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Iodine in PDB 8ing: Structure of the Ternary Complex of Lactoperoxidase with Substrate Nitric Oxide (No) and Product Nitrite Ion (NO2) at 1.98 A Resolution

Enzymatic activity of Structure of the Ternary Complex of Lactoperoxidase with Substrate Nitric Oxide (No) and Product Nitrite Ion (NO2) at 1.98 A Resolution

All present enzymatic activity of Structure of the Ternary Complex of Lactoperoxidase with Substrate Nitric Oxide (No) and Product Nitrite Ion (NO2) at 1.98 A Resolution:
1.11.1.7;

Protein crystallography data

The structure of Structure of the Ternary Complex of Lactoperoxidase with Substrate Nitric Oxide (No) and Product Nitrite Ion (NO2) at 1.98 A Resolution, PDB code: 8ing was solved by M.I.Ahmad, V.Viswanathan, M.Kumar, R.P.Singh, A.K.Singh, M.Sinha, P.Kaur, 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) 35.33 / 1.98
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.052, 80.342, 76.121, 90, 102.82, 90
R / Rfree (%) 18.3 / 23.4

Other elements in 8ing:

The structure of Structure of the Ternary Complex of Lactoperoxidase with Substrate Nitric Oxide (No) and Product Nitrite Ion (NO2) at 1.98 A Resolution also contains other interesting chemical elements:

Calcium (Ca) 1 atom
Sodium (Na) 2 atoms
Iron (Fe) 1 atom

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Iodine atom in the Structure of the Ternary Complex of Lactoperoxidase with Substrate Nitric Oxide (No) and Product Nitrite Ion (NO2) at 1.98 A Resolution (pdb code 8ing). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 13 binding sites of Iodine where determined in the Structure of the Ternary Complex of Lactoperoxidase with Substrate Nitric Oxide (No) and Product Nitrite Ion (NO2) at 1.98 A Resolution, PDB code: 8ing:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 13 in 8ing

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Iodine binding site 1 out of 13 in the Structure of the Ternary Complex of Lactoperoxidase with Substrate Nitric Oxide (No) and Product Nitrite Ion (NO2) at 1.98 A Resolution


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Structure of the Ternary Complex of Lactoperoxidase with Substrate Nitric Oxide (No) and Product Nitrite Ion (NO2) at 1.98 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I617

b:25.3
occ:0.30
 N A:NO2605 0.3 15.8 0.7
O1 A:NO2605 1.0 19.1 0.7
O2 A:NO2605 1.3 16.5 0.7
O A:NO604 2.8 40.0 1.0
NA A:NA637 3.0 37.5 1.0
O A:HOH706 3.3 53.4 1.0
O A:HOH874 3.7 33.4 1.0
CG A:GLU258 3.7 24.6 1.0
C4A A:HEM626 3.7 23.4 1.0
CD A:ARG255 3.8 25.6 1.0
NE2 A:HIS109 3.8 23.7 1.0
N A:NO604 3.9 32.0 1.0
CE1 A:HIS109 3.9 22.0 1.0
C3A A:HEM626 3.9 24.6 1.0
CB A:ARG255 3.9 27.8 1.0
NA A:HEM626 4.0 20.9 1.0
CB A:GLU258 4.0 24.6 1.0
CHB A:HEM626 4.0 20.9 1.0
CD A:GLU258 4.1 25.6 1.0
CG A:ARG255 4.1 27.2 1.0
C2A A:HEM626 4.3 24.0 1.0
O A:HOH711 4.3 29.1 0.4
C1A A:HEM626 4.3 22.0 1.0
CMA A:HEM626 4.4 26.0 1.0
OE1 A:GLU258 4.4 22.2 1.0
NE2 A:GLN105 4.5 22.0 1.0
C1B A:HEM626 4.5 20.4 1.0
OE2 A:GLU258 4.6 26.0 1.0
O A:HOH1007 4.6 42.9 1.0
O A:NO630 4.9 46.8 1.0
O A:ARG255 4.9 25.2 1.0
NE A:ARG255 5.0 24.8 1.0

