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Iodine in PDB 6l2j: Crystal Structure of Yak Lactoperoxidase at 1.93 A Resolution.

Enzymatic activity of Crystal Structure of Yak Lactoperoxidase at 1.93 A Resolution.

All present enzymatic activity of Crystal Structure of Yak Lactoperoxidase at 1.93 A Resolution.:
1.11.1.7;

Protein crystallography data

The structure of Crystal Structure of Yak Lactoperoxidase at 1.93 A Resolution., PDB code: 6l2j was solved by V.Viswanathan, P.Sharma, C.Rani, S.Sharma, T.P.Singh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 53.84 / 1.93
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.850, 78.920, 67.750, 90.00, 92.95, 90.00
R / Rfree (%) 14.5 / 19.8

Other elements in 6l2j:

The structure of Crystal Structure of Yak Lactoperoxidase at 1.93 A Resolution. also contains other interesting chemical elements:

Iron (Fe) 1 atom
Calcium (Ca) 5 atoms

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 26;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of Yak Lactoperoxidase at 1.93 A Resolution. (pdb code 6l2j). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 26 binding sites of Iodine where determined in the Crystal Structure of Yak Lactoperoxidase at 1.93 A Resolution., PDB code: 6l2j:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 26 in 6l2j

Go back to Iodine Binding Sites List in 6l2j
Iodine binding site 1 out of 26 in the Crystal Structure of Yak Lactoperoxidase at 1.93 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 1.93 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I612

b:11.6
occ:0.92
 O A:HOH1034 3.3 10.8 1.0
N A:TRP46 3.4 11.3 1.0
N A:VAL342 3.5 9.4 1.0
CH2 A:TRP452 3.7 10.0 1.0
CA A:ARG45 3.9 10.8 1.0
CB A:ASN341 3.9 10.3 1.0
CZ2 A:TRP452 3.9 9.9 1.0
N A:ASN341 3.9 10.4 1.0
CB A:VAL342 4.0 9.0 1.0
O A:ALA44 4.0 10.5 1.0
C A:ARG45 4.1 11.9 1.0
CG1 A:VAL342 4.1 9.6 1.0
N A:LEU47 4.1 11.0 1.0
O A:LEU47 4.2 11.6 1.0
CA A:ASN341 4.3 9.6 1.0
CB A:TRP46 4.3 11.3 1.0
CE A:MET446 4.3 10.8 1.0
CA A:VAL342 4.3 9.3 1.0
CA A:TRP46 4.3 11.4 1.0
C A:ASN341 4.3 9.4 1.0
CD A:ARG45 4.3 11.2 1.0
CB A:SER340 4.5 9.5 1.0
NH1 A:ARG45 4.7 10.6 1.0
CB A:ARG45 4.8 11.4 1.0
C A:ALA44 4.8 10.4 1.0
N A:ARG45 4.8 10.3 1.0
C A:TRP46 4.8 11.2 1.0
C A:SER340 4.8 9.5 1.0
CG A:TRP46 4.9 12.2 1.0
CZ3 A:TRP452 4.9 9.9 1.0
SD A:MET446 5.0 11.7 1.0

Iodine binding site 2 out of 26 in 6l2j

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Iodine binding site 2 out of 26 in the Crystal Structure of Yak Lactoperoxidase at 1.93 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 1.93 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I613

b:32.9
occ:0.40
 S A:OSM644 2.8 12.5 0.3
O A:OSM644 3.3 12.4 0.3
N A:OSM644 3.3 11.1 0.3
O A:HOH709 3.6 32.6 1.0
C A:OSM644 3.6 11.1 0.3
C A:OSM644 3.8 12.3 0.3
CE1 A:PHE381 3.9 13.6 1.0
CZ A:PHE381 3.9 13.3 1.0
CA A:ARG255 4.0 14.6 1.0
S A:OSM644 4.0 10.7 0.3
CG A:ARG255 4.1 14.8 1.0
CB A:ARG255 4.3 13.8 1.0
O A:SER254 4.3 24.2 1.0
O A:HOH1145 4.4 15.2 0.5
N A:OSM644 4.5 12.3 0.3
O1 A:PEO649 4.5 20.9 1.0
O2 A:PEO649 4.6 18.6 1.0
CG A:PRO424 4.6 25.6 1.0
N A:ARG255 4.8 16.5 1.0
C A:SER254 4.8 20.1 1.0
N A:SCN629 4.8 26.4 1.0
C A:ARG255 4.9 12.8 1.0
O A:ARG255 5.0 10.9 1.0
CD A:PRO424 5.0 25.2 1.0

