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Iodine in PDB 5ceg: X-Ray Structure of Toxin/Anti-Toxin Complex From Mesorhizobium Opportunistum

Protein crystallography data

The structure of X-Ray Structure of Toxin/Anti-Toxin Complex From Mesorhizobium Opportunistum, PDB code: 5ceg was solved by C.D.Aakre, J.Herrou, S.Crosson, M.T.Laub, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.71 / 1.59
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 43.180, 118.840, 211.420, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 19.5

Other elements in 5ceg:

The structure of X-Ray Structure of Toxin/Anti-Toxin Complex From Mesorhizobium Opportunistum also contains other interesting chemical elements:

Sodium (Na) 1 atom

Iodine Binding Sites:

The binding sites of Iodine atom in the X-Ray Structure of Toxin/Anti-Toxin Complex From Mesorhizobium Opportunistum (pdb code 5ceg). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 8 binding sites of Iodine where determined in the X-Ray Structure of Toxin/Anti-Toxin Complex From Mesorhizobium Opportunistum, PDB code: 5ceg:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iodine binding site 1 out of 8 in 5ceg

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Iodine binding site 1 out of 8 in the X-Ray Structure of Toxin/Anti-Toxin Complex From Mesorhizobium Opportunistum


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of X-Ray Structure of Toxin/Anti-Toxin Complex From Mesorhizobium Opportunistum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I102

b:16.8
occ:0.57
 O A:HOH242 3.2 24.4 1.0
NH1 A:ARG57 3.5 14.0 1.0
CG A:ARG54 4.1 13.6 1.0
CD A:ARG57 4.3 11.2 1.0
CD A:ARG54 4.3 14.3 1.0
CB A:ARG54 4.6 11.3 1.0
CZ A:ARG57 4.6 13.4 1.0
CA A:ARG54 4.9 10.3 1.0
NE A:ARG57 4.9 11.6 1.0
NE A:ARG54 5.0 19.9 1.0

Iodine binding site 2 out of 8 in 5ceg

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Iodine binding site 2 out of 8 in the X-Ray Structure of Toxin/Anti-Toxin Complex From Mesorhizobium Opportunistum


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of X-Ray Structure of Toxin/Anti-Toxin Complex From Mesorhizobium Opportunistum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I103

b:20.6
occ:0.46
 O A:HOH222 3.4 16.3 1.0
O D:HOH364 3.4 28.1 1.0
NE1 A:TRP60 3.4 11.3 1.0
CD1 A:TRP60 4.3 10.6 1.0
CG A:LYS64 4.3 16.4 1.0
CG D:ARG58 4.5 12.9 1.0
CE2 A:TRP60 4.5 11.6 1.0
CB D:ARG58 4.5 14.3 1.0
CE A:LYS64 4.5 31.7 1.0
O D:HOH328 4.7 38.5 1.0
CD D:ARG58 4.7 14.0 1.0
CB A:LYS64 4.8 15.7 1.0
CZ2 A:TRP60 4.8 13.2 1.0
CD A:LYS64 4.9 22.7 1.0

Iodine binding site 3 out of 8 in 5ceg

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Iodine binding site 3 out of 8 in the X-Ray Structure of Toxin/Anti-Toxin Complex From Mesorhizobium Opportunistum


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of X-Ray Structure of Toxin/Anti-Toxin Complex From Mesorhizobium Opportunistum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I204

b:40.5
occ:0.48
 O C:HOH208 3.0 40.0 1.0
O C:HOH257 3.2 36.7 1.0
NH1 B:ARG54 3.7 26.9 1.0
NH2 B:ARG54 3.8 20.5 1.0
CD1 C:LEU56 4.0 11.9 1.0
CD1 C:ILE53 4.1 12.2 0.4
CZ B:ARG54 4.2 23.7 1.0
CD1 B:LEU102 4.5 22.8 1.0
CB C:ASP52 4.6 9.6 1.0
O C:HOH302 4.7 35.9 1.0
CG B:LEU102 4.8 24.7 1.0
CE B:MET63 4.8 23.6 1.0
OD2 C:ASP52 5.0 13.7 1.0

Iodine binding site 4 out of 8 in 5ceg

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Iodine binding site 4 out of 8 in the X-Ray Structure of Toxin/Anti-Toxin Complex From Mesorhizobium Opportunistum


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of X-Ray Structure of Toxin/Anti-Toxin Complex From Mesorhizobium Opportunistum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I102

b:21.0
occ:0.38
 NH2 C:ARG49 3.0 21.5 0.5
NE C:ARG49 3.1 22.4 0.5
O B:HOH347 3.2 26.6 1.0
O C:HOH302 3.2 35.9 1.0
NE B:ARG101 3.3 20.4 1.0
CZ C:ARG49 3.4 20.1 0.5
CE C:LYS45 3.6 17.2 1.0
CG B:ARG101 3.9 18.9 1.0
CD C:ARG49 4.0 15.4 0.5
CD B:ARG101 4.0 19.9 1.0
CB C:ARG49 4.2 13.9 0.5
CD C:ARG49 4.2 19.2 0.5
CB C:ARG49 4.2 13.7 0.5
CZ B:ARG101 4.2 22.9 1.0
NH2 B:ARG101 4.3 21.9 1.0
CG C:ARG49 4.3 15.0 0.5
CB B:ARG101 4.3 18.5 1.0
CG C:ARG49 4.3 17.8 0.5
NZ C:LYS45 4.4 13.4 1.0
CD C:LYS45 4.4 19.7 1.0
O B:HOH417 4.4 31.7 1.0
CG C:LYS45 4.5 16.1 1.0
NH1 C:ARG49 4.7 17.2 0.5
O B:HOH317 4.8 19.8 1.0
NE C:ARG49 4.9 19.6 0.5
O C:HOH293 4.9 18.1 1.0

