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Iodine in PDB 3o2e: Crystal Structure of A Bol-Like Protein From Babesia Bovis

Protein crystallography data

The structure of Crystal Structure of A Bol-Like Protein From Babesia Bovis, PDB code: 3o2e was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.53 / 1.95
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 66.300, 66.300, 35.290, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 24.1

Other elements in 3o2e:

The structure of Crystal Structure of A Bol-Like Protein From Babesia Bovis also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of A Bol-Like Protein From Babesia Bovis (pdb code 3o2e). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 9 binding sites of Iodine where determined in the Crystal Structure of A Bol-Like Protein From Babesia Bovis, PDB code: 3o2e:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iodine binding site 1 out of 9 in 3o2e

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Iodine binding site 1 out of 9 in the Crystal Structure of A Bol-Like Protein From Babesia Bovis


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 A Bol-Like Protein From Babesia Bovis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I87

b:25.8
occ:0.94
 N A:CYS72 3.7 15.0 1.0
CB A:CYS72 4.0 14.2 1.0
SG A:CYS72 4.0 17.6 1.0
NE2 A:GLN51 4.2 34.3 1.0
CB A:LEU47 4.2 21.9 1.0
CG A:GLN51 4.3 22.6 1.0
O A:MET70 4.3 13.5 1.0
CA A:LYS71 4.3 14.2 1.0
CD2 A:LEU47 4.4 22.5 1.0
CA A:CYS72 4.4 14.7 1.0
CD1 A:LEU47 4.5 27.5 1.0
C A:LYS71 4.5 14.9 1.0
O A:LEU47 4.5 19.3 1.0
O A:CYS72 4.6 16.3 1.0
CG A:LEU47 4.6 23.1 1.0
CD A:GLN51 4.7 29.9 1.0
CA A:LEU47 4.8 20.8 1.0
CG A:MET70 4.8 15.9 1.0
C A:MET70 4.8 13.8 1.0
N A:LYS71 5.0 14.0 1.0
C A:CYS72 5.0 15.0 1.0

Iodine binding site 2 out of 9 in 3o2e

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Iodine binding site 2 out of 9 in the Crystal Structure of A Bol-Like Protein From Babesia Bovis


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 A Bol-Like Protein From Babesia Bovis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I88

b:32.5
occ:0.74
 OG A:SER5 3.0 22.9 0.5
N A:SER5 3.7 17.7 1.0
CB A:SER5 4.0 19.8 0.5
CB A:SER5 4.0 19.2 0.5
CB A:SER3 4.0 19.9 1.0
CB A:LYS4 4.1 18.4 1.0
N A:LYS4 4.2 17.4 1.0
OG A:SER3 4.3 20.7 1.0
CA A:SER5 4.4 18.3 0.5
CA A:SER5 4.4 17.8 0.5
O A:HOH113 4.5 25.0 1.0
CA A:LYS4 4.5 17.4 1.0
C A:LYS4 4.6 17.4 1.0
C A:SER3 4.9 17.9 1.0
O A:HOH139 5.0 38.5 1.0
CA A:SER3 5.0 20.0 1.0
CG A:LYS4 5.0 19.6 1.0

Iodine binding site 3 out of 9 in 3o2e

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Iodine binding site 3 out of 9 in the Crystal Structure of A Bol-Like Protein From Babesia Bovis


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 A Bol-Like Protein From Babesia Bovis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I89

b:22.9
occ:0.58
 N A:GLY44 3.4 16.8 1.0
NH2 A:ARG50 3.6 21.6 1.0
CA A:GLY44 4.1 17.5 1.0
OE2 A:GLU77 4.1 19.2 1.0
N A:LYS45 4.3 16.9 1.0
CA A:GLU43 4.3 15.7 1.0
C A:GLU43 4.3 16.6 1.0
O A:PHE42 4.3 15.8 1.0
O A:LYS45 4.4 15.7 1.0
CG2 A:THR74 4.6 15.2 1.0
C A:GLY44 4.6 17.7 1.0
CZ A:ARG50 4.9 16.2 1.0

Iodine binding site 4 out of 9 in 3o2e

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Iodine binding site 4 out of 9 in the Crystal Structure of A Bol-Like Protein From Babesia Bovis


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 A Bol-Like Protein From Babesia Bovis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I90

b:30.2
occ:0.47
 O A:HOH129 2.4 35.4 1.0
N A:ASP24 3.5 16.0 1.0
CB A:ASP24 4.0 15.6 1.0
CA A:THR23 4.1 16.6 1.0
NZ A:LYS4 4.2 33.0 1.0
CA A:ASP24 4.3 14.8 1.0
C A:THR23 4.3 15.6 1.0
O A:VAL22 4.3 15.1 1.0
CD A:LYS4 4.4 24.5 1.0
CE A:LYS4 4.5 28.2 1.0
CG2 A:THR23 4.6 18.2 1.0
O A:ASP24 4.6 15.2 1.0
O A:HOH121 4.7 37.3 1.0
CB A:THR23 4.9 16.5 1.0
C A:ASP24 4.9 14.5 1.0

Iodine binding site 5 out of 9 in 3o2e

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Iodine binding site 5 out of 9 in the Crystal Structure of A Bol-Like Protein From Babesia Bovis


