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Iodine in PDB 8y9x: Crystal Structure of the Complex of Lactoperoxidase with Four Inorganic Substrates, Scn, I, Br and Cl

Enzymatic activity of Crystal Structure of the Complex of Lactoperoxidase with Four Inorganic Substrates, Scn, I, Br and Cl

All present enzymatic activity of Crystal Structure of the Complex of Lactoperoxidase with Four Inorganic Substrates, Scn, I, Br and Cl:
1.11.1.7;

Protein crystallography data

The structure of Crystal Structure of the Complex of Lactoperoxidase with Four Inorganic Substrates, Scn, I, Br and Cl, PDB code: 8y9x was solved by V.Viswanathan, A.K.Singh, N.Pandey, M.Sinha, 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) 43.52 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.35, 80.332, 73.391, 90, 103.94, 90
R / Rfree (%) 15.1 / 19.5

Other elements in 8y9x:

The structure of Crystal Structure of the Complex of Lactoperoxidase with Four Inorganic Substrates, Scn, I, Br and Cl also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Bromine (Br) 1 atom
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 Complex of Lactoperoxidase with Four Inorganic Substrates, Scn, I, Br and Cl (pdb code 8y9x). 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 Complex of Lactoperoxidase with Four Inorganic Substrates, Scn, I, Br and Cl, PDB code: 8y9x:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 17 in 8y9x

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Iodine binding site 1 out of 17 in the Crystal Structure of the Complex of Lactoperoxidase with Four Inorganic Substrates, Scn, I, Br and Cl


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 Complex of Lactoperoxidase with Four Inorganic Substrates, Scn, I, Br and Cl within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I603

b:34.4
occ:0.35
 I A:IOD603 0.0 34.4 0.3
I A:IOD603 0.9 26.1 0.3
CG A:PRO145 3.2 25.3 1.0
ND2 A:ASN80 3.4 22.3 1.0
O A:HOH758 3.5 52.1 1.0
CB A:PRO145 3.7 26.4 1.0
CB A:ASN80 4.0 20.1 1.0
O A:LYS146 4.2 37.9 1.0
CG A:ASN80 4.2 20.7 1.0
CG A:GLU77 4.3 24.3 1.0
CE A:LYS81 4.4 32.4 1.0
CA A:GLU77 4.5 17.6 1.0
CD A:GLU77 4.6 32.0 1.0
CB A:GLU77 4.7 20.2 1.0
CD A:PRO145 4.7 24.7 1.0
OE2 A:GLU77 4.8 32.2 1.0
O A:GLU77 4.9 14.7 1.0
CG A:LYS81 4.9 25.9 1.0
N A:ASP148 5.0 26.2 1.0
CA A:PRO145 5.0 26.5 1.0

Iodine binding site 2 out of 17 in 8y9x

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Iodine binding site 2 out of 17 in the Crystal Structure of the Complex of Lactoperoxidase with Four Inorganic Substrates, Scn, I, Br and Cl


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 Complex of Lactoperoxidase with Four Inorganic Substrates, Scn, I, Br and Cl within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I603

b:26.1
occ:0.35
 I A:IOD603 0.0 26.1 0.3
I A:IOD603 0.9 34.4 0.3
ND2 A:ASN80 3.7 22.3 1.0
O A:HOH758 3.8 52.1 1.0
CE A:LYS81 3.8 32.4 1.0
CB A:ASN80 3.9 20.1 1.0
CG A:PRO145 4.1 25.3 1.0
CG A:LYS81 4.3 25.9 1.0
CG A:ASN80 4.3 20.7 1.0
CG A:GLU77 4.4 24.3 1.0
CD A:LYS81 4.5 29.4 1.0
CB A:PRO145 4.6 26.4 1.0
O A:LYS146 4.7 37.9 1.0
CD A:GLU77 4.8 32.0 1.0
NZ A:LYS81 4.8 37.2 1.0
O A:GLU77 4.8 14.7 1.0
OE2 A:GLU77 4.8 32.2 1.0
CA A:GLU77 4.9 17.6 1.0

Iodine binding site 3 out of 17 in 8y9x

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Iodine binding site 3 out of 17 in the Crystal Structure of the Complex of Lactoperoxidase with Four Inorganic Substrates, Scn, I, Br and Cl