Iodine binding site 2 out of 13 in 8ing

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Iodine binding site 2 out of 13 in the Structure of the Ternary Complex of Lactoperoxidase with Substrate Nitric Oxide (No) and Product Nitrite Ion (NO2) at 1.98 A Resolution


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Structure of the Ternary Complex of Lactoperoxidase with Substrate Nitric Oxide (No) and Product Nitrite Ion (NO2) at 1.98 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I618

b:51.8
occ:0.70
 O A:HOH920 2.0 53.0 1.0
N A:THR425 3.6 56.4 1.0
CA A:PRO236 3.6 35.5 1.0
N A:PRO236 3.9 37.2 1.0
CB A:PRO236 3.9 37.1 1.0
CB A:PHE239 4.1 35.7 1.0
C A:SER235 4.2 45.0 1.0
CA A:THR425 4.3 61.9 1.0
O A:SER235 4.3 39.5 1.0
CG A:PHE239 4.4 37.3 1.0
CD A:PRO236 4.5 36.5 1.0
CA A:PRO424 4.5 41.8 1.0
C A:PRO424 4.5 43.9 1.0
CB A:PRO234 4.5 72.5 1.0
CD2 A:PHE239 4.6 39.6 1.0
CG A:PRO234 4.7 72.5 1.0
OG1 A:THR425 4.8 72.7 1.0
CG A:PRO236 4.8 38.3 1.0
N A:SER235 4.8 59.3 1.0
C A:PRO234 4.9 65.8 1.0
CB A:PRO424 4.9 41.9 1.0
CZ A:PHE422 4.9 36.8 1.0
O A:PRO234 5.0 62.6 1.0
C A:PRO236 5.0 31.5 1.0

Iodine binding site 3 out of 13 in 8ing

Go back to Iodine Binding Sites List in 8ing
Iodine binding site 3 out of 13 in the Structure of the Ternary Complex of Lactoperoxidase with Substrate Nitric Oxide (No) and Product Nitrite Ion (NO2) at 1.98 A Resolution


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Structure of the Ternary Complex of Lactoperoxidase with Substrate Nitric Oxide (No) and Product Nitrite Ion (NO2) at 1.98 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I619

b:56.0
occ:0.50
 OD1 A:ASN410 2.4 53.4 1.0
CG A:ASN410 3.2 47.1 1.0
ND2 A:ASN473 3.7 30.7 1.0
ND2 A:ASN410 3.7 52.8 1.0
NZ A:LYS479 3.9 50.1 1.0
O A:HOH825 4.0 23.2 1.0
O A:GLN409 4.0 28.5 1.0
OD1 A:ASN473 4.0 27.9 1.0
CB A:LEU476 4.1 28.7 1.0
N A:LEU476 4.1 27.8 1.0
CG A:ASN473 4.3 27.9 1.0
CA A:ASN410 4.3 30.3 1.0
CG2 A:ILE475 4.3 37.6 1.0
CB A:ASN410 4.3 36.8 1.0
C A:GLN409 4.3 29.6 1.0
CA A:LEU476 4.4 28.0 1.0
N A:ASN410 4.5 28.1 1.0
CB A:ILE475 4.5 36.4 1.0
C A:ILE475 4.8 30.0 1.0
O A:HOH948 4.8 45.5 1.0
CB A:GLN409 4.9 26.7 1.0

Iodine binding site 4 out of 13 in 8ing

Go back to Iodine Binding Sites List in 8ing
Iodine binding site 4 out of 13 in the Structure of the Ternary Complex of Lactoperoxidase with Substrate Nitric Oxide (No) and Product Nitrite Ion (NO2) at 1.98 A Resolution


