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Iodine in PDB 3pmc: Crystal Structure of the Sporulation Inhibitor PXO2-61 From Bacillus Anthracis

Protein crystallography data

The structure of Crystal Structure of the Sporulation Inhibitor PXO2-61 From Bacillus Anthracis, PDB code: 3pmc was solved by G.R.Stranzl, E.Santelli, L.A.Bankston, C.La Clair, A.Bobkov, R.Schwarzenbacher, A.Godzik, M.Perego, M.Grynberg, R.C.Liddington, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.64 / 1.49
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 44.110, 62.620, 124.760, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 20.8

Other elements in 3pmc:

The structure of Crystal Structure of the Sporulation Inhibitor PXO2-61 From Bacillus Anthracis also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 31;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of the Sporulation Inhibitor PXO2-61 From Bacillus Anthracis (pdb code 3pmc). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 31 binding sites of Iodine where determined in the Crystal Structure of the Sporulation Inhibitor PXO2-61 From Bacillus Anthracis, PDB code: 3pmc:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 31 in 3pmc

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Iodine binding site 1 out of 31 in the Crystal Structure of the Sporulation Inhibitor PXO2-61 From Bacillus Anthracis


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Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of the Sporulation Inhibitor PXO2-61 From Bacillus Anthracis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I401

b:15.9
occ:1.00
 O A:HOH235 3.4 26.1 1.0
O A:HOH164 3.6 12.4 1.0
O A:HOH158 3.6 16.3 1.0
ND2 A:ASN87 3.6 12.6 1.0
CA A:PHE84 3.9 10.0 1.0
CG2 A:ILE39 4.0 14.7 1.0
CB A:PHE84 4.0 10.2 1.0
CD A:ARG74 4.1 12.8 1.0
CD1 A:ILE39 4.3 15.8 1.0
CG1 A:ILE39 4.3 13.6 1.0
CD1 A:PHE84 4.3 12.4 1.0
NE A:ARG74 4.3 12.2 1.0
CB A:ASN87 4.4 11.8 1.0
CG A:ASN87 4.5 13.2 1.0
N A:PHE84 4.6 10.1 1.0
O A:HOH269 4.6 28.3 1.0
CG A:PHE84 4.7 10.3 1.0
CZ A:ARG74 4.7 12.7 1.0
CB A:ILE39 4.8 13.8 1.0
NH2 A:ARG74 4.9 13.6 1.0

Iodine binding site 2 out of 31 in 3pmc

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Iodine binding site 2 out of 31 in the Crystal Structure of the Sporulation Inhibitor PXO2-61 From Bacillus Anthracis


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Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of the Sporulation Inhibitor PXO2-61 From Bacillus Anthracis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I403

b:21.6
occ:1.00
 O A:HOH223 3.5 25.2 1.0
OG1 A:THR66 3.5 19.0 1.0
CD A:LYS69 3.9 17.6 1.0
O A:HOH138 4.0 30.1 1.0
CA A:THR66 4.3 15.0 1.0
CB A:THR66 4.3 15.3 1.0
CG2 A:THR66 4.4 16.6 1.0
CD2 A:HIS45 4.6 18.8 1.0
CE A:LYS69 4.6 19.3 1.0
N A:THR66 4.7 16.2 1.0
NE2 A:HIS45 4.7 20.2 1.0
CG2 A:ILE65 4.8 22.4 1.0

Iodine binding site 3 out of 31 in 3pmc

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Iodine binding site 3 out of 31 in the Crystal Structure of the Sporulation Inhibitor PXO2-61 From Bacillus Anthracis


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 the Sporulation Inhibitor PXO2-61 From Bacillus Anthracis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I404

b:20.5
occ:1.00
 O B:HOH150 3.4 27.8 1.0
O A:HOH224 3.5 25.5 1.0
O A:HOH188 3.5 28.9 1.0
ND2 A:ASN117 3.7 14.1 1.0
O A:HOH232 3.9 29.8 1.0
O A:HOH201 4.1 28.9 1.0
CB A:ASN117 4.1 11.7 1.0
CB B:MET96 4.2 15.3 1.0
CG B:MET96 4.3 15.4 1.0
CG1 B:ILE93 4.4 15.4 1.0
CG A:ASN117 4.4 14.4 1.0
O A:HOH273 4.5 57.9 1.0
CG A:LYS114 4.5 21.2 1.0
CA A:LYS114 4.5 14.7 1.0
CA B:ILE93 4.7 13.6 1.0
NZ A:LYS114 4.7 38.6 1.0
CB A:LYS114 4.8 18.5 1.0
O A:LYS114 4.9 15.0 1.0
CE B:MET96 4.9 18.8 1.0
CG2 B:ILE93 4.9 17.6 1.0
CB B:ILE93 4.9 13.9 1.0

Iodine binding site 4 out of 31 in 3pmc

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Iodine binding site 4 out of 31 in the Crystal Structure of the Sporulation Inhibitor PXO2-61 From Bacillus Anthracis


