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Iodine in PDB 6lco: Crystal Structure of Bovine Lactoperoxidase with Substrates Thiocynate and Iodide Bound at the Distal Heme Side at 1.99 A Resolution.

Enzymatic activity of Crystal Structure of Bovine Lactoperoxidase with Substrates Thiocynate and Iodide Bound at the Distal Heme Side at 1.99 A Resolution.

All present enzymatic activity of Crystal Structure of Bovine Lactoperoxidase with Substrates Thiocynate and Iodide Bound at the Distal Heme Side at 1.99 A Resolution.:
1.11.1.7;

Protein crystallography data

The structure of Crystal Structure of Bovine Lactoperoxidase with Substrates Thiocynate and Iodide Bound at the Distal Heme Side at 1.99 A Resolution., PDB code: 6lco was solved by V.Viswanathan, H.V.Sirohi, G.S.Kushwaha, 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) 39.11 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.270, 80.441, 76.599, 90.00, 103.20, 90.00
R / Rfree (%) 20.7 / 26.1

Other elements in 6lco:

The structure of Crystal Structure of Bovine Lactoperoxidase with Substrates Thiocynate and Iodide Bound at the Distal Heme Side at 1.99 A Resolution. also contains other interesting chemical elements:

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

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of Bovine Lactoperoxidase with Substrates Thiocynate and Iodide Bound at the Distal Heme Side at 1.99 A Resolution. (pdb code 6lco). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 16 binding sites of Iodine where determined in the Crystal Structure of Bovine Lactoperoxidase with Substrates Thiocynate and Iodide Bound at the Distal Heme Side at 1.99 A Resolution., PDB code: 6lco:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 16 in 6lco

Go back to Iodine Binding Sites List in 6lco
Iodine binding site 1 out of 16 in the Crystal Structure of Bovine Lactoperoxidase with Substrates Thiocynate and Iodide Bound at the Distal Heme Side at 1.99 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 Bovine Lactoperoxidase with Substrates Thiocynate and Iodide Bound at the Distal Heme Side at 1.99 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I608

b:54.8
occ:0.70
 C A:SCN628 0.4 24.1 0.3
S A:SCN628 1.4 24.4 0.3
N A:SCN628 1.5 23.9 0.3
CA A:PRO236 3.6 46.4 1.0
N A:THR425 3.6 53.9 1.0
N A:PRO236 3.8 46.3 1.0
CB A:PRO236 3.9 47.7 1.0
O A:SER235 4.0 50.8 1.0
CB A:PHE239 4.0 46.4 1.0
C A:SER235 4.1 52.6 1.0
CA A:PRO424 4.3 52.4 1.0
CA A:THR425 4.3 59.1 1.0
CG A:PHE239 4.4 50.8 1.0
CD A:PRO236 4.4 47.7 1.0
C A:PRO424 4.4 51.3 1.0
O A:PRO234 4.5 65.9 1.0
CB A:PRO424 4.6 53.4 1.0
CD2 A:PHE239 4.6 53.4 1.0
CB A:PRO234 4.6 76.8 1.0
CG A:PRO234 4.7 79.6 1.0
C A:PRO234 4.7 66.8 1.0
CG A:PRO236 4.8 49.8 1.0
CZ A:PHE422 4.8 47.4 1.0
CG2 A:THR425 4.9 55.8 1.0
C A:PRO236 4.9 39.2 1.0
N A:SER235 4.9 58.1 1.0

Iodine binding site 2 out of 16 in 6lco

Go back to Iodine Binding Sites List in 6lco
Iodine binding site 2 out of 16 in the Crystal Structure of Bovine Lactoperoxidase with Substrates Thiocynate and Iodide Bound at the Distal Heme Side at 1.99 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 Bovine Lactoperoxidase with Substrates Thiocynate and Iodide Bound at the Distal Heme Side at 1.99 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I609

