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Iodine in PDB 2ojv: Crystal Structure of A Ternary Complex of Goat Lactoperoxidase with Cyanide and Iodide Ions at 2.4 A Resolution

Enzymatic activity of Crystal Structure of A Ternary Complex of Goat Lactoperoxidase with Cyanide and Iodide Ions at 2.4 A Resolution

All present enzymatic activity of Crystal Structure of A Ternary Complex of Goat Lactoperoxidase with Cyanide and Iodide Ions at 2.4 A Resolution:
1.11.1.7;

Protein crystallography data

The structure of Crystal Structure of A Ternary Complex of Goat Lactoperoxidase with Cyanide and Iodide Ions at 2.4 A Resolution, PDB code: 2ojv was solved by A.K.Singh, N.Singh, S.B.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) 74.54 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.197, 80.811, 77.047, 90.00, 102.96, 90.00
R / Rfree (%) 17.8 / 22.8

Other elements in 2ojv:

The structure of Crystal Structure of A Ternary Complex of Goat Lactoperoxidase with Cyanide and Iodide Ions at 2.4 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 Goat Lactoperoxidase with Cyanide and Iodide Ions at 2.4 A Resolution (pdb code 2ojv). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 8 binding sites of Iodine where determined in the Crystal Structure of A Ternary Complex of Goat Lactoperoxidase with Cyanide and Iodide Ions at 2.4 A Resolution, PDB code: 2ojv:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iodine binding site 1 out of 8 in 2ojv

Go back to Iodine Binding Sites List in 2ojv
Iodine binding site 1 out of 8 in the Crystal Structure of A Ternary Complex of Goat Lactoperoxidase with Cyanide and Iodide Ions at 2.4 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 Goat Lactoperoxidase with Cyanide and Iodide Ions at 2.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I2845

b:17.6
occ:1.00
 O A:HOH2910 3.2 12.6 1.0
N A:VAL342 3.4 8.9 1.0
N A:TRP46 3.5 14.1 1.0
CH2 A:TRP452 3.7 12.6 1.0
CB A:ASN341 3.8 10.2 1.0
CA A:ARG45 3.9 14.6 1.0
CZ2 A:TRP452 3.9 12.5 1.0
CB A:VAL342 3.9 8.7 1.0
O A:ALA44 4.0 13.4 1.0
N A:ASN341 4.1 11.1 1.0
CE A:MET446 4.1 5.5 1.0
CG1 A:VAL342 4.1 7.8 1.0
N A:LEU47 4.2 13.8 1.0
C A:ARG45 4.2 15.0 1.0
CA A:VAL342 4.2 8.9 1.0
CA A:ASN341 4.2 10.5 1.0
O A:LEU47 4.3 13.7 1.0
C A:ASN341 4.3 10.2 1.0
CB A:TRP46 4.4 13.9 1.0
CA A:TRP46 4.4 14.1 1.0
CB A:ARG45 4.5 15.3 1.0
CB A:SER340 4.6 10.2 1.0
CG A:ARG45 4.7 15.8 1.0
NH1 A:ARG45 4.8 10.9 1.0
SD A:MET446 4.8 16.6 1.0
C A:ALA44 4.8 13.7 1.0
C A:TRP46 4.8 14.6 1.0
N A:ARG45 4.8 13.4 1.0
CD A:ARG45 4.9 16.9 1.0
C A:SER340 4.9 10.7 1.0
CG A:TRP46 4.9 12.1 1.0
CZ3 A:TRP452 5.0 11.6 1.0

Iodine binding site 2 out of 8 in 2ojv

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Iodine binding site 2 out of 8 in the Crystal Structure of A Ternary Complex of Goat Lactoperoxidase with Cyanide and Iodide Ions at 2.4 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 Goat Lactoperoxidase with Cyanide and Iodide Ions at 2.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I2846

b:37.1
occ:1.00
 NZ A:LYS465 3.2 43.2 1.0
NZ A:LYS474 3.4 34.3 1.0
CB A:GLN468 4.0 22.2 1.0
N A:ALA469 4.0 20.4 1.0
CA A:ALA469 4.1 20.2 1.0
C A:GLN468 4.2 21.2 1.0
O A:GLN468 4.4 21.2 1.0
NE2 A:GLN468 4.4 27.6 1.0
CE A:LYS465 4.4 40.0 1.0
CB A:ALA469 4.6 19.9 1.0
CA A:GLN468 4.8 22.1 1.0
CE A:LYS474 4.8 35.4 1.0