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 the Sporulation Inhibitor PXO2-61 From Bacillus Anthracis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I405

b:20.6
occ:1.00
 O A:HOH219 3.5 29.2 1.0
O B:HOH178 3.5 21.6 1.0
O A:HOH166 3.5 27.9 1.0
ND2 B:ASN117 3.7 13.5 1.0
O B:HOH190 3.9 31.6 1.0
O B:HOH193 3.9 26.4 1.0
CB B:ASN117 4.1 11.6 1.0
CB A:MET96 4.3 12.9 1.0
CG A:MET96 4.3 14.8 1.0
CG1 A:ILE93 4.4 15.8 1.0
CG B:ASN117 4.4 11.7 1.0
CG B:LYS114 4.5 23.6 1.0
CA B:LYS114 4.5 15.9 1.0
CA A:ILE93 4.7 13.5 1.0
CG2 A:ILE93 4.8 17.2 1.0
CB A:ILE93 4.9 14.3 1.0
CE A:MET96 4.9 18.6 1.0
O B:LYS114 4.9 15.4 1.0
CB B:LYS114 4.9 19.1 1.0

Iodine binding site 5 out of 31 in 3pmc

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Iodine binding site 5 out of 31 in the Crystal Structure of the Sporulation Inhibitor PXO2-61 From Bacillus Anthracis


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 the Sporulation Inhibitor PXO2-61 From Bacillus Anthracis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I408

b:32.0
occ:1.00
 O A:HOH227 3.3 38.8 1.0
OH A:TYR11 3.6 31.4 1.0
CE2 A:TYR11 3.8 22.9 1.0
CB A:ARG15 4.0 25.6 1.0
CA A:PHE19 4.1 21.1 1.0
CG A:LYS18 4.1 31.1 1.0
N A:PHE19 4.1 22.0 1.0
CZ A:TYR11 4.2 24.9 1.0
CB A:PHE19 4.3 20.5 1.0
O A:ARG15 4.4 26.1 1.0
OD2 A:ASP22 4.4 29.0 0.5
CD1 A:ILE98 4.4 20.0 1.0
CD2 A:PHE19 4.5 18.0 1.0
CG A:ARG15 4.6 27.7 1.0
C A:LYS18 4.6 24.0 1.0
CB A:LYS18 4.7 27.8 1.0
CD A:ARG15 4.7 28.8 1.0
NZ A:LYS18 4.8 41.2 1.0
CG A:PHE19 4.9 16.6 1.0
O A:LYS18 5.0 24.3 1.0

Iodine binding site 6 out of 31 in 3pmc

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Iodine binding site 6 out of 31 in the Crystal Structure of the Sporulation Inhibitor PXO2-61 From Bacillus Anthracis


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 the Sporulation Inhibitor PXO2-61 From Bacillus Anthracis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I409

b:43.4
occ:1.00
 NZ A:LYS55 3.5 39.7 1.0
NE A:ARG10 3.8 43.7 1.0
NH2 A:ARG10 3.9 48.6 1.0
CB A:CYS9 3.9 26.2 1.0
CD A:LYS13 4.0 37.7 1.0
C A:CYS9 4.0 23.6 1.0
CE A:LYS55 4.0 38.3 1.0
CZ A:ARG10 4.0 47.3 1.0
CD A:LYS55 4.0 34.6 1.0
N A:ARG10 4.1 23.5 1.0
O A:CYS9 4.1 23.2 1.0
CA A:ARG10 4.1 23.7 1.0
CB A:LYS13 4.2 28.3 1.0
CG A:ARG10 4.3 33.0 1.0
NZ A:LYS13 4.4 43.0 1.0
CG A:LYS13 4.5 32.3 1.0
CG2 A:ILE51 4.5 20.5 1.0
CD A:ARG10 4.6 38.5 1.0
CA A:CYS9 4.7 23.7 1.0
CB A:ARG10 4.8 26.4 1.0
CE A:LYS13 4.9 40.8 1.0
O A:HOH338 4.9 37.0 1.0
NH1 A:ARG10 5.0 48.4 1.0

Iodine binding site 7 out of 31 in 3pmc

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Iodine binding site 7 out of 31 in the Crystal Structure of the Sporulation Inhibitor PXO2-61 From Bacillus Anthracis


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 the Sporulation Inhibitor PXO2-61 From Bacillus Anthracis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I411

b:34.9
occ:1.00
 O B:HOH314 2.3 37.0 1.0
ND2 A:ASN89 3.3 16.3 1.0
O A:HOH154 3.4 20.7 1.0
CB B:TYR125 4.0 10.8 1.0
CB A:ASN89 4.0 12.4 1.0
CG B:TYR125 4.1 11.7 1.0
CG A:ASN89 4.1 14.0 1.0
CA A:HIS86 4.3 10.9 1.0
CD1 B:TYR125 4.4 12.7 1.0
O B:ASP121 4.5 13.0 1.0
CB B:ASP121 4.6 12.0 1.0
CD2 B:TYR125 4.6 17.1 1.0
CD2 A:HIS86 4.7 17.2 1.0
C B:ASP121 4.8 11.5 1.0
CB A:HIS86 4.8 12.6 1.0
O A:HOH177 4.9 18.8 1.0
N A:HIS86 5.0 10.5 1.0