b:38.9
occ:1.00
 N A:TRP46 3.4 36.1 1.0
N A:VAL342 3.5 34.4 1.0
O A:HOH858 3.7 35.0 1.0
CH2 A:TRP452 3.7 37.2 1.0
CZ2 A:TRP452 3.9 40.7 1.0
O A:ALA44 3.9 34.2 1.0
CA A:ARG45 3.9 38.8 1.0
CB A:VAL342 3.9 32.8 1.0
CB A:ASN341 3.9 37.7 1.0
N A:ASN341 4.0 33.7 1.0
CG1 A:VAL342 4.1 35.7 1.0
C A:ARG45 4.1 39.6 1.0
N A:LEU47 4.2 35.5 1.0
CE A:MET446 4.2 35.1 1.0
O A:LEU47 4.2 40.1 1.0
CA A:VAL342 4.3 32.4 1.0
CA A:ASN341 4.3 37.8 1.0
C A:ASN341 4.3 39.6 1.0
CB A:TRP46 4.4 37.4 1.0
CA A:TRP46 4.4 39.0 1.0
CD A:ARG45 4.4 38.9 1.0
CB A:SER340 4.4 31.3 1.0
C A:ALA44 4.7 38.4 1.0
N A:ARG45 4.8 35.9 1.0
CB A:ARG45 4.8 43.0 1.0
C A:TRP46 4.8 38.2 1.0
C A:SER340 4.8 34.0 1.0
CG A:TRP46 4.9 38.3 1.0
NH1 A:ARG45 4.9 36.7 1.0
SD A:MET446 4.9 39.5 1.0
CZ3 A:TRP452 4.9 41.4 1.0
OG A:SER340 5.0 35.3 1.0

Iodine binding site 3 out of 16 in 6lco

Go back to Iodine Binding Sites List in 6lco
Iodine binding site 3 out of 16 in the Crystal Structure of Bovine Lactoperoxidase with Substrates Thiocynate and Iodide Bound at the Distal Heme Side at 1.99 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 Bovine Lactoperoxidase with Substrates Thiocynate and Iodide Bound at the Distal Heme Side at 1.99 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I610

b:50.0
occ:0.90
 NE1 A:TRP530 3.7 42.1 1.0
CZ2 A:TRP530 3.9 43.3 1.0
CB A:PHE309 3.9 38.8 1.0
CE2 A:TRP530 4.1 42.3 1.0
OE1 A:GLU531 4.2 68.0 1.0
N A:ARG310 4.3 43.1 1.0
CA A:ILE306 4.4 43.9 1.0
CB A:ARG310 4.5 48.6 1.0
CZ2 A:TRP529 4.6 46.9 1.0
CG1 A:ILE306 4.6 46.7 1.0
C A:PHE309 4.6 39.7 1.0
O A:ILE306 4.6 43.0 1.0
CA A:PHE309 4.8 38.7 1.0
CA A:ARG310 4.8 46.2 1.0
O A:GLN305 4.9 34.1 1.0
CD1 A:TRP530 4.9 45.7 1.0
CB A:ILE306 5.0 47.2 1.0

Iodine binding site 4 out of 16 in 6lco

Go back to Iodine Binding Sites List in 6lco
Iodine binding site 4 out of 16 in the Crystal Structure of Bovine Lactoperoxidase with Substrates Thiocynate and Iodide Bound at the Distal Heme Side at 1.99 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 Bovine Lactoperoxidase with Substrates Thiocynate and Iodide Bound at the Distal Heme Side at 1.99 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I611

b:57.4
occ:0.80
 ND2 A:ASN80 3.5 42.3 1.0
CG A:PRO145 3.7 40.6 1.0
CB A:ASN80 3.8 34.0 1.0
CG A:GLU77 3.9 52.8 1.0
CG A:ASN80 4.2 36.1 1.0
O A:LYS146 4.2 71.4 1.0
CB A:PRO145 4.3 46.3 1.0
CE A:LYS81 4.3 55.8 1.0
CG A:LYS81 4.4 51.5 1.0
CA A:GLU77 4.6 41.3 1.0
CB A:GLU77 4.7 49.4 1.0
CD A:GLU77 4.8 60.6 1.0
CB A:ASN147 4.8 64.7 1.0
NZ A:LYS81 4.8 56.0 1.0
O A:GLU77 4.8 42.2 1.0
CD A:LYS81 4.9 54.9 1.0

Iodine binding site 5 out of 16 in 6lco

Go back to Iodine Binding Sites List in 6lco
Iodine binding site 5 out of 16 in the Crystal Structure of Bovine Lactoperoxidase with Substrates Thiocynate and Iodide Bound at the Distal Heme Side at 1.99 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 Bovine Lactoperoxidase with Substrates Thiocynate and Iodide Bound at the Distal Heme Side at 1.99 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I612

b:53.5
occ:0.70
 S A:SCN626 2.7 47.9 0.7
C A:SCN626 3.4 32.8 0.7
NH1 A:ARG202 3.6 68.4 1.0
OG A:SER198 3.7 49.1 0.5
CA A:LEU199 4.1 45.7 1.0
CB A:LEU199 4.1 48.0 1.0
N A:LEU199 4.2 43.3 1.0
N A:SCN626 4.2 37.4 0.7
CD1 A:LEU199 4.3 50.7 1.0
CD A:ARG202 4.3 56.1 1.0
C A:SER198 4.6 47.2 1.0
CZ A:ARG202 4.7 62.0 1.0
CB A:SER198 4.7 45.5 0.5
CB A:SER198 4.8 43.9 0.5
CG A:LEU199 4.8 49.4 1.0
O A:SER198 4.9 44.8 1.0
NE A:ARG202 5.0 57.8 1.0