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 A Bol-Like Protein From Babesia Bovis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I91

b:34.9
occ:0.47
 O A:HOH137 2.3 15.7 1.0
O A:HOH138 3.5 37.5 1.0
OG1 A:THR69 3.7 16.4 1.0
N A:MET70 3.9 14.7 1.0
C A:MET70 3.9 13.8 1.0
CA A:MET70 3.9 13.5 1.0
CB A:ASN34 3.9 16.0 1.0
C A:THR69 4.1 13.9 1.0
N A:LYS71 4.1 14.0 1.0
O A:MET70 4.2 13.5 1.0
O A:ALA35 4.2 13.9 1.0
N A:ALA35 4.3 13.2 1.0
O A:THR69 4.3 12.8 1.0
CB A:THR69 4.3 15.4 1.0
CA A:ASN34 4.5 14.7 1.0
C A:ASN34 4.6 14.6 1.0
C A:ALA35 4.6 13.1 1.0
CB A:LYS71 4.7 15.4 1.0
CG A:ASN34 4.9 20.7 1.0
CA A:THR69 4.9 14.9 1.0

Iodine binding site 6 out of 9 in 3o2e

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Iodine binding site 6 out of 9 in the Crystal Structure of A Bol-Like Protein From Babesia Bovis


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 A Bol-Like Protein From Babesia Bovis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I92

b:32.9
occ:0.36
 O A:HOH106 3.3 29.9 1.0
N A:ASP49 3.6 18.7 1.0
CA A:GLY46 3.7 20.0 1.0
O A:HOH135 3.8 30.4 1.0
OD2 A:ASP49 3.8 25.1 1.0
CG A:ASP49 3.9 22.7 1.0
C A:GLY46 3.9 19.3 1.0
N A:LEU48 3.9 21.3 1.0
CB A:ASP49 4.0 20.5 1.0
CB A:LEU48 4.0 24.2 1.0
N A:GLY46 4.2 19.1 1.0
O A:GLY46 4.2 17.6 1.0
CA A:LEU48 4.3 21.7 1.0
N A:LEU47 4.3 20.7 1.0
C A:LEU48 4.4 20.1 1.0
CA A:ASP49 4.4 18.8 1.0
OD1 A:ASP49 4.4 21.9 1.0
C A:LEU47 4.9 19.9 1.0

Iodine binding site 7 out of 9 in 3o2e

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Iodine binding site 7 out of 9 in the Crystal Structure of A Bol-Like Protein From Babesia Bovis


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 A Bol-Like Protein From Babesia Bovis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I93

b:41.3
occ:0.46
 N A:MET70 3.5 14.7 1.0
CA A:THR69 3.7 14.9 1.0
O A:MET70 3.9 13.5 1.0
CB A:THR69 4.0 15.4 1.0
C A:THR69 4.1 13.9 1.0
CG2 A:THR69 4.4 16.1 1.0
CG A:MET70 4.4 15.9 1.0
O A:PHE68 4.5 18.8 1.0
OE1 A:GLN51 4.5 36.9 1.0
CA A:MET70 4.5 13.5 1.0
C A:MET70 4.7 13.8 1.0
CD A:GLN51 4.8 29.9 1.0
N A:THR69 4.9 15.0 1.0
CB A:MET70 4.9 14.1 1.0

Iodine binding site 8 out of 9 in 3o2e

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Iodine binding site 8 out of 9 in the Crystal Structure of A Bol-Like Protein From Babesia Bovis


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 A Bol-Like Protein From Babesia Bovis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I94

b:29.2
occ:0.28
 O A:HOH128 2.0 24.3 1.0
O A:HOH140 3.3 40.9 1.0
O A:HOH124 3.9 24.4 0.5
CB A:SER56 3.9 19.5 1.0
O A:ARG52 4.1 18.6 1.0
CB A:ARG52 4.5 18.3 1.0
OG A:SER56 4.5 23.2 1.0
C A:ARG52 4.5 17.4 1.0

Iodine binding site 9 out of 9 in 3o2e

Go back to Iodine Binding Sites List in 3o2e
Iodine binding site 9 out of 9 in the Crystal Structure of A Bol-Like Protein From Babesia Bovis


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 A Bol-Like Protein From Babesia Bovis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I95

b:32.2
occ:0.32
 O A:HOH106 3.1 29.9 1.0
N A:LEU47 3.5 20.7 1.0
CA A:GLY46 3.9 20.0 1.0
CG A:LEU47 4.2 23.1 1.0
C A:GLY46 4.2 19.3 1.0
CB A:LEU47 4.4 21.9 1.0
CA A:LEU47 4.5 20.8 1.0
CD1 A:LEU47 4.9 27.5 1.0

Reference:

J.Abendroth, A.S.Gardberg, J.I.Robinson, J.S.Christensen, B.L.Staker, P.J.Myler, L.J.Stewart, T.E.Edwards. Sad Phasing Using Iodide Ions in A High-Throughput Structural Genomics Environment. J.Struct.Funct.Genom. V. 12 83 2011.
ISSN: ISSN 1345-711X
PubMed: 21359836
DOI: 10.1007/S10969-011-9101-7
Page generated: Sun Aug 11 15:56:07 2024

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