Iodine binding site 8 out of 31 in 3pmc

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Iodine binding site 8 out of 31 in the Crystal Structure of the Sporulation Inhibitor PXO2-61 From Bacillus Anthracis


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 the Sporulation Inhibitor PXO2-61 From Bacillus Anthracis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I413

b:41.9
occ:1.00
 O A:HOH282 2.2 97.6 1.0
NZ A:LYS68 2.7 36.1 1.0
O A:HOH344 2.9 48.0 1.0
OG A:SER130 3.3 16.3 1.0
CE A:LYS68 3.9 30.3 1.0
CB A:SER130 4.0 13.9 1.0
CA A:SER130 4.1 11.9 1.0
CD A:LYS68 4.1 26.6 1.0
CG A:GLN134 4.2 18.4 1.0
CB A:GLU133 4.2 18.5 1.0
CG A:LYS68 4.2 20.6 1.0
O A:SER130 4.5 14.1 1.0
NE2 A:GLN134 4.6 17.7 1.0
O A:HOH328 4.8 37.1 1.0
O A:HOH335 4.8 66.9 1.0
CD A:GLN134 4.8 20.5 1.0
C A:SER130 4.8 12.0 1.0

Iodine binding site 9 out of 31 in 3pmc

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Iodine binding site 9 out of 31 in the Crystal Structure of the Sporulation Inhibitor PXO2-61 From Bacillus Anthracis


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 the Sporulation Inhibitor PXO2-61 From Bacillus Anthracis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I415

b:49.2
occ:1.00
 OG A:SER48 3.4 23.0 1.0
CB A:GLN16 3.5 30.6 1.0
O A:HOH240 3.5 27.4 1.0
O A:HOH320 3.6 19.4 0.5
CG A:GLN16 3.7 36.2 1.0
CD1 A:ILE51 3.7 20.1 1.0
CA A:SER48 4.2 14.9 1.0
CB A:SER48 4.3 16.7 1.0
CD A:GLN16 4.4 41.1 1.0
CA A:LYS13 4.4 26.5 1.0
N A:SER48 4.4 14.8 1.0
O A:LYS13 4.5 29.4 1.0
O A:LEU12 4.6 24.3 1.0
O A:HOH363 4.7 19.2 0.5
CG A:LEU47 4.7 16.4 1.0
NE2 A:GLN16 4.8 43.9 1.0
C A:LEU47 4.9 14.2 1.0
CD A:LYS13 4.9 37.7 1.0
CA A:GLN16 4.9 28.2 1.0
CD2 A:LEU47 4.9 19.4 1.0
O A:HOH243 4.9 36.5 1.0
CG A:LYS13 4.9 32.3 1.0
OE1 A:GLN16 5.0 46.1 1.0
C A:LYS13 5.0 27.9 1.0

Iodine binding site 10 out of 31 in 3pmc

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Iodine binding site 10 out of 31 in the Crystal Structure of the Sporulation Inhibitor PXO2-61 From Bacillus Anthracis


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 the Sporulation Inhibitor PXO2-61 From Bacillus Anthracis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I416

b:34.5
occ:0.50
 I A:IOD417 1.5 42.7 0.5
CG A:ARG10 3.4 33.0 1.0
CD A:ARG10 3.7 38.5 1.0
CD2 A:LEU7 3.8 25.7 1.0
O A:CYS6 4.3 30.3 1.0
CB A:ARG10 4.4 26.4 1.0
CG A:LEU7 4.4 28.4 1.0
CA A:LEU7 4.5 25.9 1.0
C A:CYS6 4.5 34.1 1.0
N A:LEU7 4.6 28.8 1.0
N A:CYS6 4.9 42.3 1.0
NE A:ARG10 4.9 43.7 1.0
NH1 A:ARG10 5.0 48.4 1.0
N A:LYS5 5.0 48.5 1.0

Reference:

G.R.Stranzl, E.Santelli, L.A.Bankston, C.La Clair, A.Bobkov, R.Schwarzenbacher, A.Godzik, M.Perego, M.Grynberg, R.C.Liddington. Structural Insights Into Inhibition of Bacillus Anthracis Sporulation By A Novel Class of Non-Heme Globin Sensor Domains. J.Biol.Chem. V. 286 8448 2011.
ISSN: ISSN 0021-9258
PubMed: 21216948
DOI: 10.1074/JBC.M110.207126
Page generated: Sun Dec 13 19:29:07 2020

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