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Structure of the Ternary Complex of Lactoperoxidase with Substrate Nitric Oxide (No) and Product Nitrite Ion (NO2) at 1.98 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I620

b:26.3
occ:0.90
 O A:HOH857 3.3 30.4 1.0
N A:TRP46 3.3 23.8 1.0
N A:VAL342 3.5 19.2 1.0
CH2 A:TRP452 3.7 25.3 1.0
CA A:ARG45 3.8 26.8 1.0
CZ2 A:TRP452 3.9 25.4 1.0
CB A:ASN341 3.9 23.1 1.0
CB A:VAL342 4.0 19.4 1.0
O A:ALA44 4.0 22.6 1.0
C A:ARG45 4.0 27.6 1.0
N A:ASN341 4.1 22.5 1.0
N A:LEU47 4.1 24.7 1.0
CE A:MET446 4.2 24.1 1.0
CG1 A:VAL342 4.2 22.6 1.0
CB A:TRP46 4.3 23.7 1.0
O A:LEU47 4.3 26.1 1.0
CA A:TRP46 4.3 25.1 1.0
CA A:ASN341 4.3 21.6 1.0
CA A:VAL342 4.3 21.6 1.0
C A:ASN341 4.4 20.8 1.0
CD A:ARG45 4.6 27.1 1.0
CB A:SER340 4.6 22.1 1.0
NH1 A:ARG45 4.7 24.2 1.0
CB A:ARG45 4.7 28.2 1.0
C A:TRP46 4.7 25.2 1.0
N A:ARG45 4.8 25.2 1.0
C A:ALA44 4.8 26.0 1.0
CG A:TRP46 4.8 24.4 1.0
SD A:MET446 4.9 25.4 1.0
CZ3 A:TRP452 4.9 22.2 1.0
C A:SER340 5.0 22.1 1.0

Iodine binding site 5 out of 13 in 8ing

Go back to Iodine Binding Sites List in 8ing
Iodine binding site 5 out of 13 in the Structure of the Ternary Complex of Lactoperoxidase with Substrate Nitric Oxide (No) and Product Nitrite Ion (NO2) at 1.98 A Resolution


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Structure of the Ternary Complex of Lactoperoxidase with Substrate Nitric Oxide (No) and Product Nitrite Ion (NO2) at 1.98 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I621

b:43.5
occ:0.35
 O1 A:NO3615 0.7 28.9 0.7
N A:NO3615 0.7 27.8 0.7
O3 A:NO3615 1.4 35.0 0.7
O2 A:NO3615 1.9 33.6 0.7
N A:PHE229 3.7 35.4 1.0
OE2 A:GLU218 3.9 76.1 1.0
N A:GLN217 3.9 39.3 1.0
O A:HOH703 4.0 43.5 1.0
CD2 A:PHE229 4.0 45.1 1.0
CG A:ASN216 4.1 40.8 1.0
OD1 A:ASN216 4.1 37.9 1.0
ND2 A:ASN216 4.1 37.0 1.0
CG A:GLU218 4.2 60.5 1.0
CA A:ASN216 4.2 39.5 1.0
CB A:PHE229 4.3 38.9 1.0
CA A:PRO228 4.3 38.5 1.0
CD A:GLU218 4.4 67.6 1.0
CG A:PHE229 4.5 41.0 1.0
C A:PRO228 4.5 37.2 1.0
CA A:PHE229 4.6 35.9 1.0
CB A:PRO228 4.6 39.8 1.0
C A:ASN216 4.6 38.8 1.0
N A:GLU218 4.7 50.0 1.0
CB A:ASN216 4.8 38.0 1.0
O A:PHE229 4.9 45.3 1.0
CE2 A:PHE229 4.9 45.0 1.0
CB A:GLN217 4.9 44.4 1.0
CA A:GLN217 4.9 46.7 1.0
CB A:GLU218 5.0 54.0 1.0

Iodine binding site 6 out of 13 in 8ing

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Iodine binding site 6 out of 13 in the Structure of the Ternary Complex of Lactoperoxidase with Substrate Nitric Oxide (No) and Product Nitrite Ion (NO2) at 1.98 A Resolution


