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Iodine in PDB 2o86: Crystal Structure of A Ternary Complex of Buffalo Lactoperoxidase with Nitrate and Iodide at 2.8 A Resolution

Enzymatic activity of Crystal Structure of A Ternary Complex of Buffalo Lactoperoxidase with Nitrate and Iodide at 2.8 A Resolution

All present enzymatic activity of Crystal Structure of A Ternary Complex of Buffalo Lactoperoxidase with Nitrate and Iodide at 2.8 A Resolution:
1.11.1.7;

Protein crystallography data

The structure of Crystal Structure of A Ternary Complex of Buffalo Lactoperoxidase with Nitrate and Iodide at 2.8 A Resolution, PDB code: 2o86 was solved by I.A.Sheikh, N.Singh, A.K.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 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.535, 80.833, 77.655, 90.00, 102.96, 90.00
R / Rfree (%) 20.9 / 21.8

Other elements in 2o86:

The structure of Crystal Structure of A Ternary Complex of Buffalo Lactoperoxidase with Nitrate and Iodide at 2.8 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 A Ternary Complex of Buffalo Lactoperoxidase with Nitrate and Iodide at 2.8 A Resolution (pdb code 2o86). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 7 binding sites of Iodine where determined in the Crystal Structure of A Ternary Complex of Buffalo Lactoperoxidase with Nitrate and Iodide at 2.8 A Resolution, PDB code: 2o86:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7;

Iodine binding site 1 out of 7 in 2o86

Go back to Iodine Binding Sites List in 2o86
Iodine binding site 1 out of 7 in the Crystal Structure of A Ternary Complex of Buffalo Lactoperoxidase with Nitrate and Iodide at 2.8 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 A Ternary Complex of Buffalo Lactoperoxidase with Nitrate and Iodide at 2.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I2001

b:49.5
occ:1.00
 N A:PHE229 3.5 36.5 1.0
OE1 A:GLU218 3.6 53.8 1.0
N A:GLN217 3.7 42.5 1.0
CA A:ASN216 3.7 39.6 1.0
CG A:ASN216 3.9 38.4 1.0
OD1 A:ASN216 4.0 40.4 1.0
ND2 A:ASN216 4.0 37.1 1.0
CA A:PRO228 4.1 34.4 1.0
C A:PRO228 4.3 35.3 1.0
C A:ASN216 4.3 41.2 1.0
CB A:PHE229 4.3 37.4 1.0
CB A:ASN216 4.3 39.5 1.0
CD2 A:PHE229 4.4 35.2 1.0
O A:HOH3175 4.4 50.9 1.0
CA A:PHE229 4.4 37.8 1.0
CB A:PRO228 4.4 34.2 1.0
CG A:PHE229 4.6 36.5 1.0
O A:PHE229 4.7 39.6 1.0
N A:GLU218 4.7 45.6 1.0
N A:ASN216 4.8 38.7 1.0
CD A:GLU218 4.8 54.1 1.0
CA A:GLN217 4.9 43.4 1.0
O A:VAL215 5.0 38.9 1.0

Iodine binding site 2 out of 7 in 2o86

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Iodine binding site 2 out of 7 in the Crystal Structure of A Ternary Complex of Buffalo Lactoperoxidase with Nitrate and Iodide at 2.8 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 A Ternary Complex of Buffalo Lactoperoxidase with Nitrate and Iodide at 2.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I2002