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 Complex of Lactoperoxidase with Four Inorganic Substrates, Scn, I, Br and Cl within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I604

b:61.5
occ:0.50
 O A:HOH1029 2.6 54.8 1.0
O A:PRO424 3.1 60.2 1.0
CA A:PRO236 3.7 31.6 1.0
CB A:PRO236 3.9 33.6 1.0
C A:PRO424 4.0 46.7 1.0
N A:PRO236 4.2 38.5 1.0
CB A:PHE239 4.4 40.1 1.0
O A:HIS426 4.5 49.9 1.0
CG A:PHE239 4.6 42.0 1.0
C A:THR425 4.6 56.4 1.0
CA A:THR425 4.6 55.4 1.0
CD A:PRO236 4.7 38.8 1.0
O A:THR425 4.7 55.0 1.0
N A:THR425 4.7 43.6 1.0
C A:SER235 4.7 45.8 1.0
CG A:PRO236 4.8 37.3 1.0
O A:SER235 4.8 41.8 1.0
CB A:PRO234 4.8 85.6 1.0
CA A:PRO424 4.9 42.4 1.0
CD1 A:PHE239 5.0 43.0 1.0
CZ A:PHE422 5.0 34.5 1.0
C A:PRO236 5.0 27.5 1.0

Iodine binding site 4 out of 17 in 8y9x

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Iodine binding site 4 out of 17 in the Crystal Structure of the Complex of Lactoperoxidase with Four Inorganic Substrates, Scn, I, Br and Cl


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 Complex of Lactoperoxidase with Four Inorganic Substrates, Scn, I, Br and Cl within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I605

b:16.6
occ:0.30
 I A:IOD605 0.0 16.6 0.3
I A:IOD605 0.7 30.3 0.5
N A:GLN217 3.3 25.9 1.0
CA A:ASN216 3.8 22.2 1.0
OD1 A:ASN216 3.8 24.8 1.0
CG A:ASN216 3.8 22.4 1.0
N A:PHE229 3.9 25.1 1.0
ND2 A:ASN216 4.0 22.1 1.0
C A:ASN216 4.1 22.6 1.0
CA A:PRO228 4.2 22.6 1.0
CA A:GLN217 4.3 30.0 1.0
CG A:GLU218 4.3 40.2 1.0
N A:GLU218 4.3 32.2 1.0
CB A:GLN217 4.3 29.6 1.0
CD2 A:PHE229 4.4 21.1 1.0
CB A:ASN216 4.4 22.2 1.0
CB A:PRO228 4.4 21.3 1.0
OE2 A:GLU218 4.5 64.4 1.0
CB A:PHE229 4.6 23.1 1.0
C A:PRO228 4.6 25.0 1.0
O A:VAL215 4.7 25.1 1.0
CD A:GLU218 4.7 52.8 1.0
CG A:PHE229 4.7 22.1 1.0
C A:GLN217 4.8 32.5 1.0
ND2 A:ASN231 4.8 70.2 1.0
CA A:PHE229 4.8 23.6 1.0
N A:ASN216 4.8 22.5 1.0
CG A:GLN217 4.8 31.4 1.0
O A:HOH976 4.9 53.7 1.0
CB A:GLU218 5.0 35.6 1.0

Iodine binding site 5 out of 17 in 8y9x

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Iodine binding site 5 out of 17 in the Crystal Structure of the Complex of Lactoperoxidase with Four Inorganic Substrates, Scn, I, Br and Cl


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 Complex of Lactoperoxidase with Four Inorganic Substrates, Scn, I, Br and Cl within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I605

b:30.3
occ:0.50
 I A:IOD605 0.0 30.3 0.5
I A:IOD605 0.7 16.6 0.3
N A:PHE229 3.6 25.1 1.0
N A:GLN217 4.1 25.9 1.0
ND2 A:ASN231 4.1 70.2 1.0
CB A:PHE229 4.2 23.1 1.0
CA A:PRO228 4.2 22.6 1.0
CB A:PRO228 4.2 21.3 1.0
O A:HOH976 4.2 53.7 1.0
CD2 A:PHE229 4.3 21.1 1.0
CG A:ASN216 4.4 22.4 1.0
ND2 A:ASN216 4.4 22.1 1.0
CA A:ASN216 4.4 22.2 1.0
CA A:PHE229 4.4 23.6 1.0
O A:PHE229 4.4 30.0 1.0
OD1 A:ASN216 4.4 24.8 1.0
C A:PRO228 4.4 25.0 1.0
OE2 A:GLU218 4.5 64.4 1.0
CG A:PHE229 4.5 22.1 1.0
CG A:GLU218 4.6 40.2 1.0
C A:ASN216 4.8 22.6 1.0
CD A:GLU218 4.8 52.8 1.0
C A:PHE229 4.9 26.6 1.0
CB A:GLN217 4.9 29.6 1.0
CB A:ASN216 5.0 22.2 1.0
N A:GLU218 5.0 32.2 1.0
CA A:GLN217 5.0 30.0 1.0

