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Iodine in PDB 3qf1: Crystal Structure of the Complex of Caprine Lactoperoxidase with Diethylenediamine at 2.6A Resolution

Enzymatic activity of Crystal Structure of the Complex of Caprine Lactoperoxidase with Diethylenediamine at 2.6A Resolution

All present enzymatic activity of Crystal Structure of the Complex of Caprine Lactoperoxidase with Diethylenediamine at 2.6A Resolution:
1.11.1.7;

Protein crystallography data

The structure of Crystal Structure of the Complex of Caprine Lactoperoxidase with Diethylenediamine at 2.6A Resolution, PDB code: 3qf1 was solved by N.Pandey, 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) 44.15 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.150, 80.180, 76.730, 90.00, 102.37, 90.00
R / Rfree (%) 23.5 / 25.6

Other elements in 3qf1:

The structure of Crystal Structure of the Complex of Caprine Lactoperoxidase with Diethylenediamine at 2.6A 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 the Complex of Caprine Lactoperoxidase with Diethylenediamine at 2.6A Resolution (pdb code 3qf1). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 10 binding sites of Iodine where determined in the Crystal Structure of the Complex of Caprine Lactoperoxidase with Diethylenediamine at 2.6A Resolution, PDB code: 3qf1:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 10 in 3qf1

Go back to Iodine Binding Sites List in 3qf1
Iodine binding site 1 out of 10 in the Crystal Structure of the Complex of Caprine Lactoperoxidase with Diethylenediamine at 2.6A 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 the Complex of Caprine Lactoperoxidase with Diethylenediamine at 2.6A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I609

b:46.1
occ:1.00
 O A:HOH691 2.8 24.0 1.0
N A:TRP46 3.4 28.0 1.0
N A:VAL342 3.6 21.0 1.0
CH2 A:TRP452 3.7 23.9 1.0
CA A:ARG45 3.8 28.8 1.0
O A:ALA44 3.9 27.9 1.0
CB A:ASN341 3.9 23.6 1.0
CZ2 A:TRP452 3.9 25.8 1.0
CB A:VAL342 3.9 20.3 1.0
CG1 A:VAL342 3.9 21.7 1.0
N A:ASN341 4.0 21.1 1.0
C A:ARG45 4.0 28.7 1.0
N A:LEU47 4.1 27.8 1.0
CE A:MET446 4.2 28.5 1.0
CA A:ASN341 4.3 21.2 1.0
C A:ASN341 4.3 22.1 1.0
O A:LEU47 4.3 23.9 1.0
CA A:TRP46 4.3 27.8 1.0
CB A:TRP46 4.3 27.8 1.0
CA A:VAL342 4.4 21.1 1.0
CB A:SER340 4.4 21.3 1.0
CD A:ARG45 4.5 32.0 1.0
CB A:ARG45 4.7 29.3 1.0
C A:ALA44 4.7 28.6 1.0
C A:TRP46 4.7 29.2 1.0
N A:ARG45 4.7 28.1 1.0
NH1 A:ARG45 4.7 37.5 1.0
C A:SER340 4.8 21.7 1.0
OG A:SER340 4.9 23.1 1.0
CG A:TRP46 4.9 29.0 1.0
CZ3 A:TRP452 5.0 21.8 1.0

Iodine binding site 2 out of 10 in 3qf1

Go back to Iodine Binding Sites List in 3qf1
Iodine binding site 2 out of 10 in the Crystal Structure of the Complex of Caprine Lactoperoxidase with Diethylenediamine at 2.6A 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 the Complex of Caprine Lactoperoxidase with Diethylenediamine at 2.6A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I610