Iodine binding site 3 out of 26 in 6l2j

Go back to Iodine Binding Sites List in 6l2j
Iodine binding site 3 out of 26 in the Crystal Structure of Yak Lactoperoxidase at 1.93 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 1.93 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I614

b:24.4
occ:0.60
 S A:OSM645 2.3 25.1 0.9
O A:OSM645 3.1 33.6 0.9
NH1 A:ARG202 3.7 33.4 1.0
O A:HOH1098 3.7 32.6 1.0
C A:OSM645 3.7 24.2 0.9
CA A:LEU199 4.0 17.4 1.0
CB A:LEU199 4.0 19.0 1.0
CD A:ARG202 4.1 27.4 1.0
N A:OSM645 4.2 21.7 0.9
CD1 A:LEU199 4.2 20.8 1.0
N A:LEU199 4.3 16.8 1.0
O A:HOH1311 4.5 28.8 1.0
OG A:SER198 4.6 19.7 1.0
CG A:LEU199 4.7 19.7 1.0
CZ A:ARG202 4.7 31.3 1.0
C A:SER198 4.8 18.2 1.0
NE A:ARG202 4.9 28.1 1.0

Iodine binding site 4 out of 26 in 6l2j

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Iodine binding site 4 out of 26 in the Crystal Structure of Yak Lactoperoxidase at 1.93 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 1.93 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I615

b:25.8
occ:0.40
 N A:ASP336 3.4 14.7 1.0
O A:HOH1188 3.5 29.1 1.0
O6 A:NAG603 3.9 34.3 1.0
CA A:VAL335 3.9 14.7 1.0
CD A:GLN521 4.0 14.5 1.0
OE1 A:GLN521 4.1 16.9 1.0
CB A:ASP336 4.1 15.9 1.0
C A:VAL335 4.1 14.6 1.0
NE2 A:GLN521 4.2 14.9 1.0
CG1 A:VAL335 4.3 16.7 1.0
CG A:GLN521 4.3 13.4 1.0
CA A:ASP336 4.3 15.4 1.0
C6 A:NAG603 4.5 33.3 1.0
CB A:VAL335 4.5 15.8 1.0
O A:ASP336 4.6 16.5 1.0
O A:SER334 4.7 14.8 1.0
CG2 A:VAL335 4.7 16.6 1.0
O A:HOH880 4.8 25.1 1.0
O A:HOH836 4.8 24.7 1.0
C A:ASP336 5.0 16.0 1.0

Iodine binding site 5 out of 26 in 6l2j

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Iodine binding site 5 out of 26 in the Crystal Structure of Yak Lactoperoxidase at 1.93 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 1.93 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I616

b:30.4
occ:0.50
 CZ A:PHE229 4.0 14.9 1.0
CG2 A:ILE387 4.1 21.6 1.0
CE2 A:PHE229 4.1 14.4 1.0
CB A:ALA219 4.4 17.9 1.0
CB A:GLU218 4.6 24.4 1.0
CG2 A:VAL246 4.7 15.0 1.0
CG1 A:VAL246 4.9 15.1 1.0
CB A:ILE387 4.9 21.7 1.0
CG1 A:ILE387 4.9 22.8 1.0
O A:GLU218 4.9 19.7 1.0

Iodine binding site 6 out of 26 in 6l2j

Go back to Iodine Binding Sites List in 6l2j
Iodine binding site 6 out of 26 in the Crystal Structure of Yak Lactoperoxidase at 1.93 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 1.93 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I617

b:12.9
occ:0.65
 C A:SCN634 0.6 6.2 0.3
S A:SCN634 1.2 6.2 0.3
N A:SCN634 1.7 6.5 0.3
N A:GLY223 3.6 14.6 1.0
CB A:TRP220 4.0 16.9 1.0
O A:HOH788 4.0 30.8 1.0
CA A:GLY223 4.1 15.1 1.0
O A:HOH1038 4.2 29.5 1.0
C A:HIS222 4.5 15.0 1.0
CA A:HIS222 4.6 15.2 1.0
N A:HIS222 4.6 13.9 1.0
CG A:TRP220 4.8 17.8 1.0
O A:HOH1082 4.8 24.6 1.0
O A:TRP220 5.0 15.3 1.0
C A:TRP220 5.0 14.3 1.0

Iodine binding site 7 out of 26 in 6l2j

Go back to Iodine Binding Sites List in 6l2j
Iodine binding site 7 out of 26 in the Crystal Structure of Yak Lactoperoxidase at 1.93 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 1.93 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I618

b:14.7
occ:0.80
 C A:SCN635 0.5 2.5 0.2
S A:SCN635 1.2 2.5 0.2
N A:SCN635 1.6 2.5 0.2
O A:HOH1100 3.5 20.7 1.0
ND2 A:ASN80 3.6 13.0 1.0
O A:HOH1151 3.8 36.8 1.0
CG A:PRO145 3.9 15.5 1.0
CB A:ASN80 4.0 12.4 1.0
CG A:GLU77 4.2 12.8 1.0
CB A:PRO145 4.2 15.0 1.0
CE A:LYS81 4.2 17.9 1.0
CG A:ASN80 4.3 12.7 1.0
CB A:ASN147 4.5 22.9 1.0
CA A:GLU77 4.5 11.3 1.0
CG A:LYS81 4.5 16.1 1.0
C A:ASN147 4.6 20.1 1.0
CB A:GLU77 4.7 11.5 1.0
N A:ASP148 4.7 17.4 1.0
CD A:GLU77 4.8 14.7 1.0
O A:ASN147 4.8 21.8 1.0
CD A:LYS81 4.8 16.8 1.0
O A:GLU77 4.9 11.3 1.0
CA A:ASP148 4.9 15.7 1.0
CA A:ASN147 5.0 20.5 1.0