Iodine binding site 3 out of 8 in 2ojv

Go back to Iodine Binding Sites List in 2ojv
Iodine binding site 3 out of 8 in the Crystal Structure of A Ternary Complex of Goat Lactoperoxidase with Cyanide and Iodide Ions at 2.4 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 Goat Lactoperoxidase with Cyanide and Iodide Ions at 2.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I2847

b:47.4
occ:1.00
 OG1 A:THR463 3.3 26.1 1.0
N A:LYS462 3.3 24.5 1.0
N A:THR463 3.4 26.0 1.0
CG2 A:THR463 3.9 24.9 1.0
CB A:THR463 4.0 25.1 1.0
CA A:GLY466 4.0 21.8 1.0
CA A:LYS462 4.0 25.8 1.0
CB A:LYS462 4.1 26.3 1.0
C A:LYS462 4.2 26.3 1.0
CA A:THR463 4.3 25.1 1.0
C A:PRO461 4.4 23.6 1.0
N A:GLY466 4.4 23.4 1.0
CA A:PRO461 4.6 22.7 1.0
CG A:LYS462 4.8 29.4 1.0
O A:THR463 4.8 24.3 1.0
O A:HOH3057 4.9 44.0 1.0
O A:GLN460 5.0 22.1 1.0
C A:THR463 5.0 25.2 1.0

Iodine binding site 4 out of 8 in 2ojv

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Iodine binding site 4 out of 8 in the Crystal Structure of A Ternary Complex of Goat Lactoperoxidase with Cyanide and Iodide Ions at 2.4 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 Goat Lactoperoxidase with Cyanide and Iodide Ions at 2.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I2848

b:61.2
occ:1.00
 NH2 A:ARG202 2.8 47.1 1.0
NE A:ARG202 3.2 44.6 1.0
CZ A:ARG202 3.5 47.6 1.0
CB A:SER198 4.0 23.7 1.0
O A:SER198 4.1 25.1 1.0
C A:SER198 4.1 24.5 1.0
OG A:SER198 4.2 26.2 1.0
N A:LEU199 4.4 24.8 1.0
CD A:ARG202 4.5 39.7 1.0
CA A:LEU199 4.5 24.7 1.0
CA A:SER198 4.7 24.1 1.0
NH1 A:ARG202 4.8 48.6 1.0
CG A:ARG202 4.8 33.8 1.0
CB A:ARG202 4.9 29.6 1.0

Iodine binding site 5 out of 8 in 2ojv

Go back to Iodine Binding Sites List in 2ojv
Iodine binding site 5 out of 8 in the Crystal Structure of A Ternary Complex of Goat Lactoperoxidase with Cyanide and Iodide Ions at 2.4 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 Goat Lactoperoxidase with Cyanide and Iodide Ions at 2.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I2849

b:62.7
occ:1.00
 ND2 A:ASN80 3.4 14.5 1.0
O A:HOH2855 3.5 41.3 1.0
O A:HOH3174 3.5 32.3 1.0
CB A:ASN80 3.8 14.8 1.0
CG A:PRO145 3.8 22.2 1.0
CG A:ASN80 4.1 15.6 1.0
O A:HOH3018 4.1 47.8 1.0
O A:LYS146 4.2 32.2 1.0
CB A:PRO145 4.2 23.4 1.0
CE A:LYS81 4.3 25.6 1.0
CG A:GLU77 4.4 22.1 1.0
O A:ASN147 4.6 29.3 1.0
CG A:LYS81 4.7 19.5 1.0
CA A:GLU77 4.8 17.5 1.0

Iodine binding site 6 out of 8 in 2ojv

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Iodine binding site 6 out of 8 in the Crystal Structure of A Ternary Complex of Goat Lactoperoxidase with Cyanide and Iodide Ions at 2.4 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 Goat Lactoperoxidase with Cyanide and Iodide Ions at 2.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I2850

b:63.9
occ:1.00
 NH2 A:ARG397 3.3 26.7 1.0
NE A:ARG397 3.4 29.6 1.0
N A:THR560 3.4 25.7 1.0
O A:GLU363 3.6 33.1 1.0
CZ A:ARG397 3.8 28.0 1.0
CG2 A:ILE559 3.9 24.2 1.0
OG1 A:THR560 3.9 28.0 1.0
N A:LYS561 4.0 27.5 1.0
CA A:GLU363 4.0 32.6 1.0
CA A:ILE559 4.0 24.8 1.0
CB A:GLU363 4.2 33.2 1.0
C A:ILE559 4.2 25.0 1.0
C A:GLU363 4.3 32.9 1.0
CE2 A:TYR365 4.3 27.1 1.0
CA A:THR560 4.4 26.7 1.0
CB A:LYS561 4.4 28.9 1.0
CD A:ARG397 4.5 25.8 1.0
CG A:LYS561 4.5 31.5 1.0
C A:THR560 4.6 26.8 1.0
CB A:ILE559 4.6 24.9 1.0
O A:HIS558 4.6 24.6 1.0
CB A:THR560 4.7 27.6 1.0
CA A:LYS561 4.8 28.2 1.0
CD2 A:TYR365 4.9 28.4 1.0
OE1 A:GLU363 4.9 40.9 1.0
CG A:ARG397 4.9 22.3 1.0
O A:LYS561 5.0 28.9 1.0

