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Iodine in PDB 6ky7: Crystal Structure of Yak Lactoperoxidase at 2.27 A Resolution

Protein crystallography data

The structure of Crystal Structure of Yak Lactoperoxidase at 2.27 A Resolution, PDB code: 6ky7 was solved by P.K.Singh, 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) 52.79 / 2.27
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.080, 80.640, 76.130, 90.00, 102.80, 90.00
R / Rfree (%) 19.6 / 26.6

Other elements in 6ky7:

The structure of Crystal Structure of Yak Lactoperoxidase at 2.27 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 - 13;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of Yak Lactoperoxidase at 2.27 A Resolution (pdb code 6ky7). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 13 binding sites of Iodine where determined in the Crystal Structure of Yak Lactoperoxidase at 2.27 A Resolution, PDB code: 6ky7:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 13 in 6ky7

Go back to Iodine Binding Sites List in 6ky7
Iodine binding site 1 out of 13 in the Crystal Structure of Yak Lactoperoxidase at 2.27 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 2.27 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I607

b:51.1
occ:0.40
 S A:SCN626 1.0 30.8 0.6
C A:SCN626 2.4 34.1 0.6
N A:SCN626 3.5 35.3 0.6
CE1 A:HIS109 3.5 35.4 1.0
NE2 A:HIS109 3.6 37.3 1.0
O2 A:PEO628 3.6 42.2 1.0
O1 A:PEO628 3.7 60.6 1.0
CG A:GLU258 3.7 43.1 1.0
CB A:GLU258 3.8 42.8 1.0
CD A:ARG255 3.9 48.5 1.0
CB A:ARG255 3.9 49.6 1.0
C4A A:HEM606 3.9 41.6 1.0
O A:HOH971 3.9 42.8 1.0
CG A:ARG255 4.0 51.3 1.0
O A:HOH967 4.1 56.7 1.0
CD A:GLU258 4.1 41.1 1.0
CHB A:HEM606 4.1 39.1 1.0
NA A:HEM606 4.2 41.4 1.0
C3A A:HEM606 4.2 39.1 1.0
NE2 A:GLN105 4.2 29.9 1.0
OE1 A:GLU258 4.2 46.8 1.0
C1A A:HEM606 4.5 39.9 1.0
C2A A:HEM606 4.5 39.7 1.0
C1B A:HEM606 4.6 37.9 1.0
O A:ARG255 4.7 46.1 1.0
CMA A:HEM606 4.7 34.1 1.0
ND1 A:HIS109 4.7 33.6 1.0
OE2 A:GLU258 4.8 44.7 1.0
CD2 A:HIS109 4.9 35.4 1.0
NB A:HEM606 5.0 38.2 1.0
CA A:ARG255 5.0 48.0 1.0

Iodine binding site 2 out of 13 in 6ky7

Go back to Iodine Binding Sites List in 6ky7
Iodine binding site 2 out of 13 in the Crystal Structure of Yak Lactoperoxidase at 2.27 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 2.27 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I608

b:67.1
occ:0.50
 N A:SCN626 2.6 35.3 0.6
C A:SCN626 3.4 34.1 0.6
CE1 A:PHE381 3.8 43.9 1.0
CZ A:PHE381 3.9 47.6 1.0
C A:SCN625 4.2 58.9 1.0
CA A:ARG255 4.2 48.0 1.0
CG A:PRO424 4.2 50.8 1.0
CG A:ARG255 4.3 51.3 1.0
N A:SCN625 4.4 62.6 1.0
O A:ALA254 4.4 62.1 1.0
S A:SCN625 4.5 56.5 1.0
CB A:ARG255 4.5 49.6 1.0
CD A:PRO424 4.7 52.1 1.0
S A:SCN626 4.8 30.8 0.6
O A:HOH967 4.9 56.7 1.0
C A:ALA254 5.0 52.4 1.0
N A:ARG255 5.0 50.9 1.0

