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Iodine in PDB 2gjm: Crystal Structure of Buffalo Lactoperoxidase at 2.75A Resolution

Enzymatic activity of Crystal Structure of Buffalo Lactoperoxidase at 2.75A Resolution

All present enzymatic activity of Crystal Structure of Buffalo Lactoperoxidase at 2.75A Resolution:
1.11.1.7;

Protein crystallography data

The structure of Crystal Structure of Buffalo Lactoperoxidase at 2.75A Resolution, PDB code: 2gjm was solved by I.A.Sheikh, A.S.Ethayathulla, A.K.Singh, N.Singh, S.Sharma, T.P.Singh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.75
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.240, 80.472, 77.348, 90.00, 102.71, 90.00
R / Rfree (%) 18.2 / 21.6

Other elements in 2gjm:

The structure of Crystal Structure of Buffalo Lactoperoxidase at 2.75A 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 Buffalo Lactoperoxidase at 2.75A Resolution (pdb code 2gjm). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 8 binding sites of Iodine where determined in the Crystal Structure of Buffalo Lactoperoxidase at 2.75A Resolution, PDB code: 2gjm:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iodine binding site 1 out of 8 in 2gjm

Go back to Iodine Binding Sites List in 2gjm
Iodine binding site 1 out of 8 in the Crystal Structure of Buffalo Lactoperoxidase at 2.75A 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 Buffalo Lactoperoxidase at 2.75A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I2001

b:47.6
occ:0.50
 ND2 A:ASN66 3.4 23.5 1.0
O A:HOH2189 3.4 53.4 1.0
CB A:ASN66 3.8 22.5 1.0
CE A:LYS67 4.0 25.7 1.0
CG A:PRO131 4.0 32.0 1.0
CG A:GLU63 4.0 26.4 1.0
O A:LYS132 4.0 36.3 1.0
CG A:ASN66 4.1 23.4 1.0
CB A:PRO131 4.5 32.6 1.0
NZ A:LYS67 4.6 25.6 1.0
O A:ASN133 4.8 33.7 1.0
CD A:GLU63 4.8 28.8 1.0
CD A:LYS67 4.9 24.4 1.0
OE2 A:GLU63 4.9 30.0 1.0
CG A:LYS67 4.9 23.2 1.0

Iodine binding site 2 out of 8 in 2gjm

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Iodine binding site 2 out of 8 in the Crystal Structure of Buffalo Lactoperoxidase at 2.75A 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 Buffalo Lactoperoxidase at 2.75A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I2002

b:42.3
occ:0.50
 OG A:SER182 3.4 31.1 1.0
CB A:SER182 3.7 29.1 1.0
CD A:PRO181 3.8 26.8 1.0
N A:SER182 3.9 27.8 1.0
CB A:GLU180 4.0 27.4 1.0
OE2 A:GLU180 4.2 32.5 1.0
N A:PRO181 4.3 26.7 1.0
CG A:GLU180 4.4 29.6 1.0
CA A:SER182 4.4 28.5 1.0
CD A:GLU180 4.5 31.6 1.0
CG A:PRO181 4.7 26.5 1.0
CA A:GLU180 4.8 25.9 1.0
CB A:PRO181 4.8 27.2 1.0
C A:GLU180 4.8 26.3 1.0
C A:PRO181 4.9 27.4 1.0
CA A:PRO181 5.0 27.0 1.0

Iodine binding site 3 out of 8 in 2gjm

Go back to Iodine Binding Sites List in 2gjm
Iodine binding site 3 out of 8 in the Crystal Structure of Buffalo Lactoperoxidase at 2.75A 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 Buffalo Lactoperoxidase at 2.75A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I2003

b:47.8
occ:0.50
 NH2 A:ARG186 3.3 37.8 1.0
NE A:ARG186 3.4 36.2 1.0
CZ A:ARG186 3.8 37.2 1.0
CA A:LEU183 4.2 27.2 1.0
OG A:SER182 4.3 31.1 1.0
O A:SER182 4.4 29.4 1.0
CD1 A:LEU183 4.4 24.5 1.0
CB A:LEU183 4.4 26.1 1.0
N A:LEU183 4.5 27.9 1.0
C A:SER182 4.6 28.5 1.0
CD A:ARG186 4.6 33.9 1.0
CG A:ARG186 4.7 32.9 1.0
CB A:ARG186 4.8 31.0 1.0

