with Nitric Oxide and Nitrite Ion at 1.95 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 Ternary Complex of Lactoperoxidase with Nitric Oxide and Nitrite Ion at 1.95 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I619

b:52.5
occ:0.35
 N A:NO3614 0.5 30.6 0.7
O3 A:NO3614 0.9 34.9 0.7
O2 A:NO3614 1.3 33.8 0.7
O1 A:NO3614 1.7 24.5 0.7
O A:HOH721 2.9 68.5 1.0
N A:GLN217 3.5 57.0 1.0
CG A:ASN216 3.8 57.1 1.0
N A:PHE229 3.8 46.0 1.0
ND2 A:ASN216 3.9 56.1 1.0
CA A:ASN216 3.9 60.2 1.0
OD1 A:ASN216 3.9 54.3 1.0
C A:ASN216 4.2 55.1 1.0
CD2 A:PHE229 4.2 60.9 1.0
CA A:PRO228 4.2 49.6 1.0
CB A:GLN217 4.4 62.2 1.0
OE2 A:GLU218 4.4 97.1 1.0
CB A:PRO228 4.4 50.0 1.0
CA A:GLN217 4.4 64.4 1.0
CB A:ASN216 4.5 57.6 1.0
CB A:PHE229 4.6 52.8 1.0
C A:PRO228 4.6 50.4 1.0
N A:GLU218 4.6 70.1 1.0
CG A:GLU218 4.6 76.9 1.0
O A:VAL215 4.7 62.7 1.0
CA A:PHE229 4.8 45.5 1.0
CG A:PHE229 4.8 58.1 1.0
CD A:GLU218 4.8 85.8 1.0
CG A:GLN217 4.8 60.8 1.0
O A:HOH1011 4.8 67.7 1.0
O A:PHE229 5.0 57.0 1.0
N A:ASN216 5.0 60.8 1.0

Iodine binding site 5 out of 17 in 9it8

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Iodine binding site 5 out of 17 in the Crystal Structure of the Ternary Complex of Lactoperoxidase with Nitric Oxide and Nitrite Ion at 1.95 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 Ternary Complex of Lactoperoxidase with Nitric Oxide and Nitrite Ion at 1.95 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I620

b:55.3
occ:0.45
 O2 A:NO3612 0.6 34.9 0.5
N A:NO3612 1.0 30.4 0.5
O3 A:NO3612 1.6 37.4 0.5
O1 A:NO3612 2.2 36.2 0.5
N A:SER198 3.6 46.0 1.0
CD A:PRO197 3.6 49.8 1.0
CB A:SER198 3.7 54.4 1.0
CB A:GLU196 4.0 58.3 1.0
N A:PRO197 4.0 52.8 1.0
CG A:PRO197 4.2 49.4 1.0
CB A:PRO197 4.2 48.3 1.0
CA A:SER198 4.3 49.9 1.0
CA A:PRO197 4.5 46.4 1.0
C A:GLU196 4.6 51.0 1.0
C A:PRO197 4.6 42.4 1.0
CA A:GLU196 4.7 50.8 1.0
CG A:GLU196 4.8 67.8 1.0

Iodine binding site 6 out of 17 in 9it8

Go back to Iodine Binding Sites List in 9it8
Iodine binding site 6 out of 17 in the Crystal Structure of the Ternary Complex of Lactoperoxidase with Nitric Oxide and Nitrite Ion at 1.95 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 Ternary Complex of Lactoperoxidase with Nitric Oxide and Nitrite Ion at 1.95 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I621

b:50.2
occ:0.50
 O1 A:NO3613 0.6 25.8 0.4
N A:NO3613 0.7 28.1 0.4
O2 A:NO3613 1.5 28.2 0.4
O3 A:NO3613 1.7 31.7 0.4
ND2 A:ASN80 3.6 41.4 1.0
CG A:PRO145 3.7 45.9 1.0
CB A:ASN80 4.0 39.0 1.0
CG A:GLU77 4.1 56.7 1.0
CB A:PRO145 4.2 46.4 1.0
O A:LYS146 4.2 70.2 1.0
CE A:LYS81 4.3 58.4 1.0
CG A:ASN80 4.3 40.1 1.0
CA A:GLU77 4.7 38.5 1.0
CG A:LYS81 4.7 54.0 1.0
CB A:ASN147 4.8 74.8 1.0
CB A:GLU77 4.8 48.7 1.0
CD A:GLU77 4.9 63.5 1.0
O A:ASN147 4.9 65.4 1.0
CD A:LYS81 4.9 56.4 1.0
O A:GLU77 5.0 43.8 1.0
C A:ASN147 5.0 62.3 1.0

Iodine binding site 7 out of 17 in 9it8

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Iodine binding site 7 out of 17 in the Crystal Structure of the Ternary Complex of Lactoperoxidase with Nitric Oxide and Nitrite Ion at 1.95 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 Ternary Complex of Lactoperoxidase with Nitric Oxide and Nitrite Ion at 1.95 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I622

