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Iodine in PDB 7de5: Crystal Structure of Yak Lactoperoxidase at 1.55 A Resolution.

Enzymatic activity of Crystal Structure of Yak Lactoperoxidase at 1.55 A Resolution.

All present enzymatic activity of Crystal Structure of Yak Lactoperoxidase at 1.55 A Resolution.:
1.11.1.7;

Protein crystallography data

The structure of Crystal Structure of Yak Lactoperoxidase at 1.55 A Resolution., PDB code: 7de5 was solved by P.K.Singh, V.Viswanathan, P.Sharma, C.Rani, N.Ahmad, 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) 43.25 / 1.55
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.910, 78.980, 67.820, 90.00, 92.96, 90.00
R / Rfree (%) 18.7 / 22.6

Other elements in 7de5:

The structure of Crystal Structure of Yak Lactoperoxidase at 1.55 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 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 48;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of Yak Lactoperoxidase at 1.55 A Resolution. (pdb code 7de5). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 48 binding sites of Iodine where determined in the Crystal Structure of Yak Lactoperoxidase at 1.55 A Resolution., PDB code: 7de5:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 48 in 7de5

Go back to Iodine Binding Sites List in 7de5
Iodine binding site 1 out of 48 in the Crystal Structure of Yak Lactoperoxidase at 1.55 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 Yak Lactoperoxidase at 1.55 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I604

b:15.4
occ:0.54
 I A:IOD604 0.0 15.4 0.5
I A:IOD604 0.0 12.8 0.3
I A:IOD604 0.1 9.8 0.2
O A:HOH949 3.4 13.7 1.0
N A:TRP46 3.5 11.1 1.0
N A:VAL342 3.5 9.6 1.0
CH2 A:TRP452 3.8 8.3 1.0
CB A:ASN341 3.9 10.2 1.0
CA A:ARG45 3.9 11.2 1.0
O A:ALA44 3.9 11.6 1.0
CZ2 A:TRP452 3.9 8.4 1.0
CB A:VAL342 4.0 9.9 1.0
N A:ASN341 4.0 9.4 1.0
CG1 A:VAL342 4.0 11.1 1.0
N A:LEU47 4.1 11.6 1.0
C A:ARG45 4.2 11.4 1.0
O A:LEU47 4.2 12.7 1.0
CA A:ASN341 4.3 9.7 1.0
CE A:MET446 4.3 12.3 1.0
CB A:TRP46 4.3 12.1 1.0
CD A:ARG45 4.3 11.7 1.0
C A:ASN341 4.3 9.6 1.0
CA A:VAL342 4.3 9.4 1.0
CA A:TRP46 4.4 12.2 1.0
CB A:SER340 4.6 9.9 1.0
CB A:ARG45 4.7 11.9 1.0
NH1 A:ARG45 4.7 12.1 1.0
C A:TRP46 4.8 12.3 1.0
C A:ALA44 4.8 10.3 1.0
N A:ARG45 4.8 10.3 1.0
CG A:TRP46 4.9 13.1 1.0
C A:SER340 4.9 9.5 1.0
SD A:MET446 4.9 13.3 1.0
CZ3 A:TRP452 5.0 8.9 1.0
CG A:ARG45 5.0 11.6 1.0

Iodine binding site 2 out of 48 in 7de5

Go back to Iodine Binding Sites List in 7de5
Iodine binding site 2 out of 48 in the Crystal Structure of Yak Lactoperoxidase at 1.55 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 Yak Lactoperoxidase at 1.55 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I604