b:82.2
occ:1.00
 N A:PHE229 3.7 52.5 1.0
CD2 A:PHE229 3.8 56.1 1.0
ND2 A:ASN216 4.0 57.1 1.0
CG A:ASN216 4.0 56.1 1.0
OD1 A:ASN216 4.0 58.3 1.0
O A:HOH779 4.0 73.3 1.0
N A:GLN217 4.0 55.5 1.0
CA A:ASN216 4.2 55.8 1.0
CB A:PHE229 4.3 55.6 1.0
CA A:PRO228 4.3 52.1 1.0
CG A:PHE229 4.5 56.4 1.0
C A:PRO228 4.6 51.6 1.0
CB A:PRO228 4.6 52.8 1.0
CA A:PHE229 4.6 55.5 1.0
CG A:GLU218 4.6 72.0 1.0
C A:ASN216 4.6 55.5 1.0
N A:GLU218 4.7 62.1 1.0
CE2 A:PHE229 4.7 56.5 1.0
CB A:ASN216 4.7 55.6 1.0
O A:PHE229 4.8 57.0 1.0
O A:VAL215 4.9 52.5 1.0
CB A:GLU218 5.0 67.2 1.0

Iodine binding site 3 out of 10 in 3qf1

Go back to Iodine Binding Sites List in 3qf1
Iodine binding site 3 out of 10 in the Crystal Structure of the Complex of Caprine Lactoperoxidase with Diethylenediamine at 2.6A 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 the Complex of Caprine Lactoperoxidase with Diethylenediamine at 2.6A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I611

b:79.0
occ:1.00
 CG2 A:ILE559 3.7 50.0 1.0
N A:THR560 3.7 54.4 1.0
NE A:ARG397 3.7 49.3 1.0
O A:GLU363 3.9 56.7 1.0
CA A:ILE559 4.0 53.4 1.0
OG1 A:THR560 4.0 57.0 1.0
CE2 A:TYR365 4.2 61.7 1.0
NH2 A:ARG397 4.2 51.1 1.0
N A:LYS561 4.3 53.2 1.0
C A:ILE559 4.3 54.6 1.0
OE1 A:GLU363 4.4 68.1 1.0
CB A:ILE559 4.4 51.7 1.0
CZ A:ARG397 4.4 49.5 1.0
CG A:LYS561 4.4 56.7 1.0
CA A:GLU363 4.5 59.3 1.0
CD A:ARG397 4.6 47.3 1.0
O A:HIS558 4.6 53.2 1.0
C A:GLU363 4.6 58.9 1.0
CA A:THR560 4.7 53.9 1.0
CD1 A:ILE559 4.8 49.8 1.0
CB A:LYS561 4.8 55.0 1.0
CD2 A:TYR365 4.9 61.7 1.0
CB A:GLU363 4.9 60.8 1.0
OH A:TYR365 4.9 62.0 1.0
C A:THR560 4.9 54.2 1.0
O A:LYS561 5.0 52.2 1.0
CB A:THR560 5.0 54.9 1.0
CZ A:TYR365 5.0 62.1 1.0

Iodine binding site 4 out of 10 in 3qf1

Go back to Iodine Binding Sites List in 3qf1
Iodine binding site 4 out of 10 in the Crystal Structure of the Complex of Caprine Lactoperoxidase with Diethylenediamine at 2.6A 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 the Complex of Caprine Lactoperoxidase with Diethylenediamine at 2.6A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I612

b:58.8
occ:1.00
 O A:HOH778 3.3 33.3 1.0
ND2 A:ASN80 3.5 40.2 1.0
O A:HOH624 3.7 35.9 1.0
CB A:ASN80 3.7 36.9 1.0
CG A:PRO145 3.8 41.9 1.0
CG A:GLU77 4.0 48.8 1.0
CB A:PRO145 4.1 42.5 1.0
CG A:ASN80 4.1 39.2 1.0
O A:LYS146 4.5 44.1 1.0
CE A:LYS81 4.5 40.3 1.0
O A:ASN147 4.6 46.5 1.0
CA A:GLU77 4.7 44.0 1.0
CG A:LYS81 4.7 36.9 1.0
CB A:ASN147 4.8 47.2 1.0
CB A:GLU77 4.8 45.7 1.0
C A:ASN147 4.9 46.2 1.0
CD A:GLU77 4.9 52.3 1.0
O A:GLU77 5.0 42.7 1.0