Iodine binding site 8 out of 26 in 6l2j

Go back to Iodine Binding Sites List in 6l2j
Iodine binding site 8 out of 26 in the Crystal Structure of Yak Lactoperoxidase at 1.93 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 1.93 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I619

b:21.3
occ:0.50
 OG A:SER198 3.1 19.7 1.0
CB A:SER198 3.7 19.5 1.0
N A:SER198 3.8 17.8 1.0
OE1 A:GLU196 3.9 35.3 1.0
CD A:PRO197 4.0 20.1 1.0
CB A:GLU196 4.1 21.0 1.0
N A:PRO197 4.2 17.9 1.0
CA A:SER198 4.4 18.1 1.0
CB A:PRO197 4.5 19.2 1.0
CG A:PRO197 4.6 21.1 1.0
C A:GLU196 4.7 17.2 1.0
CG A:GLU196 4.8 25.1 1.0
CA A:GLU196 4.8 17.5 1.0
C A:PRO197 4.8 18.1 1.0
CD A:GLU196 4.8 29.9 1.0
CA A:PRO197 4.8 19.1 1.0

Iodine binding site 9 out of 26 in 6l2j

Go back to Iodine Binding Sites List in 6l2j
Iodine binding site 9 out of 26 in the Crystal Structure of Yak Lactoperoxidase at 1.93 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 1.93 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I620

b:12.7
occ:0.40
 O A:OSM644 1.0 11.4 0.3
N A:OSM644 1.1 12.3 0.3
S A:OSM644 1.5 10.7 0.3
C A:OSM644 2.5 12.3 0.3
O1 A:PEO648 2.5 24.5 1.0
C A:OSM644 3.2 11.1 0.3
S A:OSM644 3.3 12.5 0.3
C4A A:HEM601 3.6 10.0 1.0
CG A:GLU258 3.7 11.7 1.0
O2 A:PEO648 3.7 22.4 1.0
CE1 A:HIS109 3.7 9.3 1.0
O A:HOH1094 3.8 20.5 1.0
NE2 A:HIS109 3.8 9.9 1.0
CD A:ARG255 3.9 14.0 1.0
CHB A:HEM601 3.9 9.2 1.0
NA A:HEM601 3.9 9.2 1.0
C3A A:HEM601 3.9 9.7 1.0
CB A:GLU258 4.0 10.9 1.0
CB A:ARG255 4.0 13.8 1.0
CD A:GLU258 4.0 12.2 1.0
N A:OSM644 4.0 11.1 0.3
O A:HOH765 4.1 20.6 0.5
O A:HOH1145 4.1 15.2 0.5
CG A:ARG255 4.1 14.8 1.0
C1A A:HEM601 4.2 9.7 1.0
C2A A:HEM601 4.2 10.0 1.0
NE2 A:GLN105 4.3 8.3 1.0
OE1 A:GLU258 4.3 11.2 1.0
C1B A:HEM601 4.4 9.3 1.0
CMA A:HEM601 4.5 10.1 1.0
OE2 A:GLU258 4.5 12.8 1.0
O A:OSM644 4.6 12.4 0.3
NB A:HEM601 4.8 8.8 1.0
O A:ARG255 4.9 10.9 1.0
ND1 A:HIS109 5.0 9.8 1.0
CHA A:HEM601 5.0 9.6 1.0
FE A:HEM601 5.0 9.8 1.0

Iodine binding site 10 out of 26 in 6l2j

Go back to Iodine Binding Sites List in 6l2j
Iodine binding site 10 out of 26 in the Crystal Structure of Yak Lactoperoxidase at 1.93 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 1.93 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I621

b:20.5
occ:0.60
 O A:HOH895 2.9 27.2 1.0
OG A:SER359 3.3 11.2 1.0
CB A:SER359 3.7 12.6 1.0
CB A:ALA372 4.0 13.6 1.0
NZ A:LYS402 4.1 19.5 1.0
CD2 A:LEU361 4.1 17.1 1.0
CB A:GLU373 4.2 14.9 1.0
CE A:LYS402 4.3 17.3 1.0
CG A:PRO367 4.4 20.6 1.0
CB A:PRO367 4.4 21.0 1.0
N A:GLU373 4.5 13.4 1.0
CA A:PRO367 4.6 18.6 1.0
C A:ALA372 4.7 13.2 1.0
CA A:GLU373 4.7 13.9 1.0
O A:HOH1141 4.8 33.7 1.0
CA A:SER359 4.8 12.1 1.0
O A:ARG360 4.9 13.2 1.0
OE1 A:GLU373 5.0 19.8 1.0

Reference:

V.Viswanathan, P.Sharma, C.Rani, S.Sharma, T.P.Singh. Crystal Structure of Yak Lactoperoxidase at 1.93 A Resolution. To Be Published.
Page generated: Sun Aug 11 23:32:07 2024

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