b:9.8
occ:0.19
 I A:IOD604 0.0 9.8 0.2
I A:IOD604 0.0 12.8 0.3
I A:IOD604 0.1 15.4 0.5
O A:HOH949 3.4 13.7 1.0
N A:TRP46 3.5 11.1 1.0
N A:VAL342 3.6 9.6 1.0
CH2 A:TRP452 3.8 8.3 1.0
CA A:ARG45 3.8 11.2 1.0
O A:ALA44 3.9 11.6 1.0
CB A:ASN341 3.9 10.2 1.0
N A:ASN341 4.0 9.4 1.0
CB A:VAL342 4.0 9.9 1.0
CZ2 A:TRP452 4.0 8.4 1.0
CG1 A:VAL342 4.0 11.1 1.0
N A:LEU47 4.1 11.6 1.0
C A:ARG45 4.1 11.4 1.0
O A:LEU47 4.2 12.7 1.0
CB A:TRP46 4.2 12.1 1.0
CA A:ASN341 4.3 9.7 1.0
CD A:ARG45 4.3 11.7 1.0
CE A:MET446 4.3 12.3 1.0
CA A:TRP46 4.3 12.2 1.0
C A:ASN341 4.3 9.6 1.0
CA A:VAL342 4.4 9.4 1.0
CB A:SER340 4.5 9.9 1.0
CB A:ARG45 4.7 11.9 1.0
C A:TRP46 4.7 12.3 1.0
C A:ALA44 4.7 10.3 1.0
NH1 A:ARG45 4.8 12.1 1.0
N A:ARG45 4.8 10.3 1.0
CG A:TRP46 4.8 13.1 1.0
C A:SER340 4.9 9.5 1.0
SD A:MET446 5.0 13.3 1.0
CG A:ARG45 5.0 11.6 1.0
CZ3 A:TRP452 5.0 8.9 1.0

Iodine binding site 3 out of 48 in 7de5

Go back to Iodine Binding Sites List in 7de5
Iodine binding site 3 out of 48 in the Crystal Structure of Yak Lactoperoxidase at 1.55 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 Yak Lactoperoxidase at 1.55 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I604

b:12.8
occ:0.27
 I A:IOD604 0.0 12.8 0.3
I A:IOD604 0.0 15.4 0.5
I A:IOD604 0.0 9.8 0.2
O A:HOH949 3.4 13.7 1.0
N A:TRP46 3.5 11.1 1.0
N A:VAL342 3.5 9.6 1.0
CH2 A:TRP452 3.8 8.3 1.0
CA A:ARG45 3.9 11.2 1.0
CB A:ASN341 3.9 10.2 1.0
O A:ALA44 3.9 11.6 1.0
CB A:VAL342 4.0 9.9 1.0
CZ2 A:TRP452 4.0 8.4 1.0
N A:ASN341 4.0 9.4 1.0
CG1 A:VAL342 4.0 11.1 1.0
N A:LEU47 4.1 11.6 1.0
C A:ARG45 4.1 11.4 1.0
O A:LEU47 4.2 12.7 1.0
CB A:TRP46 4.3 12.1 1.0
CA A:ASN341 4.3 9.7 1.0
CE A:MET446 4.3 12.3 1.0
CD A:ARG45 4.3 11.7 1.0
C A:ASN341 4.3 9.6 1.0
CA A:TRP46 4.3 12.2 1.0
CA A:VAL342 4.3 9.4 1.0
CB A:SER340 4.6 9.9 1.0
CB A:ARG45 4.7 11.9 1.0
NH1 A:ARG45 4.7 12.1 1.0
C A:TRP46 4.8 12.3 1.0
C A:ALA44 4.8 10.3 1.0
N A:ARG45 4.8 10.3 1.0
CG A:TRP46 4.9 13.1 1.0
C A:SER340 4.9 9.5 1.0
SD A:MET446 4.9 13.3 1.0
CZ3 A:TRP452 5.0 8.9 1.0
CG A:ARG45 5.0 11.6 1.0

Iodine binding site 4 out of 48 in 7de5

Go back to Iodine Binding Sites List in 7de5
Iodine binding site 4 out of 48 in the Crystal Structure of Yak Lactoperoxidase at 1.55 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 Yak Lactoperoxidase at 1.55 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I605

b:24.3
occ:0.59
 I A:IOD639 2.3 61.3 0.7
NH1 A:ARG202 3.7 30.6 1.0
O A:HOH1227 3.7 28.6 1.0
CB A:LEU199 4.0 16.5 1.0
CA A:LEU199 4.0 16.2 1.0
I A:IOD639 4.1 61.4 0.3
CD1 A:LEU199 4.1 17.1 1.0
CD A:ARG202 4.2 27.1 1.0
N A:LEU199 4.2 14.8 1.0
O A:HOH1274 4.4 26.9 1.0
CG A:LEU199 4.6 17.2 1.0
OG A:SER198 4.6 20.3 1.0
CZ A:ARG202 4.8 29.3 1.0
C A:SER198 4.8 16.7 1.0
NE A:ARG202 4.9 27.8 1.0