Iodine binding site 6 out of 17 in 8y9x

Go back to Iodine Binding Sites List in 8y9x
Iodine binding site 6 out of 17 in the Crystal Structure of the Complex of Lactoperoxidase with Four Inorganic Substrates, Scn, I, Br and Cl


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 Complex of Lactoperoxidase with Four Inorganic Substrates, Scn, I, Br and Cl within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I606

b:22.1
occ:0.70
 O A:HOH1094 3.3 41.8 1.0
O A:HOH710 3.5 27.1 1.0
O A:HOH979 3.8 35.2 1.0
NE1 A:TRP530 3.8 18.8 1.0
CB A:PHE309 3.8 16.9 1.0
CZ2 A:TRP530 4.0 24.1 1.0
CE2 A:TRP530 4.3 21.3 1.0
N A:ARG310 4.3 20.6 1.0
CB A:ARG310 4.4 22.9 1.0
CA A:ILE306 4.4 16.4 1.0
C A:PHE309 4.6 18.5 1.0
CZ2 A:TRP529 4.6 17.3 1.0
CG1 A:ILE306 4.7 21.9 1.0
O A:ILE306 4.7 18.7 1.0
CA A:ARG310 4.7 20.7 1.0
CA A:PHE309 4.8 16.6 1.0
O A:GLN305 4.8 14.7 1.0
CB A:ILE306 4.9 18.6 1.0
CG A:PHE309 5.0 15.5 1.0
OE1 A:GLU531 5.0 34.4 1.0

Iodine binding site 7 out of 17 in 8y9x

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Iodine binding site 7 out of 17 in the Crystal Structure of the Complex of Lactoperoxidase with Four Inorganic Substrates, Scn, I, Br and Cl


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 Complex of Lactoperoxidase with Four Inorganic Substrates, Scn, I, Br and Cl within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I607

b:21.9
occ:0.45
 I A:IOD607 0.0 21.9 0.5
I A:IOD607 0.8 16.2 0.5
NE A:ARG397 3.5 24.9 1.0
NH2 A:ARG397 3.6 25.7 1.0
N A:THR560 3.7 19.1 1.0
CA A:ILE559 3.8 19.9 1.0
CG A:GLU363 3.9 24.2 1.0
CZ A:ARG397 4.0 25.3 1.0
CA A:GLU363 4.0 20.8 1.0
O A:HIS558 4.1 30.6 1.0
CB A:GLU363 4.1 23.5 1.0
NZ A:LYS561 4.1 40.7 1.0
CD A:LYS561 4.1 37.9 1.0
CG2 A:ILE559 4.1 19.5 1.0
O A:GLU363 4.2 23.8 1.0
CE A:LYS561 4.2 42.0 1.0
C A:ILE559 4.3 18.7 1.0
OG1 A:THR560 4.3 20.3 1.0
CB A:ILE559 4.4 20.2 1.0
N A:LYS561 4.4 22.7 1.0
CD A:ARG397 4.5 22.2 1.0
CG1 A:ILE559 4.6 21.6 1.0
C A:GLU363 4.6 22.7 1.0
CE1 A:TYR365 4.6 23.8 1.0
CA A:THR560 4.7 22.1 1.0
N A:ILE559 4.8 19.6 1.0
C A:HIS558 4.9 25.8 1.0

Iodine binding site 8 out of 17 in 8y9x

Go back to Iodine Binding Sites List in 8y9x
Iodine binding site 8 out of 17 in the Crystal Structure of the Complex of Lactoperoxidase with Four Inorganic Substrates, Scn, I, Br and Cl


