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Iodine in PDB 7ve3: Structure of the Complex of Sheep Lactoperoxidase with Hypoiodite at 2.70 A Resolution

Enzymatic activity of Structure of the Complex of Sheep Lactoperoxidase with Hypoiodite at 2.70 A Resolution

All present enzymatic activity of Structure of the Complex of Sheep Lactoperoxidase with Hypoiodite at 2.70 A Resolution:
1.11.1.7;

Protein crystallography data

The structure of Structure of the Complex of Sheep Lactoperoxidase with Hypoiodite at 2.70 A Resolution, PDB code: 7ve3 was solved by P.K.Singh, S.Yamini, R.P.Singh, A.K.Singh, 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) 43.97 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.942, 80.179, 76.122, 90, 102.86, 90
R / Rfree (%) 19.5 / 27.7

Other elements in 7ve3:

The structure of Structure of the Complex of Sheep Lactoperoxidase with Hypoiodite at 2.70 A Resolution also contains other interesting chemical elements:

Calcium (Ca) 1 atom
Iron (Fe) 1 atom

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Iodine atom in the Structure of the Complex of Sheep Lactoperoxidase with Hypoiodite at 2.70 A Resolution (pdb code 7ve3). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 17 binding sites of Iodine where determined in the Structure of the Complex of Sheep Lactoperoxidase with Hypoiodite at 2.70 A Resolution, PDB code: 7ve3:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 17 in 7ve3

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Iodine binding site 1 out of 17 in the Structure of the Complex of Sheep Lactoperoxidase with Hypoiodite at 2.70 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 Complex of Sheep Lactoperoxidase with Hypoiodite at 2.70 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I605

b:76.3
occ:0.45
 O A:HOH855 3.4 57.9 1.0
NH1 A:ARG96 3.6 55.9 1.0
NH2 A:ARG96 3.6 55.9 1.0
ND2 A:ASN95 4.0 56.3 1.0
CZ A:ARG96 4.1 64.5 1.0
NH1 A:ARG506 4.1 52.9 1.0
CA A:ARG504 4.2 69.2 1.0
O A:ARG504 4.2 65.5 1.0
NH2 A:ARG506 4.3 53.0 1.0
C A:ARG504 4.4 65.4 1.0
CZ A:ARG506 4.5 55.7 1.0
CB A:ARG504 4.7 76.5 1.0
O A:HOH718 4.9 64.3 1.0
CB A:ASN95 4.9 58.7 1.0
CG A:ASN95 4.9 64.9 1.0

Iodine binding site 2 out of 17 in 7ve3

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Iodine binding site 2 out of 17 in the Structure of the Complex of Sheep Lactoperoxidase with Hypoiodite at 2.70 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 Complex of Sheep Lactoperoxidase with Hypoiodite at 2.70 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I606

b:61.5
occ:0.60
 I A:IOD607 2.7 89.9 0.4
NH1 A:ARG202 3.3 80.2 1.0
OG A:SER198 3.4 62.9 0.5
N A:LEU199 4.0 60.9 1.0
CA A:LEU199 4.1 62.3 1.0
CD1 A:LEU199 4.1 66.0 1.0
CB A:LEU199 4.3 65.7 1.0
CB A:SER198 4.4 64.7 0.5
CB A:SER198 4.4 64.0 0.5
C A:SER198 4.4 64.5 0.5
C A:SER198 4.4 64.2 0.5
CZ A:ARG202 4.5 75.8 1.0
CD A:ARG202 4.6 69.3 1.0
O A:SER198 4.7 64.6 0.5
O A:SER198 4.7 64.3 0.5
CG A:LEU199 4.8 68.0 1.0
NE A:ARG202 5.0 72.9 1.0