Iodine binding site 5 out of 48 in 7de5

Go back to Iodine Binding Sites List in 7de5
Iodine binding site 5 out of 48 in the Crystal Structure of Yak Lactoperoxidase at 1.55 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 Yak Lactoperoxidase at 1.55 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I606

b:23.4
occ:0.36
 O A:HOH1164 3.4 32.4 1.0
N A:ASP336 3.5 15.1 1.0
CD A:GLN521 3.9 15.6 1.0
O6 A:NAG603 4.0 32.5 1.0
CA A:VAL335 4.0 14.6 1.0
OE1 A:GLN521 4.1 18.1 1.0
CB A:ASP336 4.1 15.0 1.0
NE2 A:GLN521 4.1 16.1 1.0
C A:VAL335 4.2 15.1 1.0
CG A:GLN521 4.3 13.6 1.0
CA A:ASP336 4.4 15.4 1.0
CG1 A:VAL335 4.5 16.5 1.0
C6 A:NAG603 4.6 29.7 1.0
CB A:VAL335 4.6 15.1 1.0
O A:HOH837 4.7 28.0 1.0
O A:ASP336 4.7 17.0 1.0
O A:SER334 4.7 17.8 1.0
CG2 A:VAL335 4.7 16.0 1.0
O A:HOH817 4.8 23.3 1.0

Iodine binding site 6 out of 48 in 7de5

Go back to Iodine Binding Sites List in 7de5
Iodine binding site 6 out of 48 in the Crystal Structure of Yak Lactoperoxidase at 1.55 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 Yak Lactoperoxidase at 1.55 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I607

b:29.9
occ:0.48
 CG2 A:ILE387 4.0 21.0 1.0
CZ A:PHE229 4.0 16.1 1.0
CE2 A:PHE229 4.1 15.3 1.0
CB A:ALA219 4.4 18.9 1.0
CB A:GLU218 4.6 20.1 1.0
CG2 A:VAL246 4.8 15.0 1.0
O A:GLU218 4.8 17.8 1.0
CG1 A:VAL246 4.9 16.0 1.0
CB A:ILE387 4.9 20.4 1.0
CG1 A:ILE387 4.9 23.0 1.0

Iodine binding site 7 out of 48 in 7de5

Go back to Iodine Binding Sites List in 7de5
Iodine binding site 7 out of 48 in the Crystal Structure of Yak Lactoperoxidase at 1.55 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 Yak Lactoperoxidase at 1.55 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I608

b:18.7
occ:0.59
 I A:IOD608 0.0 18.7 0.6
I A:IOD608 0.0 21.4 0.2
I A:IOD608 0.0 22.1 0.2
O A:HOH1066 3.6 19.8 1.0
ND2 A:ASN80 3.6 14.5 1.0
CG A:PRO145 3.8 17.2 1.0
O A:HOH1121 3.9 37.1 1.0
CB A:ASN80 4.0 12.7 1.0
CE A:LYS81 4.1 18.0 1.0
CG A:GLU77 4.2 14.5 1.0
CB A:PRO145 4.2 15.8 1.0
CG A:ASN80 4.3 14.6 1.0
CG A:LYS81 4.5 14.7 1.0
C A:ASN147 4.6 19.2 1.0
CA A:GLU77 4.6 12.2 1.0
CB A:ASN147 4.6 21.6 1.0
O A:ASN147 4.7 21.4 1.0
CB A:GLU77 4.7 12.5 1.0
N A:ASP148 4.7 17.6 1.0
CD A:GLU77 4.8 17.1 1.0
CD A:LYS81 4.8 16.6 1.0
O A:GLU77 4.9 11.6 1.0
CA A:ASN147 5.0 20.1 1.0