Iodine binding site 6 out of 16 in 6lco

Go back to Iodine Binding Sites List in 6lco
Iodine binding site 6 out of 16 in the Crystal Structure of Bovine Lactoperoxidase with Substrates Thiocynate and Iodide Bound at the Distal Heme Side at 1.99 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 Bovine Lactoperoxidase with Substrates Thiocynate and Iodide Bound at the Distal Heme Side at 1.99 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I613

b:65.1
occ:0.50
 CD A:GLU363 0.8 40.1 0.5
OE1 A:GLU363 1.1 31.8 0.5
OE2 A:GLU363 1.2 26.2 0.5
CG A:GLU363 2.3 45.3 0.5
CB A:GLU363 3.3 51.7 0.5
CE A:LYS561 3.4 88.2 1.0
N A:THR560 3.5 59.6 1.0
CD A:LYS561 3.6 80.7 1.0
CG2 A:ILE559 3.7 54.9 1.0
N A:LYS561 3.8 61.4 1.0
CA A:GLU363 3.9 58.2 0.5
CG A:LYS561 3.9 79.7 1.0
CA A:ILE559 3.9 58.0 1.0
CA A:GLU363 3.9 59.1 0.5
O A:GLU363 3.9 70.3 1.0
CG A:GLU363 4.0 49.9 0.5
CB A:GLU363 4.0 54.1 0.5
OG1 A:THR560 4.1 54.1 1.0
NE A:ARG397 4.1 57.4 1.0
C A:ILE559 4.2 61.4 1.0
CB A:LYS561 4.2 74.4 1.0
CB A:ILE559 4.3 58.7 1.0
CE1 A:TYR365 4.4 55.9 1.0
CA A:THR560 4.4 60.7 1.0
C A:GLU363 4.4 57.1 1.0
C A:THR560 4.5 59.5 1.0
CA A:LYS561 4.6 66.8 1.0
O A:LYS561 4.7 64.5 1.0
O A:HIS558 4.7 62.1 1.0
NH2 A:ARG397 4.7 59.4 1.0
OH A:TYR365 4.8 54.3 1.0
NZ A:LYS561 4.8 91.2 1.0
CG1 A:ILE559 4.8 58.4 1.0
CB A:THR560 4.9 60.8 1.0
CZ A:ARG397 4.9 57.9 1.0
CD A:ARG397 4.9 52.7 1.0

Iodine binding site 7 out of 16 in 6lco

Go back to Iodine Binding Sites List in 6lco
Iodine binding site 7 out of 16 in the Crystal Structure of Bovine Lactoperoxidase with Substrates Thiocynate and Iodide Bound at the Distal Heme Side at 1.99 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 Bovine Lactoperoxidase with Substrates Thiocynate and Iodide Bound at the Distal Heme Side at 1.99 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I614

b:49.4
occ:0.60
 N A:LYS462 3.5 43.1 1.0
OG1 A:THR463 3.6 42.8 1.0
CA A:GLY466 3.9 48.1 1.0
N A:THR463 4.0 45.8 1.0
CA A:PRO461 4.1 46.6 1.0
O A:HOH1010 4.1 47.3 1.0
C A:PRO461 4.3 46.4 1.0
CG2 A:THR463 4.4 43.1 1.0
CA A:LYS462 4.4 48.8 1.0
CB A:THR463 4.5 43.7 1.0
N A:GLY466 4.5 46.5 1.0
CB A:LYS462 4.5 47.5 1.0
C A:LYS462 4.7 46.7 1.0
CG A:LYS462 4.8 56.6 1.0
CA A:THR463 4.8 44.9 1.0
CB A:PRO461 4.9 48.1 1.0
O A:GLN460 5.0 43.4 1.0

Iodine binding site 8 out of 16 in 6lco

Go back to Iodine Binding Sites List in 6lco
Iodine binding site 8 out of 16 in the Crystal Structure of Bovine Lactoperoxidase with Substrates Thiocynate and Iodide Bound at the Distal Heme Side at 1.99 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 Bovine Lactoperoxidase with Substrates Thiocynate and Iodide Bound at the Distal Heme Side at 1.99 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I615

b:74.3
occ:0.50
 S A:SCN625 0.8 31.8 0.5
C A:SCN625 2.3 33.3 0.5
N A:SCN625 3.5 35.1 0.5
NE2 A:HIS377 3.7 48.3 1.0
CD2 A:HIS377 3.7 47.9 1.0
ND1 A:HIS429 4.1 46.5 1.0
CG A:HIS429 4.1 46.4 1.0
CB A:HIS429 4.4 44.4 1.0
CE1 A:HIS429 4.4 55.5 1.0
CD2 A:HIS429 4.5 52.1 1.0
NE2 A:HIS429 4.7 56.0 1.0
CG2 A:THR378 4.9 43.5 1.0
CE1 A:HIS377 5.0 53.1 1.0
CG A:HIS377 5.0 47.7 1.0