Iodine binding site 3 out of 17 in 7ve3

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Iodine binding site 3 out of 17 in the Structure of the Complex of Sheep Lactoperoxidase with Hypoiodite at 2.70 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 Complex of Sheep Lactoperoxidase with Hypoiodite at 2.70 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I607

b:89.9
occ:0.40
 OG A:SER198 2.1 62.9 0.5
I A:IOD606 2.7 61.5 0.6
CB A:SER198 3.6 64.0 0.5
CB A:SER198 3.6 64.7 0.5
CD A:ARG202 3.9 69.3 1.0
O A:SER198 4.0 64.6 0.5
C A:SER198 4.0 64.5 0.5
O A:SER198 4.0 64.3 0.5
C A:SER198 4.0 64.2 0.5
CA A:SER198 4.2 63.2 0.5
CA A:SER198 4.2 62.9 0.5
NH1 A:ARG202 4.5 80.2 1.0
N A:LEU199 4.5 60.9 1.0
CB A:ARG202 4.5 68.2 1.0
NE A:ARG202 4.8 72.9 1.0
CG A:ARG202 4.9 70.7 1.0
OG A:SER198 4.9 63.7 0.5
CA A:LEU199 5.0 62.3 1.0

Iodine binding site 4 out of 17 in 7ve3

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Iodine binding site 4 out of 17 in the Structure of the Complex of Sheep Lactoperoxidase with Hypoiodite at 2.70 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 Complex of Sheep Lactoperoxidase with Hypoiodite at 2.70 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I608

b:74.5
occ:0.87
 CG A:PRO145 3.8 53.1 1.0
CB A:ASN80 3.8 55.9 1.0
ND2 A:ASN80 3.8 64.6 1.0
O A:HOH754 3.9 68.4 1.0
CE A:LYS81 4.0 65.2 1.0
CG A:GLU77 4.0 66.1 1.0
CB A:PRO145 4.2 59.1 1.0
CG A:ASN80 4.2 61.5 1.0
CG A:LYS81 4.5 60.9 1.0
NZ A:LYS81 4.7 65.8 1.0
CD A:LYS81 4.7 66.2 1.0
CA A:GLU77 4.7 52.9 1.0
CB A:GLU77 4.8 56.8 1.0
CD A:GLU77 4.9 78.2 1.0
O A:GLU77 4.9 59.0 1.0
CB A:ASN147 5.0 76.5 1.0

Iodine binding site 5 out of 17 in 7ve3

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Iodine binding site 5 out of 17 in the Structure of the Complex of Sheep Lactoperoxidase with Hypoiodite at 2.70 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 Complex of Sheep Lactoperoxidase with Hypoiodite at 2.70 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I609

b:85.0
occ:0.55
 N A:ALA566 3.4 60.5 1.0
N A:PHE567 3.5 54.7 1.0
C A:HIS565 3.5 62.6 1.0
CA A:HIS565 3.5 64.6 1.0
CB A:HIS565 3.7 69.3 1.0
NE2 A:GLN568 3.7 82.5 1.0
CB A:PHE567 3.8 58.3 1.0
CD2 A:PHE567 3.8 56.0 1.0
CG A:PHE567 4.0 57.7 1.0
CB A:ASP311 4.1 66.3 1.0
CA A:PHE567 4.2 57.5 1.0
O A:HIS565 4.2 63.0 1.0
CG A:ASP311 4.4 72.1 1.0
CA A:ALA566 4.5 61.7 1.0
C A:ALA566 4.5 61.0 1.0
OD1 A:ASP311 4.6 81.5 1.0
N A:GLN568 4.7 59.5 1.0
CD A:GLN568 4.7 86.8 1.0
CE2 A:PHE567 4.7 53.2 1.0
CG A:HIS565 4.8 85.3 1.0
ND1 A:HIS565 4.9 88.0 1.0
CG A:GLN568 4.9 80.0 1.0
O A:ASP311 4.9 71.9 1.0
N A:HIS565 5.0 74.1 1.0
C A:PHE567 5.0 55.8 1.0