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Structure of the Ternary Complex of Lactoperoxidase with Substrate Nitric Oxide (No) and Product Nitrite Ion (NO2) at 1.98 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I622

b:34.0
occ:0.45
 N A:NO3613 0.4 20.3 0.6
O1 A:NO3613 1.0 21.7 0.6
O2 A:NO3613 1.1 22.0 0.6
O3 A:NO3613 1.6 23.2 0.6
N A:SEP198 3.8 37.3 1.0
CD A:PRO197 3.9 44.7 1.0
CB A:SEP198 4.0 44.9 1.0
CB A:GLU196 4.1 42.0 1.0
N A:PRO197 4.2 45.6 1.0
CG A:PRO197 4.3 45.0 1.0
CB A:PRO197 4.4 46.4 1.0
CA A:SEP198 4.5 40.1 1.0
C A:PRO197 4.7 35.6 1.0
CA A:PRO197 4.7 43.0 1.0
C A:GLU196 4.8 40.9 1.0
CA A:GLU196 4.9 39.4 1.0
CG A:GLU196 5.0 46.9 1.0

Iodine binding site 7 out of 13 in 8ing

Go back to Iodine Binding Sites List in 8ing
Iodine binding site 7 out of 13 in the Structure of the Ternary Complex of Lactoperoxidase with Substrate Nitric Oxide (No) and Product Nitrite Ion (NO2) at 1.98 A Resolution


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Structure of the Ternary Complex of Lactoperoxidase with Substrate Nitric Oxide (No) and Product Nitrite Ion (NO2) at 1.98 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I623

b:35.6
occ:0.50
 N A:NO3614 0.7 17.3 0.4
O1 A:NO3614 1.0 15.9 0.4
O3 A:NO3614 1.2 16.3 0.4
O2 A:NO3614 1.9 22.1 0.4
O A:HOH704 3.0 46.2 1.0
ND2 A:ASN80 3.5 31.6 1.0
CG A:PRO145 3.8 33.1 1.0
CB A:ASN80 3.8 28.2 1.0
CG A:ASN80 4.2 31.0 1.0
O A:LYS146 4.3 50.9 1.0
CB A:PRO145 4.4 34.2 1.0
CE A:LYS81 4.4 42.9 1.0
CG A:GLU77 4.4 31.1 1.0
CG A:LYS81 4.5 35.0 1.0
CD A:LYS81 4.6 36.9 1.0
CA A:GLU77 4.7 26.3 1.0
O A:GLU77 4.9 30.6 1.0
CB A:GLU77 4.9 26.9 1.0
CD A:GLU77 5.0 36.9 1.0

Iodine binding site 8 out of 13 in 8ing

Go back to Iodine Binding Sites List in 8ing
Iodine binding site 8 out of 13 in the Structure of the Ternary Complex of Lactoperoxidase with Substrate Nitric Oxide (No) and Product Nitrite Ion (NO2) at 1.98 A Resolution


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Structure of the Ternary Complex of Lactoperoxidase with Substrate Nitric Oxide (No) and Product Nitrite Ion (NO2) at 1.98 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I624

b:30.6
occ:0.40
 N A:NO3612 0.6 19.6 0.5
O1 A:NO3612 1.0 20.1 0.5
O3 A:NO3612 1.2 19.9 0.5
O2 A:NO3612 1.7 22.4 0.5
NE A:ARG397 3.4 42.2 1.0
N A:THR560 3.7 38.4 1.0
O A:GLU363 3.8 40.5 1.0
NH2 A:ARG397 3.8 41.4 1.0
OG1 A:THR560 3.9 41.7 1.0
CA A:GLU363 3.9 44.2 1.0
N A:LYS561 4.0 41.2 1.0
CZ A:ARG397 4.1 39.6 1.0
CG A:LYS561 4.1 51.8 1.0
CA A:VAL559 4.2 35.8 1.0
CB A:GLU363 4.2 47.8 1.0
CB A:LYS561 4.2 45.3 1.0
CG A:GLU363 4.2 53.7 1.0
CG1 A:VAL559 4.2 33.6 1.0
CD A:ARG397 4.3 41.6 1.0
CE1 A:TYR365 4.3 37.3 1.0
C A:GLU363 4.3 37.5 1.0
C A:VAL559 4.4 38.1 1.0
CA A:THR560 4.6 40.4 1.0
CA A:LYS561 4.7 40.2 1.0
C A:THR560 4.7 39.7 1.0
O A:LYS561 4.7 35.4 1.0
CB A:VAL559 4.7 34.1 1.0
CB A:THR560 4.8 42.7 1.0
O A:HIS558 4.9 46.0 1.0
CD1 A:TYR365 5.0 37.1 1.0