Iodine binding site 5 out of 10 in 3qf1

Go back to Iodine Binding Sites List in 3qf1
Iodine binding site 5 out of 10 in the Crystal Structure of the Complex of Caprine Lactoperoxidase with Diethylenediamine at 2.6A 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 the Complex of Caprine Lactoperoxidase with Diethylenediamine at 2.6A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I615

b:54.1
occ:1.00
 O A:HOH728 3.2 40.4 1.0
NE1 A:TRP530 3.8 51.0 1.0
O A:HOH694 3.9 30.2 1.0
CB A:PHE309 4.0 30.3 1.0
N A:ARG310 4.3 34.5 1.0
CZ2 A:TRP530 4.3 50.6 1.0
CZ2 A:TRP529 4.4 41.4 1.0
CE2 A:TRP530 4.4 50.5 1.0
CB A:ARG310 4.4 37.5 1.0
CA A:ILE306 4.5 37.2 1.0
C A:PHE309 4.5 34.0 1.0
O A:GLN305 4.5 38.7 1.0
CG1 A:ILE306 4.6 37.5 1.0
CA A:ARG310 4.7 36.6 1.0
O A:ILE306 4.8 37.4 1.0
CA A:PHE309 4.8 33.0 1.0
CD1 A:TRP530 4.9 50.0 1.0

Iodine binding site 6 out of 10 in 3qf1

Go back to Iodine Binding Sites List in 3qf1
Iodine binding site 6 out of 10 in the Crystal Structure of the Complex of Caprine Lactoperoxidase with Diethylenediamine at 2.6A 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 the Complex of Caprine Lactoperoxidase with Diethylenediamine at 2.6A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I616

b:83.5
occ:1.00
 OG1 A:THR463 3.2 40.7 1.0
N A:LYS462 3.5 45.4 1.0
CA A:GLY466 3.8 42.2 1.0
N A:THR463 4.1 42.4 1.0
CA A:PRO461 4.3 42.8 1.0
CB A:THR463 4.3 40.8 1.0
N A:GLY466 4.4 42.3 1.0
C A:PRO461 4.4 43.9 1.0
CA A:LYS462 4.4 45.4 1.0
CG2 A:THR463 4.4 39.9 1.0
CB A:LYS462 4.4 46.2 1.0
C A:LYS462 4.7 44.1 1.0
CG A:LYS462 4.7 49.2 1.0
CA A:THR463 4.9 41.8 1.0
O A:GLN460 5.0 44.2 1.0

Iodine binding site 7 out of 10 in 3qf1

Go back to Iodine Binding Sites List in 3qf1
Iodine binding site 7 out of 10 in the Crystal Structure of the Complex of Caprine Lactoperoxidase with Diethylenediamine at 2.6A 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 the Complex of Caprine Lactoperoxidase with Diethylenediamine at 2.6A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I617

b:64.6
occ:0.50
 N A:ALA566 3.5 43.6 1.0
N A:PHE567 3.5 40.9 1.0
C A:HIS565 3.6 45.9 1.0
CA A:HIS565 3.6 48.1 1.0
CD2 A:PHE567 3.7 43.8 1.0
O A:HOH742 3.8 42.1 1.0
CB A:PHE567 3.9 42.7 1.0
CB A:HIS565 4.0 51.2 1.0
CG A:PHE567 4.1 44.6 1.0
CB A:ASP311 4.1 40.9 1.0
CA A:PHE567 4.2 42.5 1.0
O A:HIS565 4.3 45.3 1.0
CG A:ASP311 4.3 42.0 1.0
CA A:ALA566 4.4 41.0 1.0
OD1 A:ASP311 4.5 43.9 1.0
C A:ALA566 4.5 40.7 1.0
O A:HOH783 4.5 57.4 1.0
CE2 A:PHE567 4.6 42.0 1.0
N A:GLN568 4.7 45.9 1.0
ND1 A:HIS565 4.8 53.0 1.0
CG A:HIS565 4.8 53.4 1.0
OD2 A:ASP311 4.9 41.8 1.0
C A:PHE567 4.9 44.2 1.0
CB A:ALA566 5.0 39.5 1.0