Iodine binding site 6 out of 17 in 7ve3

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Iodine binding site 6 out of 17 in the Structure of the Complex of Sheep Lactoperoxidase with Hypoiodite at 2.70 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 Complex of Sheep Lactoperoxidase with Hypoiodite at 2.70 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I610

b:68.0
occ:0.56
 ND2 A:ASN216 2.6 84.9 1.0
N A:PHE229 3.7 57.9 1.0
CG A:ASN216 3.8 71.9 1.0
N A:GLN217 4.1 70.7 1.0
CA A:PRO228 4.1 55.3 1.0
CA A:ASN216 4.3 70.8 1.0
CB A:PRO228 4.3 54.4 1.0
CD2 A:PHE229 4.4 78.4 1.0
C A:PRO228 4.4 54.8 1.0
CB A:PHE229 4.5 68.4 1.0
CB A:ASN216 4.6 71.6 1.0
CA A:PHE229 4.6 64.4 1.0
OD1 A:ASN216 4.7 77.1 1.0
CG A:PHE229 4.8 72.4 1.0
C A:ASN216 4.8 70.2 1.0
O A:PHE229 4.8 72.2 1.0
O A:VAL215 4.8 60.2 1.0
CG A:GLU218 4.9 95.5 1.0
N A:GLU218 4.9 82.1 1.0

Iodine binding site 7 out of 17 in 7ve3

Go back to Iodine Binding Sites List in 7ve3
Iodine binding site 7 out of 17 in the Structure of the Complex of Sheep Lactoperoxidase with Hypoiodite at 2.70 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 Complex of Sheep Lactoperoxidase with Hypoiodite at 2.70 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I612

b:67.7
occ:0.50
 I A:61D612 0.0 67.7 0.5
O A:61D612 2.1 55.4 0.5
O A:61D613 3.5 58.0 0.4
O A:HOH752 3.6 61.9 0.8
CD A:ARG255 3.6 53.9 1.0
O A:HOH725 3.7 40.6 1.0
CB A:ARG255 3.7 50.7 1.0
CG A:ARG255 3.8 55.0 1.0
O A:HOH820 3.8 60.4 1.0
C4A A:HEM601 3.8 41.5 1.0
CG A:GLU258 3.8 45.7 1.0
C3A A:HEM601 3.9 40.2 1.0
CE1 A:HIS109 3.9 44.7 1.0
NE2 A:HIS109 3.9 45.4 1.0
CB A:GLU258 4.0 44.0 1.0
NA A:HEM601 4.1 42.8 1.0
C2A A:HEM601 4.1 40.6 1.0
C1A A:HEM601 4.2 40.3 1.0
CHB A:HEM601 4.2 43.8 1.0
CMA A:HEM601 4.4 37.0 1.0
CD A:GLU258 4.4 45.9 1.0
C1B A:HEM601 4.8 42.4 1.0
OE1 A:GLU258 4.8 49.1 1.0
O A:HOH720 4.8 75.8 1.0
NE A:ARG255 4.9 50.1 1.0
CAA A:HEM601 4.9 34.8 1.0
NE2 A:GLN105 4.9 43.3 1.0
CHA A:HEM601 4.9 37.0 1.0
O A:ARG255 4.9 50.1 1.0
OE2 A:GLU258 5.0 46.3 1.0
CA A:ARG255 5.0 52.1 1.0

Iodine binding site 8 out of 17 in 7ve3

Go back to Iodine Binding Sites List in 7ve3
Iodine binding site 8 out of 17 in the Structure of the Complex of Sheep Lactoperoxidase with Hypoiodite at 2.70 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 Complex of Sheep Lactoperoxidase with Hypoiodite at 2.70 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I613