b:62.4
occ:0.40
 N A:NO3611 0.7 28.1 0.5
O3 A:NO3611 1.0 26.2 0.5
O2 A:NO3611 1.2 26.2 0.5
O1 A:NO3611 1.9 29.8 0.5
N A:THR560 3.4 60.3 1.0
CG2 A:ILE559 3.7 61.0 1.0
N A:LYS561 3.8 66.3 1.0
CA A:ILE559 3.8 63.5 1.0
NE A:ARG397 3.8 57.3 1.0
CG A:LYS561 4.0 96.0 1.0
O A:GLU363 4.0 65.9 1.0
CB A:LYS561 4.1 84.8 1.0
C A:ILE559 4.1 65.3 1.0
OG1 A:THR560 4.1 67.0 1.0
CE1 A:TYR365 4.1 51.0 1.0
CB A:ILE559 4.2 65.3 1.0
CA A:THR560 4.3 59.5 1.0
NH2 A:ARG397 4.5 65.2 1.0
CA A:GLU363 4.5 72.3 1.0
C A:THR560 4.5 60.1 1.0
CA A:LYS561 4.5 70.1 1.0
CG1 A:ILE559 4.5 71.0 1.0
CD A:ARG397 4.6 53.3 1.0
CZ A:ARG397 4.6 57.9 1.0
CB A:GLU363 4.7 76.2 1.0
CB A:THR560 4.7 59.7 1.0
OH A:TYR365 4.7 51.8 1.0
C A:GLU363 4.7 68.2 1.0
O A:LYS561 4.7 64.4 1.0
O A:HIS558 4.8 68.4 1.0
CZ A:TYR365 4.9 47.5 1.0
CG2 A:THR560 4.9 55.1 1.0
CD1 A:TYR365 5.0 53.9 1.0

Iodine binding site 8 out of 17 in 9it8

Go back to Iodine Binding Sites List in 9it8
Iodine binding site 8 out of 17 in the Crystal Structure of the Ternary Complex of Lactoperoxidase with Nitric Oxide and Nitrite Ion at 1.95 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 Ternary Complex of Lactoperoxidase with Nitric Oxide and Nitrite Ion at 1.95 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I623

b:56.3
occ:0.30
 N A:NO3607 0.7 38.4 0.7
O2 A:NO3607 0.8 35.1 0.7
O1 A:NO3607 1.4 32.5 0.7
O3 A:NO3607 1.8 58.9 0.7
N A:LYS462 3.6 47.0 1.0
OG1 A:THR463 3.7 49.4 1.0
CA A:GLY466 3.8 42.8 1.0
N A:THR463 4.1 46.9 1.0
O A:HOH967 4.2 60.4 1.0
CA A:PRO461 4.2 50.2 1.0
N A:GLY466 4.4 45.0 1.0
C A:PRO461 4.5 45.5 1.0
CA A:LYS462 4.5 50.2 1.0
CB A:LYS462 4.5 53.6 1.0
CB A:THR463 4.7 50.3 1.0
CG2 A:THR463 4.7 54.9 1.0
C A:LYS462 4.7 46.8 1.0
CB A:PRO461 4.9 52.6 1.0
CA A:THR463 4.9 47.4 1.0

Iodine binding site 9 out of 17 in 9it8

Go back to Iodine Binding Sites List in 9it8
Iodine binding site 9 out of 17 in the Crystal Structure of the Ternary Complex of Lactoperoxidase with Nitric Oxide and Nitrite Ion at 1.95 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 Ternary Complex of Lactoperoxidase with Nitric Oxide and Nitrite Ion at 1.95 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I629

b:48.2
occ:0.55
 N A:NO3633 0.7 25.1 0.5
O2 A:NO3633 1.0 21.9 0.5
O1 A:NO3633 1.2 21.9 0.5
O3 A:NO3633 1.8 33.8 0.5
NE1 A:TRP530 3.7 56.5 1.0
CB A:PHE309 3.9 41.4 1.0
CZ2 A:TRP530 4.2 56.3 1.0
N A:ARG310 4.2 48.1 1.0
CE2 A:TRP530 4.3 57.4 1.0
CA A:ILE306 4.4 51.2 1.0
CB A:ARG310 4.4 55.2 1.0
C A:PHE309 4.5 42.5 1.0
CG1 A:ILE306 4.5 60.9 1.0
CZ2 A:TRP529 4.6 56.2 1.0
O A:ILE306 4.6 52.2 1.0
CA A:ARG310 4.7 52.6 1.0
CA A:PHE309 4.7 40.6 1.0
O A:GLN305 4.8 45.6 1.0
CD1 A:TRP530 4.9 55.5 1.0
CB A:ILE306 4.9 56.8 1.0

Iodine binding site 10 out of 17 in 9it8

Go back to Iodine Binding Sites List in 9it8
Iodine binding site 10 out of 17 in the Crystal Structure of the Ternary Complex of Lactoperoxidase with Nitric Oxide and Nitrite Ion at 1.95 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 the Ternary Complex of Lactoperoxidase with Nitric Oxide and Nitrite Ion at 1.95 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I630

b:47.5
occ:0.35
 I A:IOD631 1.3 60.1 0.3
I A:IOD632 2.1 66.0 0.3
CD2 A:HIS377 3.7 44.0 1.0
NE2 A:HIS377 3.8 44.0 1.0
CD2 A:HIS429 3.8 44.3 1.0
NE2 A:HIS429 3.9 49.5 1.0
CG A:HIS429 4.0 44.1 1.0
CE1 A:HIS429 4.2 47.3 1.0
ND1 A:HIS429 4.2 49.3 1.0
CG2 A:THR378 4.3 45.4 1.0
CB A:HIS429 4.6 43.2 1.0
CA A:THR378 4.7 41.2 1.0
O A:HOH892 4.7 54.4 1.0
CG A:HIS377 4.9 39.2 1.0
CB A:THR378 4.9 39.6 1.0
O A:HIS377 4.9 44.4 1.0

Reference:

A.Maurya, N.Ahmad, P.Sharma, S.Sharma, T.P.Singh. Crystal Structure of the Ternary Complex of Lactoperoxidase with Nitric Oxide and Nitrite Ion at 1.95 A Resolution To Be Published.
Page generated: Sat Sep 28 22:03:46 2024

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