Iodine binding site 4 out of 8 in 2gjm

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Iodine binding site 4 out of 8 in the Crystal Structure of Buffalo Lactoperoxidase at 2.75A 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 Buffalo Lactoperoxidase at 2.75A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I2004

b:33.9
occ:0.50
 ND2 A:ASN200 3.1 33.9 1.0
N A:PHE213 3.4 32.1 1.0
N A:GLN201 4.0 35.6 1.0
CB A:PHE213 4.0 34.3 1.0
OE1 A:GLU202 4.1 46.3 1.0
CA A:ASN200 4.1 33.5 1.0
CD2 A:PHE213 4.1 34.2 1.0
CA A:PRO212 4.1 29.0 1.0
CG A:ASN200 4.1 33.4 1.0
C A:PRO212 4.3 30.5 1.0
CA A:PHE213 4.3 34.3 1.0
O A:HOH2126 4.4 46.7 1.0
CG A:PHE213 4.4 34.2 1.0
CB A:PRO212 4.5 28.1 1.0
O A:VAL199 4.5 32.3 1.0
C A:ASN200 4.6 34.5 1.0
O A:PHE213 4.6 35.5 1.0
CB A:ASN200 4.7 33.3 1.0
N A:GLU202 4.9 38.9 1.0
C A:PHE213 5.0 36.0 1.0
OD1 A:ASN200 5.0 34.4 1.0

Iodine binding site 5 out of 8 in 2gjm

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Iodine binding site 5 out of 8 in the Crystal Structure of Buffalo Lactoperoxidase at 2.75A 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 Buffalo Lactoperoxidase at 2.75A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I2005

b:37.9
occ:0.50
 O A:HOH2191 2.6 44.5 1.0
NE1 A:TRP514 3.4 27.5 1.0
O A:HOH2188 3.4 40.3 1.0
CZ2 A:TRP514 3.7 27.5 1.0
CB A:PHE293 3.9 14.4 1.0
CE2 A:TRP514 3.9 28.0 1.0
OE1 A:GLU515 4.1 35.8 1.0
O A:HOH2190 4.2 40.8 1.0
O A:GLN289 4.4 20.9 1.0
CZ2 A:TRP513 4.4 22.4 1.0
N A:ARG294 4.4 16.1 1.0
CA A:ILE290 4.4 18.8 1.0
CB A:ARG294 4.6 15.9 1.0
CD1 A:TRP514 4.6 27.7 1.0
C A:PHE293 4.6 15.6 1.0
CD A:GLU515 4.8 35.2 1.0
O A:ILE290 4.8 18.2 1.0
CG1 A:ILE290 4.8 18.4 1.0
CA A:PHE293 4.8 15.2 1.0
CA A:ARG294 4.8 16.6 1.0
CG A:PHE293 4.9 13.2 1.0

Iodine binding site 6 out of 8 in 2gjm

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Iodine binding site 6 out of 8 in the Crystal Structure of Buffalo Lactoperoxidase at 2.75A 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 Buffalo Lactoperoxidase at 2.75A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I2006

b:37.5
occ:0.50
 NE A:ARG382 3.5 27.9 1.0
N A:THR544 3.5 31.6 1.0
CG2 A:ILE543 3.5 28.0 1.0
CA A:ILE543 3.7 29.7 1.0
OG1 A:THR544 3.7 35.0 1.0
O A:GLU348 3.8 37.7 1.0
NH2 A:ARG382 4.0 29.3 1.0
C A:ILE543 4.1 30.5 1.0
N A:LYS545 4.1 31.6 1.0
CZ A:ARG382 4.2 28.6 1.0
CB A:ILE543 4.3 29.0 1.0
CE2 A:TYR350 4.3 41.5 1.0
CA A:GLU348 4.4 36.8 1.0
CD A:ARG382 4.4 26.3 1.0
C A:GLU348 4.5 37.5 1.0
CA A:THR544 4.5 32.5 1.0
O A:HIS542 4.6 29.8 1.0
CB A:LYS545 4.6 31.2 1.0
CD1 A:ILE543 4.6 27.7 1.0
CG A:LYS545 4.7 31.6 1.0
CB A:GLU348 4.7 37.8 1.0
CB A:THR544 4.7 33.5 1.0
C A:THR544 4.8 32.2 1.0
OH A:TYR350 4.9 41.8 1.0
O A:LYS545 4.9 30.5 1.0
N A:ILE543 4.9 29.8 1.0
CA A:LYS545 5.0 31.3 1.0
CZ A:TYR350 5.0 41.1 1.0