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 Complex of Lactoperoxidase with Four Inorganic Substrates, Scn, I, Br and Cl within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I607

b:16.2
occ:0.45
 I A:IOD607 0.0 16.2 0.5
I A:IOD607 0.8 21.9 0.5
CD A:LYS561 3.5 37.9 1.0
CE A:LYS561 3.6 42.0 1.0
N A:THR560 3.6 19.1 1.0
NZ A:LYS561 3.7 40.7 1.0
NE A:ARG397 3.8 24.9 1.0
N A:LYS561 3.8 22.7 1.0
O A:GLU363 3.9 23.8 1.0
CG2 A:ILE559 4.1 19.5 1.0
CE1 A:TYR365 4.1 23.8 1.0
CA A:ILE559 4.1 19.9 1.0
OG1 A:THR560 4.2 20.3 1.0
CA A:GLU363 4.2 20.8 1.0
NH2 A:ARG397 4.2 25.7 1.0
CB A:LYS561 4.3 25.6 1.0
C A:ILE559 4.4 18.7 1.0
CB A:GLU363 4.4 23.5 1.0
CG A:GLU363 4.4 24.2 1.0
CG A:LYS561 4.5 31.5 1.0
CZ A:ARG397 4.5 25.3 1.0
C A:GLU363 4.5 22.7 1.0
CB A:ILE559 4.5 20.2 1.0
CA A:THR560 4.6 22.1 1.0
C A:THR560 4.6 23.0 1.0
CA A:LYS561 4.6 24.2 1.0
CD A:ARG397 4.7 22.2 1.0
O A:HIS558 4.7 30.6 1.0
O A:LYS561 4.7 20.8 1.0
OH A:TYR365 4.8 21.2 1.0
CZ A:TYR365 4.9 22.8 1.0
CD1 A:TYR365 4.9 20.6 1.0
CG1 A:ILE559 4.9 21.6 1.0
CB A:THR560 5.0 23.9 1.0

Iodine binding site 9 out of 17 in 8y9x

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Iodine binding site 9 out of 17 in the Crystal Structure of the Complex of Lactoperoxidase with Four Inorganic Substrates, Scn, I, Br and Cl


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 Complex of Lactoperoxidase with Four Inorganic Substrates, Scn, I, Br and Cl within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I608

b:66.7
occ:0.70
 NH1 A:ARG96 3.6 21.4 1.0
ND2 A:ASN95 3.8 36.9 1.0
NH2 A:ARG96 3.8 18.7 1.0
NH1 A:ARG506 3.9 22.3 1.0
NH2 A:ARG506 4.1 19.3 1.0
O6 A:NAG625 4.1 49.0 1.0
O5 A:NAG625 4.1 48.1 1.0
CZ A:ARG96 4.2 20.8 1.0
CA A:ARG504 4.3 29.1 1.0
C1 A:NAG625 4.3 42.7 1.0
CZ A:ARG506 4.4 20.1 1.0
O A:ARG504 4.6 23.5 1.0
C2 A:NAG625 4.6 47.1 1.0
C A:ARG504 4.7 22.0 1.0
O7 A:NAG625 4.8 52.4 1.0
CB A:ASN95 4.8 24.5 1.0
CG A:ASN95 4.8 29.9 1.0
CG A:ARG504 4.9 41.3 1.0
CB A:ARG504 4.9 33.8 1.0

Iodine binding site 10 out of 17 in 8y9x

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Iodine binding site 10 out of 17 in the Crystal Structure of the Complex of Lactoperoxidase with Four Inorganic Substrates, Scn, I, Br and Cl


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 Complex of Lactoperoxidase with Four Inorganic Substrates, Scn, I, Br and Cl within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I609

b:29.3
occ:0.35
 I A:IOD609 0.0 29.3 0.3
I A:IOD609 1.0 24.6 0.3
O4 A:PEG619 3.7 45.4 1.0
C4 A:PEG619 3.8 45.4 1.0
N A:LYS462 3.9 25.7 1.0
CA A:GLY466 3.9 20.6 1.0
OG1 A:THR463 4.0 24.0 1.0
CA A:PRO461 4.3 23.9 1.0
C3 A:PEG619 4.4 45.9 1.0
N A:GLY466 4.5 20.9 1.0
N A:THR463 4.6 24.9 1.0
C A:PRO461 4.6 23.2 1.0
CG2 A:THR463 4.8 28.9 1.0
CA A:LYS462 4.9 29.0 1.0
CB A:LYS462 4.9 31.2 1.0
CB A:THR463 4.9 26.6 1.0
CB A:PRO461 5.0 24.7 1.0
O A:GLN460 5.0 26.6 1.0

Reference:

V.Viswanathan, A.K.Singh, N.Pandey, M.Sinha, P.Kaur, S.Sharma, T.P.Singh. Structural Evidence For the Order of Preference of Inorganic Substrates in Mammalian Heme Peroxidases: Crystal Structure of the Complex of Lactoperoxidase with Four Inorganic Substrates, Scn, I, Br and Cl To Be Published.
Page generated: Mon Aug 12 03:13:29 2024

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