b:76.1
occ:0.43
 I A:61D613 0.0 76.1 0.4
O A:61D613 2.1 58.0 0.4
O A:61D612 3.5 55.4 0.5
CE1 A:PHE381 3.6 49.8 1.0
CZ A:PHE381 3.7 55.2 1.0
O A:HOH720 4.0 75.8 1.0
CA A:ARG255 4.2 52.1 1.0
CG A:ARG255 4.2 55.0 1.0
CB A:ARG255 4.3 50.7 1.0
O A:HOH849 4.4 54.8 1.0
CG A:PRO424 4.4 61.4 1.0
O A:HOH800 4.4 41.7 1.0
O A:SER254 4.6 59.6 1.0
O A:HOH752 4.7 61.9 0.8
CD A:PRO424 4.9 61.8 1.0
CD1 A:PHE381 4.9 48.7 1.0
N A:ARG255 4.9 58.3 1.0
CB A:GLU258 5.0 44.0 1.0
CE2 A:PHE381 5.0 53.2 1.0
C A:SER254 5.0 59.9 1.0

Iodine binding site 9 out of 17 in 7ve3

Go back to Iodine Binding Sites List in 7ve3
Iodine binding site 9 out of 17 in the Structure of the Complex of Sheep Lactoperoxidase with Hypoiodite at 2.70 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 Complex of Sheep Lactoperoxidase with Hypoiodite at 2.70 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I614

b:101.9
occ:0.50
 I A:61D614 0.0 101.9 0.5
O A:61D614 2.1 89.2 0.5
O A:HOH849 2.7 54.8 1.0
O A:HOH705 3.3 23.6 0.5
ND2 A:ASN230 3.5 81.9 1.0
CB A:CYS248 3.8 64.1 1.0
CD A:PRO236 3.8 53.4 1.0
SG A:CYS248 3.9 69.6 1.0
CG A:ASN230 4.4 73.8 1.0
CG A:PRO236 4.5 57.3 1.0
OG A:SER235 4.7 71.4 1.0
CA A:SER235 4.7 64.5 1.0
CB A:ASN230 4.7 69.8 1.0
O A:HOH800 4.9 41.7 1.0
O A:PRO234 5.0 79.6 1.0
N A:PRO236 5.0 58.3 1.0
O A:ASN230 5.0 90.8 1.0

Iodine binding site 10 out of 17 in 7ve3

Go back to Iodine Binding Sites List in 7ve3
Iodine binding site 10 out of 17 in the Structure of the Complex of Sheep Lactoperoxidase with Hypoiodite at 2.70 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 Complex of Sheep Lactoperoxidase with Hypoiodite at 2.70 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I615

b:68.6
occ:0.84
 I A:61D615 0.0 68.6 0.8
O A:61D615 2.1 60.6 0.8
O A:HOH813 3.4 66.6 1.0
N A:THR425 3.6 67.3 1.0
CA A:PRO236 3.6 53.0 1.0
CB A:PRO236 3.8 50.6 1.0
N A:PRO236 3.9 58.3 1.0
CB A:PHE239 4.1 56.3 1.0
CA A:THR425 4.2 70.4 1.0
O A:HOH774 4.2 68.4 1.0
CG A:PHE239 4.3 61.3 1.0
CB A:PRO234 4.3 87.1 1.0
C A:SER235 4.3 61.5 1.0
CA A:PRO424 4.4 57.8 1.0
CD2 A:PHE239 4.4 59.4 1.0
CD A:PRO236 4.4 53.4 1.0
O A:SER235 4.5 57.6 1.0
C A:PRO424 4.5 58.7 1.0
CG A:PRO234 4.5 93.2 1.0
CG A:PRO236 4.5 57.3 1.0
CG2 A:THR425 4.5 65.1 1.0
CB A:PRO424 4.7 60.1 1.0
C A:PRO234 4.9 81.0 1.0
CB A:THR425 5.0 66.4 1.0
C A:PRO236 5.0 53.9 1.0

Reference:

P.K.Singh, S.Yamini, R.P.Singh, A.K.Singh, M.Sinha, P.Kaur, S.Sharma, T.P.Singh. Structure of the Complex of Sheep Lactoperoxidase with Hypoiodite at 2.70 A Resolution To Be Published.
Page generated: Mon Aug 12 02:15:42 2024

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