Iodine binding site 3 out of 13 in 6ky7

Go back to Iodine Binding Sites List in 6ky7
Iodine binding site 3 out of 13 in the Crystal Structure of Yak Lactoperoxidase at 2.27 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 2.27 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I609

b:60.4
occ:1.00
 O A:HOH778 3.7 43.2 1.0
NE1 A:TRP530 3.7 58.7 1.0
O A:HOH883 3.9 62.3 1.0
CB A:PHE309 3.9 42.3 1.0
CZ2 A:TRP530 3.9 60.3 1.0
CE2 A:TRP530 4.2 59.1 1.0
CA A:ILE306 4.3 51.4 1.0
N A:ARG310 4.4 50.9 1.0
CB A:ARG310 4.5 53.1 1.0
CZ2 A:TRP529 4.6 63.5 1.0
C A:PHE309 4.6 44.8 1.0
O A:ILE306 4.6 51.1 1.0
CG1 A:ILE306 4.7 63.5 1.0
O A:GLN305 4.8 52.4 1.0
CA A:PHE309 4.8 46.0 1.0
CA A:ARG310 4.8 50.5 1.0
CB A:ILE306 4.9 57.6 1.0
CD1 A:TRP530 5.0 57.5 1.0

Iodine binding site 4 out of 13 in 6ky7

Go back to Iodine Binding Sites List in 6ky7
Iodine binding site 4 out of 13 in the Crystal Structure of Yak Lactoperoxidase at 2.27 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 2.27 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I610

b:59.7
occ:0.50
 O A:HOH921 3.2 45.1 1.0
OG A:SER359 3.3 38.9 1.0
CB A:SER359 3.6 42.0 1.0
CB A:GLU373 4.1 47.0 1.0
NZ A:LYS402 4.1 49.6 1.0
CB A:ALA372 4.2 59.0 1.0
CD2 A:LEU361 4.2 49.9 1.0
CE A:LYS402 4.3 45.2 1.0
N A:GLU373 4.4 46.2 1.0
CB A:PRO367 4.4 60.2 1.0
CG A:PRO367 4.4 57.9 1.0
CA A:PRO367 4.6 57.3 1.0
CA A:GLU373 4.6 46.3 1.0
CA A:SER359 4.6 43.7 1.0
C A:ALA372 4.7 49.7 1.0
O A:ARG360 4.8 42.0 1.0
CG A:GLU373 4.8 49.4 1.0
OE2 A:GLU373 5.0 53.5 1.0

Iodine binding site 5 out of 13 in 6ky7

Go back to Iodine Binding Sites List in 6ky7
Iodine binding site 5 out of 13 in the Crystal Structure of Yak Lactoperoxidase at 2.27 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 2.27 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I611

b:65.8
occ:0.80
 N A:PHE229 3.8 55.3 1.0
N A:GLN217 3.8 61.8 1.0
CG A:GLU218 3.8 77.3 1.0
OE2 A:GLU218 3.9 81.2 1.0
ND2 A:ASN216 3.9 55.9 1.0
CG A:ASN216 4.0 55.3 1.0
CA A:ASN216 4.0 59.7 1.0
OD1 A:ASN216 4.2 57.1 1.0
CD A:GLU218 4.3 79.4 1.0
CA A:PRO228 4.3 53.0 1.0
CD2 A:PHE229 4.3 63.4 1.0
CB A:PHE229 4.4 53.8 1.0
C A:ASN216 4.4 57.5 1.0
CB A:PRO228 4.5 49.7 1.0
C A:PRO228 4.5 55.6 1.0
CB A:ASN216 4.6 56.6 1.0
CA A:PHE229 4.6 54.1 1.0
N A:GLU218 4.7 69.6 1.0
CG A:PHE229 4.7 59.2 1.0
O A:VAL215 4.8 61.4 1.0
CA A:GLN217 4.8 65.5 1.0
CB A:GLN217 4.9 62.9 1.0
O A:PHE229 4.9 53.9 1.0