Iodine binding site 8 out of 10 in 3qf1

Go back to Iodine Binding Sites List in 3qf1
Iodine binding site 8 out of 10 in the Crystal Structure of the Complex of Caprine Lactoperoxidase with Diethylenediamine at 2.6A 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 the Complex of Caprine Lactoperoxidase with Diethylenediamine at 2.6A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1618

b:80.3
occ:1.00
 CD2 A:HIS377 3.6 27.2 1.0
NE2 A:HIS377 3.7 25.4 1.0
CG A:HIS429 3.8 40.3 1.0
CD2 A:HIS429 3.9 38.6 1.0
ND1 A:HIS429 4.0 39.2 1.0
CG2 A:THR378 4.1 35.4 1.0
NE2 A:HIS429 4.1 37.7 1.0
CE1 A:HIS429 4.2 38.5 1.0
CB A:HIS429 4.3 39.6 1.0
O A:HIS377 4.8 36.6 1.0
CG A:HIS377 4.9 28.9 1.0
CA A:THR378 4.9 36.1 1.0
CE1 A:HIS377 4.9 27.2 1.0

Iodine binding site 9 out of 10 in 3qf1

Go back to Iodine Binding Sites List in 3qf1
Iodine binding site 9 out of 10 in the Crystal Structure of the Complex of Caprine Lactoperoxidase with Diethylenediamine at 2.6A 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 the Complex of Caprine Lactoperoxidase with Diethylenediamine at 2.6A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I619

b:73.6
occ:1.00
 CA A:PRO236 3.6 55.3 1.0
CB A:PRO236 3.6 54.5 1.0
N A:THR425 3.6 52.4 1.0
N A:PRO236 3.8 56.3 1.0
CB A:PHE239 4.0 44.1 1.0
C A:SER235 4.1 57.4 1.0
CG A:PHE239 4.2 42.3 1.0
CA A:THR425 4.2 54.1 1.0
CD1 A:PHE239 4.3 42.0 1.0
O A:SER235 4.3 58.3 1.0
CA A:PRO424 4.5 48.7 1.0
C A:PRO424 4.5 50.5 1.0
CD A:PRO236 4.6 54.1 1.0
CG A:PRO236 4.6 54.9 1.0
CZ A:PHE422 4.7 41.5 1.0
CE2 A:PHE422 4.9 41.0 1.0
C A:PRO236 4.9 54.7 1.0
CB A:PRO424 5.0 47.6 1.0
N A:SER235 5.0 61.8 1.0
CD2 A:PHE239 5.0 41.3 1.0
O A:PRO234 5.0 63.0 1.0
C A:PRO234 5.0 63.4 1.0

Iodine binding site 10 out of 10 in 3qf1

Go back to Iodine Binding Sites List in 3qf1
Iodine binding site 10 out of 10 in the Crystal Structure of the Complex of Caprine Lactoperoxidase with Diethylenediamine at 2.6A 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 the Complex of Caprine Lactoperoxidase with Diethylenediamine at 2.6A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I620

b:47.5
occ:0.50
 NE A:ARG202 2.3 43.8 1.0
CZ A:ARG202 2.5 42.8 1.0
CD A:ARG202 2.8 49.7 1.0
NH2 A:ARG202 3.1 39.7 1.0
NH1 A:ARG202 3.2 36.9 1.0
CD1 A:LEU199 4.0 37.9 1.0
CA A:LEU199 4.1 40.8 1.0
CB A:LEU199 4.2 40.4 1.0
N A:LEU199 4.2 42.0 1.0
O A:SEP198 4.3 48.0 1.0
CG A:ARG202 4.4 48.6 1.0
C A:SEP198 4.4 48.9 1.0
CG A:LEU199 4.8 41.1 1.0
CB A:ARG202 4.8 49.6 1.0
O A:HOH750 5.0 59.2 1.0

Reference:

N.Pandey, R.P.Singh, A.K.Singh, M.Sinha, P.Kaur, S.Sharma, T.P.Singh. Crystal Structure of the Complex of Caprine Lactoperoxidase with Diethylenediamine at 2.6A Resolution To Be Published.
Page generated: Sun Aug 11 16:14:17 2024

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