Iodine binding site 7 out of 8 in 2ojv

Go back to Iodine Binding Sites List in 2ojv
Iodine binding site 7 out of 8 in the Crystal Structure of A Ternary Complex of Goat Lactoperoxidase with Cyanide and Iodide Ions at 2.4 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 Goat Lactoperoxidase with Cyanide and Iodide Ions at 2.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I2851

b:59.7
occ:1.00
 N A:PHE229 3.4 25.5 1.0
O A:HOH3094 3.5 30.7 1.0
ND2 A:ASN216 3.5 29.0 1.0
O A:HOH3137 3.5 34.7 1.0
CG A:ASN216 3.6 29.8 1.0
N A:GLN217 3.6 30.9 1.0
CA A:ASN216 3.8 29.4 1.0
OD1 A:ASN216 3.8 32.0 1.0
CB A:PHE229 4.1 26.9 1.0
O A:HOH3151 4.2 48.6 1.0
CA A:PRO228 4.2 23.6 1.0
CB A:ASN216 4.2 29.4 1.0
CD2 A:PHE229 4.2 25.5 1.0
C A:ASN216 4.2 29.8 1.0
OE1 A:GLU218 4.3 49.1 1.0
C A:PRO228 4.3 24.4 1.0
CA A:PHE229 4.3 27.4 1.0
CG A:PHE229 4.4 26.3 1.0
ND2 A:ASN231 4.6 44.1 1.0
CB A:PRO228 4.6 23.9 1.0
O A:PHE229 4.7 29.3 1.0
CA A:GLN217 4.7 32.8 1.0
CB A:GLN217 4.7 33.1 1.0
N A:GLU218 4.8 33.9 1.0
N A:ASN216 4.9 28.7 1.0
O A:VAL215 5.0 28.2 1.0
CG A:GLN217 5.0 34.8 1.0

Iodine binding site 8 out of 8 in 2ojv

Go back to Iodine Binding Sites List in 2ojv
Iodine binding site 8 out of 8 in the Crystal Structure of A Ternary Complex of Goat Lactoperoxidase with Cyanide and Iodide Ions at 2.4 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 A Ternary Complex of Goat Lactoperoxidase with Cyanide and Iodide Ions at 2.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I2852

b:45.2
occ:1.00
 N A:CYN2844 2.8 17.7 1.0
O A:HOH3152 3.2 24.1 1.0
O A:HOH3050 3.4 17.6 1.0
C4A A:HEM2853 3.6 13.7 1.0
C A:CYN2844 3.6 16.5 1.0
C3A A:HEM2853 3.7 12.8 1.0
CG A:GLU258 3.7 14.0 1.0
CB A:ARG255 3.8 17.6 1.0
NA A:HEM2853 3.8 12.7 1.0
CG A:ARG255 3.8 16.1 1.0
CHB A:HEM2853 3.9 14.2 1.0
CB A:GLU258 4.0 15.2 1.0
NE2 A:HIS109 4.0 6.2 1.0
C2A A:HEM2853 4.0 13.1 1.0
C1A A:HEM2853 4.1 13.4 1.0
CD A:GLU258 4.1 14.3 1.0
CE1 A:HIS109 4.2 5.7 1.0
CMA A:HEM2853 4.3 8.6 1.0
OE1 A:GLU258 4.4 12.0 1.0
C1B A:HEM2853 4.5 12.4 1.0
OE2 A:GLU258 4.6 12.0 1.0
NE2 A:GLN105 4.6 11.0 1.0
NE A:ARG255 4.7 18.6 1.0
CD A:ARG255 4.9 19.3 1.0
CHA A:HEM2853 4.9 12.4 1.0
NB A:HEM2853 4.9 14.5 1.0
CAA A:HEM2853 4.9 15.9 1.0

Reference:

A.K.Singh, N.Singh, S.B.Singh, S.Sharma, P.Kaur, T.P.Singh. Crystal Structure of A Ternary Complex of Goat Lactoperoxidase with Cyanide and Iodide Ions at 2.4 A Resolution To Be Published.
Page generated: Sun Aug 11 14:13:01 2024

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