Iodine binding site 9 out of 13 in 8ing

Go back to Iodine Binding Sites List in 8ing
Iodine binding site 9 out of 13 in the Structure of the Ternary Complex of Lactoperoxidase with Substrate Nitric Oxide (No) and Product Nitrite Ion (NO2) at 1.98 A Resolution


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Structure of the Ternary Complex of Lactoperoxidase with Substrate Nitric Oxide (No) and Product Nitrite Ion (NO2) at 1.98 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I625

b:40.6
occ:0.30
 N A:NO3607 0.8 33.8 0.7
O2 A:NO3607 1.0 30.8 0.7
O1 A:NO3607 1.3 30.7 0.7
O3 A:NO3607 2.0 43.2 0.7
OG1 A:THR463 3.6 37.3 1.0
O A:HOH804 3.6 55.7 1.0
N A:LYS462 3.7 40.0 1.0
CA A:GLY466 3.8 34.1 1.0
N A:THR463 4.1 38.8 1.0
CA A:PRO461 4.3 37.6 1.0
N A:GLY466 4.3 31.0 1.0
CG2 A:THR463 4.3 39.1 1.0
CB A:THR463 4.4 38.5 1.0
C A:PRO461 4.5 40.0 1.0
CA A:LYS462 4.6 39.9 1.0
CB A:LYS462 4.7 44.5 1.0
C A:LYS462 4.8 39.9 1.0
O A:HOH773 4.8 47.1 1.0
CA A:THR463 4.8 38.8 1.0
CB A:PRO461 4.9 39.5 1.0
C A:GLY466 5.0 27.9 1.0

Iodine binding site 10 out of 13 in 8ing

Go back to Iodine Binding Sites List in 8ing
Iodine binding site 10 out of 13 in the Structure of the Ternary Complex of Lactoperoxidase with Substrate Nitric Oxide (No) and Product Nitrite Ion (NO2) at 1.98 A Resolution


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Structure of the Ternary Complex of Lactoperoxidase with Substrate Nitric Oxide (No) and Product Nitrite Ion (NO2) at 1.98 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I633

b:37.2
occ:0.80
 O A:HOH1045 1.2 18.2 1.0
NE1 A:TRP530 3.6 32.8 1.0
CZ2 A:TRP530 3.8 35.3 1.0
CB A:PHE309 3.8 29.3 1.0
CE2 A:TRP530 4.1 33.3 1.0
CA A:ILE306 4.3 29.1 1.0
CZ2 A:TRP529 4.4 33.4 1.0
N A:ARG310 4.4 32.7 1.0
CG1 A:ILE306 4.5 32.1 1.0
O A:ILE306 4.6 32.4 1.0
C A:PHE309 4.7 26.8 1.0
CB A:ARG310 4.7 35.6 1.0
O A:GLN305 4.7 26.3 1.0
CA A:PHE309 4.7 26.9 1.0
CD1 A:TRP530 4.8 32.6 1.0
CB A:ILE306 4.8 29.9 1.0
CA A:ARG310 4.9 33.4 1.0
CG A:PHE309 5.0 26.3 1.0
CG2 A:ILE306 5.0 30.9 1.0

Reference:

M.I.Ahmad, V.Viswanathan, M.Kumar, R.P.Singh, A.K.Singh, M.Sinha, P.Kaur, P.Sharma, S.Sharma, T.P.Singh. Structure of the Ternary Complex of Lactoperoxidase with Substrate Nitric Oxide (No) and Product Nitrite Ion (NO2) at 1.98 A Resolution To Be Published.
Page generated: Mon Aug 12 02:47:57 2024

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