Iodine binding site 7 out of 8 in 2gjm

Go back to Iodine Binding Sites List in 2gjm
Iodine binding site 7 out of 8 in the Crystal Structure of Buffalo Lactoperoxidase at 2.75A 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 Buffalo Lactoperoxidase at 2.75A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I2007

b:10.7
occ:0.50
 O A:HOH2081 3.3 21.0 1.0
N A:TRP32 3.4 15.9 1.0
N A:VAL327 3.5 13.6 1.0
CH2 A:TRP436 3.7 14.3 1.0
CB A:VAL327 3.8 13.8 1.0
CB A:ASN326 3.8 11.5 1.0
CG1 A:VAL327 3.9 15.0 1.0
CA A:ARG31 3.9 15.4 1.0
N A:ASN326 3.9 12.2 1.0
CZ2 A:TRP436 4.0 13.5 1.0
O A:ALA30 4.0 15.4 1.0
CE A:MET430 4.1 12.8 1.0
C A:ARG31 4.1 15.9 1.0
C A:ASN326 4.2 13.2 1.0
CA A:ASN326 4.2 12.8 1.0
N A:LEU33 4.2 15.9 1.0
CA A:VAL327 4.2 13.3 1.0
CD A:ARG31 4.2 15.9 1.0
CB A:TRP32 4.4 14.7 1.0
CA A:TRP32 4.4 15.6 1.0
O A:LEU33 4.5 15.1 1.0
CB A:SER325 4.5 12.3 1.0
CB A:ARG31 4.7 15.0 1.0
SD A:MET430 4.7 14.4 1.0
C A:SER325 4.7 12.6 1.0
NH1 A:ARG31 4.7 15.1 1.0
C A:TRP32 4.8 16.1 1.0
CZ3 A:TRP436 4.9 13.8 1.0
C A:ALA30 4.9 14.8 1.0
N A:ARG31 4.9 14.9 1.0
CG A:ARG31 4.9 15.7 1.0
CG A:TRP32 4.9 14.8 1.0

Iodine binding site 8 out of 8 in 2gjm

Go back to Iodine Binding Sites List in 2gjm
Iodine binding site 8 out of 8 in the Crystal Structure of Buffalo Lactoperoxidase at 2.75A 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 Buffalo Lactoperoxidase at 2.75A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I2008

b:24.4
occ:0.50
 N A:LYS446 3.2 28.2 1.0
OG1 A:THR447 3.4 29.7 1.0
N A:THR447 3.5 29.8 1.0
CA A:GLY450 4.0 26.0 1.0
CA A:PRO445 4.0 26.4 1.0
CA A:LYS446 4.0 29.2 1.0
CG2 A:THR447 4.1 28.9 1.0
C A:PRO445 4.1 27.2 1.0
CB A:THR447 4.2 29.7 1.0
CB A:LYS446 4.2 29.6 1.0
C A:LYS446 4.2 29.2 1.0
CA A:THR447 4.4 29.3 1.0
N A:GLY450 4.5 27.0 1.0
O A:HOH2115 4.7 24.6 1.0
CB A:PRO445 4.7 25.8 1.0
CG A:LYS446 4.8 31.4 1.0
O A:THR447 4.8 28.2 1.0
O A:GLN444 5.0 24.8 1.0

Reference:

I.A.Sheikh, A.S.Ethayathulla, A.K.Singh, N.Singh, S.Sharma, T.P.Singh. Crystal Structure of Buffalo Lactoperoxidase at 2.75A Resolution To Be Published.
Page generated: Sun Aug 11 13:52:11 2024

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