Iodine binding site 8 out of 48 in 7de5

Go back to Iodine Binding Sites List in 7de5
Iodine binding site 8 out of 48 in the Crystal Structure of Yak Lactoperoxidase at 1.55 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 Yak Lactoperoxidase at 1.55 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I608

b:22.1
occ:0.19
 I A:IOD608 0.0 22.1 0.2
I A:IOD608 0.0 21.4 0.2
I A:IOD608 0.0 18.7 0.6
O A:HOH1066 3.6 19.8 1.0
ND2 A:ASN80 3.6 14.5 1.0
CG A:PRO145 3.8 17.2 1.0
O A:HOH1121 3.9 37.1 1.0
CB A:ASN80 4.0 12.7 1.0
CG A:GLU77 4.2 14.5 1.0
CE A:LYS81 4.2 18.0 1.0
CB A:PRO145 4.2 15.8 1.0
CG A:ASN80 4.3 14.6 1.0
CG A:LYS81 4.5 14.7 1.0
CA A:GLU77 4.5 12.2 1.0
C A:ASN147 4.6 19.2 1.0
CB A:ASN147 4.6 21.6 1.0
O A:ASN147 4.7 21.4 1.0
N A:ASP148 4.7 17.6 1.0
CB A:GLU77 4.7 12.5 1.0
CD A:GLU77 4.8 17.1 1.0
CD A:LYS81 4.9 16.6 1.0
O A:GLU77 4.9 11.6 1.0
CA A:ASN147 5.0 20.1 1.0
CA A:ASP148 5.0 16.3 1.0

Iodine binding site 9 out of 48 in 7de5

Go back to Iodine Binding Sites List in 7de5
Iodine binding site 9 out of 48 in the Crystal Structure of Yak Lactoperoxidase at 1.55 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 Yak Lactoperoxidase at 1.55 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I608

b:21.4
occ:0.22
 I A:IOD608 0.0 21.4 0.2
I A:IOD608 0.0 22.1 0.2
I A:IOD608 0.0 18.7 0.6
O A:HOH1066 3.6 19.8 1.0
ND2 A:ASN80 3.6 14.5 1.0
CG A:PRO145 3.8 17.2 1.0
O A:HOH1121 3.9 37.1 1.0
CB A:ASN80 4.0 12.7 1.0
CG A:GLU77 4.2 14.5 1.0
CE A:LYS81 4.2 18.0 1.0
CB A:PRO145 4.2 15.8 1.0
CG A:ASN80 4.3 14.6 1.0
CG A:LYS81 4.5 14.7 1.0
CA A:GLU77 4.6 12.2 1.0
C A:ASN147 4.6 19.2 1.0
CB A:ASN147 4.6 21.6 1.0
O A:ASN147 4.7 21.4 1.0
CB A:GLU77 4.7 12.5 1.0
N A:ASP148 4.7 17.6 1.0
CD A:GLU77 4.8 17.1 1.0
CD A:LYS81 4.8 16.6 1.0
O A:GLU77 4.9 11.6 1.0
CA A:ASN147 5.0 20.1 1.0
CA A:ASP148 5.0 16.3 1.0

Iodine binding site 10 out of 48 in 7de5

Go back to Iodine Binding Sites List in 7de5
Iodine binding site 10 out of 48 in the Crystal Structure of Yak Lactoperoxidase at 1.55 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 Yak Lactoperoxidase at 1.55 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I609

b:19.9
occ:0.48
 OG A:SER198 3.0 20.3 1.0
CB A:SER198 3.7 18.8 1.0
N A:SER198 3.8 18.3 1.0
CD A:PRO197 4.0 18.9 1.0
CB A:GLU196 4.1 20.9 1.0
OE1 A:GLU196 4.1 35.4 1.0
CD A:GLU196 4.3 30.0 1.0
N A:PRO197 4.3 17.0 1.0
CA A:SER198 4.4 16.8 1.0
CG A:GLU196 4.4 26.1 1.0
CB A:PRO197 4.6 18.5 1.0
C A:GLU196 4.7 16.1 1.0
CG A:PRO197 4.7 20.1 1.0
CA A:GLU196 4.7 17.2 1.0
C A:PRO197 4.8 17.7 1.0
OE2 A:GLU196 4.8 38.3 1.0
CA A:PRO197 4.8 18.5 1.0

Reference:

V.Viswanathan, C.Rani, N.Ahmad, P.Singh, P.Sharma, P.Kaur, S.Sharma, T.P.Singh. Crystal Structure of Yak Lactoperoxidase at 1.55 A Resolution. To Be Published.
Page generated: Mon Aug 12 00:58:29 2024

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