Iodine binding site 6 out of 13 in 6ky7

Go back to Iodine Binding Sites List in 6ky7
Iodine binding site 6 out of 13 in the Crystal Structure of Yak Lactoperoxidase at 2.27 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 2.27 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I612

b:69.1
occ:1.00
 ND2 A:ASN80 3.8 36.5 1.0
CG A:PRO145 3.8 44.2 1.0
CG A:GLU77 4.1 62.1 1.0
CB A:ASN80 4.1 35.7 1.0
O A:LYS146 4.3 65.7 1.0
CB A:PRO145 4.3 46.3 1.0
CE A:LYS81 4.3 60.0 1.0
CG A:ASN80 4.4 38.4 1.0
CA A:GLU77 4.5 47.4 1.0
CG A:LYS81 4.6 53.6 1.0
O A:HOH973 4.6 62.9 1.0
CB A:GLU77 4.7 54.7 1.0
CD A:LYS81 4.9 57.1 1.0
CD A:GLU77 4.9 66.3 1.0
O A:GLU77 4.9 45.7 1.0
CB A:ASN147 5.0 70.0 1.0

Iodine binding site 7 out of 13 in 6ky7

Go back to Iodine Binding Sites List in 6ky7
Iodine binding site 7 out of 13 in the Crystal Structure of Yak Lactoperoxidase at 2.27 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 2.27 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I613

b:44.1
occ:1.00
 N A:TRP46 3.4 43.0 1.0
N A:VAL342 3.6 31.1 1.0
CH2 A:TRP452 3.7 38.4 1.0
CZ2 A:TRP452 3.9 38.5 1.0
CA A:ARG45 3.9 42.4 1.0
CB A:ASN341 3.9 35.1 1.0
N A:ASN341 3.9 32.5 1.0
O A:ALA44 4.0 40.8 1.0
CB A:VAL342 4.0 29.7 1.0
N A:LEU47 4.1 41.2 1.0
CE A:MET446 4.1 41.8 1.0
CG1 A:VAL342 4.1 31.9 1.0
C A:ARG45 4.1 43.9 1.0
O A:LEU47 4.2 50.3 1.0
CA A:ASN341 4.3 33.5 1.0
CA A:TRP46 4.3 42.8 1.0
CB A:TRP46 4.3 40.2 1.0
CA A:VAL342 4.3 33.5 1.0
C A:ASN341 4.4 38.2 1.0
CD A:ARG45 4.4 41.2 1.0
NH1 A:ARG45 4.7 40.3 1.0
C A:TRP46 4.7 40.9 1.0
CB A:SER340 4.7 35.8 1.0
C A:ALA44 4.8 42.9 1.0
N A:ARG45 4.8 43.8 1.0
CB A:ARG45 4.8 43.3 1.0
C A:SER340 4.9 35.4 1.0
OG A:SER340 4.9 36.0 1.0
CZ3 A:TRP452 4.9 40.6 1.0
CG A:TRP46 4.9 38.5 1.0

Iodine binding site 8 out of 13 in 6ky7

Go back to Iodine Binding Sites List in 6ky7
Iodine binding site 8 out of 13 in the Crystal Structure of Yak Lactoperoxidase at 2.27 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 2.27 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I614