Iodine binding site 9 out of 16 in 6lco

Go back to Iodine Binding Sites List in 6lco
Iodine binding site 9 out of 16 in the Crystal Structure of Bovine Lactoperoxidase with Substrates Thiocynate and Iodide Bound at the Distal Heme Side at 1.99 A Resolution.


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 Bovine Lactoperoxidase with Substrates Thiocynate and Iodide Bound at the Distal Heme Side at 1.99 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I616

b:63.1
occ:0.55
 O A:HOH998 3.2 56.9 1.0
N A:PHE229 3.8 47.8 1.0
N A:GLN217 3.8 59.3 1.0
OD1 A:ASN216 3.9 57.0 1.0
CG A:ASN216 3.9 55.6 1.0
CA A:ASN216 4.0 55.6 1.0
ND2 A:ASN216 4.1 56.1 1.0
CD2 A:PHE229 4.2 55.6 1.0
CA A:PRO228 4.2 50.5 1.0
C A:ASN216 4.4 55.7 1.0
OE2 A:GLU218 4.4 83.0 1.0
CB A:PHE229 4.4 47.4 1.0
CB A:PRO228 4.4 53.1 1.0
C A:PRO228 4.5 48.9 1.0
CB A:ASN216 4.6 54.5 1.0
CG A:PHE229 4.6 51.5 1.0
CA A:PHE229 4.7 48.7 1.0
CD A:GLU218 4.7 84.3 1.0
N A:GLU218 4.7 67.6 1.0
O A:PHE229 4.8 56.1 1.0
CG A:GLU218 4.8 75.4 1.0
O A:VAL215 4.8 54.2 1.0
CA A:GLN217 4.8 67.2 1.0
CB A:GLN217 4.9 64.2 1.0
N A:ASN216 5.0 54.5 1.0
CE2 A:PHE229 5.0 57.0 1.0

Iodine binding site 10 out of 16 in 6lco

Go back to Iodine Binding Sites List in 6lco
Iodine binding site 10 out of 16 in the Crystal Structure of Bovine Lactoperoxidase with Substrates Thiocynate and Iodide Bound at the Distal Heme Side at 1.99 A Resolution.


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 Bovine Lactoperoxidase with Substrates Thiocynate and Iodide Bound at the Distal Heme Side at 1.99 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I617

b:77.5
occ:0.50
 C A:SCN629 0.3 36.5 0.5
N A:SCN629 1.4 35.9 0.5
S A:SCN629 1.5 48.6 0.5
N A:ALA566 3.5 49.6 1.0
N A:PHE567 3.6 43.5 1.0
CA A:HIS565 3.6 51.4 1.0
C A:HIS565 3.6 48.8 1.0
CD2 A:PHE567 3.7 50.8 1.0
O A:HOH756 3.9 48.5 1.0
CB A:HIS565 4.0 55.6 1.0
CB A:PHE567 4.0 43.4 1.0
O A:HOH893 4.1 44.8 1.0
CG A:PHE567 4.2 47.7 1.0
O A:HOH875 4.2 51.2 1.0
CB A:ASP311 4.2 45.5 1.0
CA A:PHE567 4.3 47.2 1.0
O A:HIS565 4.4 51.0 1.0
CG A:ASP311 4.4 48.5 1.0
CA A:ALA566 4.5 46.3 1.0
C A:ALA566 4.5 46.5 1.0
CE2 A:PHE567 4.6 54.0 1.0
OD1 A:ASP311 4.8 56.8 1.0
OD2 A:ASP311 4.8 51.0 1.0
N A:GLN568 4.8 47.7 1.0
ND1 A:HIS565 4.9 66.7 1.0
CB A:ALA566 4.9 51.0 1.0
CG A:HIS565 4.9 60.6 1.0
N A:HIS565 4.9 54.1 1.0

Reference:

V.Viswanathan, H.V.Sirohi, G.S.Kushwaha, M.Sinha, P.Kaur, S.Sharma, T.P.Singh. Crystal Structure of Bovine Lactoperoxidase with Substrates Thiocynate and Iodide Bound at the Distal Heme Side at 1.99 A Resolution. To Be Published.
Page generated: Sun Aug 11 23:32:46 2024

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