b:43.2
occ:1.00
 O A:HOH3009 3.0 20.3 1.0
CG A:GLU258 3.7 29.5 1.0
C4A A:HEM3008 3.8 27.7 1.0
CG A:ARG255 3.8 31.0 1.0
CB A:ARG255 3.9 31.0 1.0
CD A:ARG255 3.9 30.0 1.0
NE2 A:HIS109 3.9 22.6 1.0
CE1 A:HIS109 3.9 24.8 1.0
CB A:GLU258 3.9 30.0 1.0
NA A:HEM3008 4.0 27.8 1.0
C3A A:HEM3008 4.0 28.2 1.0
CHB A:HEM3008 4.1 27.1 1.0
C1A A:HEM3008 4.3 26.9 1.0
C2A A:HEM3008 4.3 27.9 1.0
CD A:GLU258 4.4 29.4 1.0
CMA A:HEM3008 4.6 26.6 1.0
C1B A:HEM3008 4.7 26.1 1.0
OE1 A:GLU258 4.8 31.1 1.0
O A:ARG255 4.8 30.1 1.0
OE2 A:GLU258 4.9 31.1 1.0
CA A:ARG255 4.9 30.6 1.0

Iodine binding site 3 out of 7 in 2o86

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Iodine binding site 3 out of 7 in the Crystal Structure of A Ternary Complex of Buffalo Lactoperoxidase with Nitrate and Iodide at 2.8 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 A Ternary Complex of Buffalo Lactoperoxidase with Nitrate and Iodide at 2.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I2003

b:58.6
occ:1.00
 O A:PRO424 3.0 48.5 1.0
CA A:PRO236 3.7 45.2 1.0
CG A:PRO236 3.7 45.8 1.0
CB A:PRO236 3.7 44.8 1.0
N A:PRO236 3.9 46.0 1.0
O A:THR425 4.1 51.1 1.0
C A:PRO424 4.2 47.6 1.0
CD A:PRO236 4.3 45.5 1.0
C A:SER235 4.4 47.1 1.0
CB A:PHE239 4.5 48.5 1.0
CG A:PHE239 4.7 51.7 1.0
O A:SER235 4.8 46.4 1.0
C A:THR425 4.8 51.2 1.0
CD2 A:PHE239 4.9 54.6 1.0
CA A:THR425 4.9 51.3 1.0

Iodine binding site 4 out of 7 in 2o86

Go back to Iodine Binding Sites List in 2o86
Iodine binding site 4 out of 7 in the Crystal Structure of A Ternary Complex of Buffalo Lactoperoxidase with Nitrate and Iodide at 2.8 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 A Ternary Complex of Buffalo Lactoperoxidase with Nitrate and Iodide at 2.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I2004

b:58.7
occ:1.00
 NH2 A:ARG397 3.2 27.3 1.0
O A:GLU363 3.4 46.0 1.0
NE A:ARG397 3.6 25.9 1.0
NZ A:LYS561 3.7 53.0 1.0
N A:THR560 3.8 41.5 1.0
CZ A:ARG397 3.9 27.7 1.0
CG2 A:ILE559 4.0 39.6 1.0
CA A:ILE559 4.1 40.7 1.0
OG1 A:THR560 4.1 42.3 1.0
CA A:GLU363 4.2 45.9 1.0
O A:HOH3197 4.2 46.2 1.0
C A:GLU363 4.2 46.1 1.0
CB A:GLU363 4.4 46.8 1.0
C A:ILE559 4.5 41.2 1.0
N A:LYS561 4.5 41.0 1.0
CE2 A:TYR365 4.5 45.0 1.0
CB A:ILE559 4.6 40.5 1.0
O A:HIS558 4.7 41.4 1.0
CD1 A:ILE559 4.7 38.6 1.0
CG A:GLU363 4.8 49.3 1.0
CD A:ARG397 4.8 26.1 1.0
CA A:THR560 4.8 41.7 1.0
OE1 A:GLU363 4.9 59.6 1.0