b:81.6
occ:1.00
 N A:THR560 3.5 58.6 1.0
O A:HOH914 3.6 56.4 1.0
O A:GLU363 3.6 65.1 1.0
NE A:ARG397 3.7 59.1 1.0
CG2 A:ILE559 3.8 60.3 1.0
CA A:ILE559 3.9 60.2 1.0
CA A:GLU363 4.0 73.6 1.0
N A:LYS561 4.0 68.5 1.0
CB A:GLU363 4.0 75.5 1.0
CE1 A:TYR365 4.2 53.2 1.0
C A:ILE559 4.2 64.0 1.0
CB A:ILE559 4.3 61.0 1.0
C A:GLU363 4.3 65.5 1.0
OG1 A:THR560 4.3 65.3 1.0
NH2 A:ARG397 4.4 61.7 1.0
CB A:LYS561 4.5 90.9 1.0
CD A:ARG397 4.5 61.6 1.0
CZ A:ARG397 4.5 61.6 1.0
CA A:THR560 4.5 59.8 1.0
CG1 A:ILE559 4.6 65.2 1.0
C A:THR560 4.7 63.8 1.0
O A:HIS558 4.8 66.2 1.0
CG A:LYS561 4.8 0.3 1.0
CB A:THR560 4.8 62.6 1.0
CA A:LYS561 4.8 78.4 1.0
CG2 A:THR560 4.9 57.2 1.0
OH A:TYR365 4.9 55.6 1.0
CD1 A:TYR365 4.9 53.7 1.0
O A:LYS561 4.9 79.7 1.0
CZ A:TYR365 5.0 52.0 1.0

Iodine binding site 9 out of 13 in 6ky7

Go back to Iodine Binding Sites List in 6ky7
Iodine binding site 9 out of 13 in the Crystal Structure of Yak Lactoperoxidase at 2.27 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 2.27 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I615

b:56.7
occ:0.90
 O A:PRO424 2.5 69.1 1.0
C A:PRO424 3.6 54.5 1.0
CA A:PRO236 3.7 41.6 1.0
CB A:PRO236 3.8 43.3 1.0
N A:PRO236 4.0 47.2 1.0
CB A:PHE239 4.1 49.2 1.0
CB A:PRO234 4.2 76.0 1.0
CG A:PRO234 4.3 78.3 1.0
CG A:PHE239 4.3 51.5 1.0
CA A:PRO424 4.3 53.7 1.0
C A:SER235 4.3 51.4 1.0
O A:SER235 4.4 52.4 1.0
CD2 A:PHE239 4.4 51.2 1.0
CD A:PRO236 4.6 46.7 1.0
N A:THR425 4.6 56.5 1.0
CA A:THR425 4.6 64.0 1.0
O A:PRO234 4.6 58.9 1.0
CG A:PRO236 4.7 46.7 1.0
C A:PRO234 4.7 65.8 1.0
CB A:PRO424 4.9 53.1 1.0
CZ A:PHE422 4.9 40.2 1.0
N A:SER235 5.0 58.2 1.0

Iodine binding site 10 out of 13 in 6ky7

Go back to Iodine Binding Sites List in 6ky7
Iodine binding site 10 out of 13 in the Crystal Structure of Yak Lactoperoxidase at 2.27 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 2.27 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I616

b:74.3
occ:0.80
 N A:LYS462 3.6 53.3 1.0
OG1 A:THR463 3.7 48.5 1.0
CA A:GLY466 3.9 41.6 1.0
CA A:PRO461 4.1 54.8 1.0
O A:HOH1011 4.2 44.2 1.0
N A:THR463 4.2 50.9 1.0
C A:PRO461 4.4 54.9 1.0
N A:GLY466 4.5 43.1 1.0
CA A:LYS462 4.5 55.6 1.0
CB A:LYS462 4.6 54.7 1.0
CB A:THR463 4.7 48.9 1.0
CG2 A:THR463 4.8 51.0 1.0
CB A:PRO461 4.8 57.2 1.0
CG A:LYS462 4.8 59.5 1.0
C A:LYS462 4.9 51.5 1.0

Reference:

P.K.Singh, V.Viswanathan, P.Sharma, C.Rani, S.Sharma, T.P.Singh. Crystal Structure of Yak Lactoperoxidase at 2.27 A Resolution To Be Published.
Page generated: Sun Aug 11 23:31:22 2024

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