Iodine binding site 5 out of 7 in 2o86

Go back to Iodine Binding Sites List in 2o86
Iodine binding site 5 out of 7 in the Crystal Structure of A Ternary Complex of Buffalo Lactoperoxidase with Nitrate and Iodide at 2.8 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 A Ternary Complex of Buffalo Lactoperoxidase with Nitrate and Iodide at 2.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I2005

b:34.4
occ:1.00
 O A:HOH3082 3.1 29.2 1.0
N A:TRP46 3.5 28.1 1.0
N A:VAL342 3.6 28.3 1.0
CH2 A:TRP452 3.8 27.1 1.0
CB A:ASN341 3.9 28.2 1.0
CG1 A:VAL342 3.9 28.8 1.0
CZ2 A:TRP452 4.0 25.2 1.0
CE A:MET446 4.0 38.0 1.0
CB A:VAL342 4.0 28.4 1.0
CA A:ARG45 4.0 29.2 1.0
N A:ASN341 4.1 27.9 1.0
N A:LEU47 4.2 28.6 1.0
C A:ARG45 4.2 28.8 1.0
O A:ALA44 4.3 30.1 1.0
CA A:ASN341 4.3 28.3 1.0
O A:LEU47 4.3 30.0 1.0
C A:ASN341 4.4 28.4 1.0
CA A:VAL342 4.4 28.1 1.0
CD A:ARG45 4.4 26.3 1.0
CA A:TRP46 4.4 27.2 1.0
CB A:TRP46 4.4 26.7 1.0
NH1 A:ARG45 4.7 29.9 1.0
CB A:SER340 4.8 26.7 1.0
CB A:ARG45 4.8 29.3 1.0
C A:TRP46 4.8 27.8 1.0
CG A:ARG45 5.0 28.7 1.0
C A:SER340 5.0 27.7 1.0
CG A:TRP46 5.0 23.3 1.0
SD A:MET446 5.0 37.1 1.0

Iodine binding site 6 out of 7 in 2o86

Go back to Iodine Binding Sites List in 2o86
Iodine binding site 6 out of 7 in the Crystal Structure of A Ternary Complex of Buffalo Lactoperoxidase with Nitrate and Iodide at 2.8 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 A Ternary Complex of Buffalo Lactoperoxidase with Nitrate and Iodide at 2.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I2006

b:50.1
occ:1.00
 OG1 A:THR463 3.2 28.9 1.0
N A:LYS462 3.6 32.8 1.0
N A:THR463 4.1 33.8 1.0
CA A:GLY466 4.1 31.5 1.0
CA A:PRO461 4.3 32.9 1.0
CB A:THR463 4.3 33.6 1.0
CG2 A:THR463 4.4 33.9 1.0
CA A:LYS462 4.4 34.1 1.0
CB A:LYS462 4.4 34.8 1.0
C A:PRO461 4.5 32.8 1.0
N A:GLY466 4.6 32.5 1.0
C A:LYS462 4.6 33.9 1.0
CA A:THR463 4.8 33.3 1.0

Iodine binding site 7 out of 7 in 2o86

Go back to Iodine Binding Sites List in 2o86
Iodine binding site 7 out of 7 in the Crystal Structure of A Ternary Complex of Buffalo Lactoperoxidase with Nitrate and Iodide at 2.8 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 A Ternary Complex of Buffalo Lactoperoxidase with Nitrate and Iodide at 2.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I2007

b:52.1
occ:1.00
 OG A:SER359 3.1 32.0 1.0
NZ A:LYS402 3.2 31.8 1.0
CG A:PRO367 3.6 55.0 1.0
CB A:SER359 4.0 30.4 1.0
CD2 A:LEU361 4.1 30.7 1.0
CB A:PRO367 4.2 54.9 1.0
CE A:LYS402 4.2 32.5 1.0
OE2 A:GLU373 4.3 49.3 1.0
CD A:PRO367 4.4 54.3 1.0
CB A:ALA372 4.5 45.3 1.0
CA A:PRO367 4.6 54.6 1.0
CB A:GLU373 4.6 40.0 1.0
N A:PRO367 4.9 54.1 1.0

Reference:

I.A.Sheikh, N.Singh, A.K.Singh, S.Sharma, P.Kaur, T.P.Singh. Crystal Structure of A Ternary Complex of Buffalo Lactoperoxidase with Nitrate and Iodide at 2.8 A Resolution To Be Published.
Page generated: Sun Aug 11 14:10:07 2024

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