Iodine binding site 5 out of 8 in 5ceg

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Iodine binding site 5 out of 8 in the X-Ray Structure of Toxin/Anti-Toxin Complex From Mesorhizobium Opportunistum


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of X-Ray Structure of Toxin/Anti-Toxin Complex From Mesorhizobium Opportunistum within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I204

b:0.6
occ:0.72
 O C:HOH293 3.1 18.1 1.0
O D:HOH427 3.1 46.5 1.0
O D:HOH397 3.6 21.0 1.0
CD2 D:LEU102 3.7 37.4 1.0
CG D:LEU102 4.0 25.8 1.0
O D:PRO68 4.1 17.3 1.0
CA D:GLY95 4.1 13.4 1.0
C D:GLY95 4.1 16.3 1.0
CD1 D:LEU102 4.1 35.7 1.0
O D:HOH376 4.2 31.1 1.0
N D:ARG96 4.3 11.4 1.0
O B:HOH347 4.4 26.6 1.0
O D:GLY95 4.5 15.5 1.0
CA D:PRO68 4.6 18.8 1.0
CG D:ARG96 4.7 13.0 1.0
O D:HOH303 4.7 7.9 1.0
C D:PRO68 4.7 17.0 1.0
CB D:PRO68 4.8 18.0 1.0
N D:GLY95 4.8 14.4 1.0
CA D:ARG96 5.0 11.1 1.0

Iodine binding site 6 out of 8 in 5ceg

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Iodine binding site 6 out of 8 in the X-Ray Structure of Toxin/Anti-Toxin Complex From Mesorhizobium Opportunistum


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of X-Ray Structure of Toxin/Anti-Toxin Complex From Mesorhizobium Opportunistum within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I205

b:25.9
occ:0.50
 O D:MET63 3.7 18.6 1.0
N D:VAL65 3.7 12.8 1.0
CZ D:PHE103 3.8 23.5 0.6
CG1 D:VAL65 3.9 19.1 0.3
CG2 D:VAL52 4.0 19.0 0.7
CE1 D:PHE103 4.0 23.1 0.6
O B:HOH426 4.0 38.7 1.0
CG2 D:VAL65 4.1 19.7 0.7
CZ D:PHE103 4.1 24.1 0.4
CA D:LEU64 4.1 12.4 1.0
CE2 D:PHE103 4.1 22.6 0.4
CB D:VAL65 4.4 19.1 0.3
CB D:VAL65 4.4 19.1 0.7
CD1 D:LEU64 4.4 18.2 1.0
C D:LEU64 4.4 13.7 1.0
C D:MET63 4.5 16.0 1.0
CG1 D:VAL52 4.5 18.0 0.3
CG2 B:VAL65 4.5 18.4 1.0
N D:VAL52 4.6 14.2 1.0
CA D:VAL65 4.7 16.1 0.3
CA D:VAL65 4.7 16.1 0.7
CB D:VAL52 4.7 20.1 0.7
N D:LEU64 4.7 12.6 1.0
CB D:VAL52 4.8 20.5 0.3
CB B:VAL65 4.9 14.2 1.0
CA D:GLY51 4.9 19.9 1.0
O B:HOH318 4.9 28.4 1.0

Iodine binding site 7 out of 8 in 5ceg

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Iodine binding site 7 out of 8 in the X-Ray Structure of Toxin/Anti-Toxin Complex From Mesorhizobium Opportunistum


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of X-Ray Structure of Toxin/Anti-Toxin Complex From Mesorhizobium Opportunistum within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I206

b:18.5
occ:0.77
 O D:HOH374 3.4 35.3 1.0
N D:ARG49 3.6 14.6 1.0
O B:HOH356 3.7 25.2 1.0
C D:GLN47 3.7 16.3 1.0
CA D:GLN47 3.8 17.7 1.0
CB D:GLN47 3.9 18.6 1.0
CB D:ARG49 4.0 15.4 1.0
N D:PRO48 4.0 16.3 1.0
CG B:GLN47 4.0 22.6 1.0
CE B:MET50 4.0 19.9 1.0
CA D:ARG49 4.1 15.8 1.0
O D:GLN47 4.1 18.1 1.0
C D:ARG49 4.2 15.7 1.0
CD D:PRO48 4.2 16.4 1.0
CB B:GLN47 4.3 17.3 1.0
N D:MET50 4.3 16.8 1.0
SD B:MET50 4.4 21.2 1.0
CG D:GLN47 4.5 24.7 1.0
C D:PRO48 4.7 19.4 1.0
O D:ARG49 4.8 18.5 1.0
CG D:ARG49 4.8 21.1 1.0
CB B:MET50 4.8 21.5 1.0
CG D:PRO48 4.8 22.2 1.0
CA D:PRO48 4.9 17.4 1.0
CD B:GLN47 5.0 30.8 1.0
CA D:MET50 5.0 16.1 1.0

Iodine binding site 8 out of 8 in 5ceg

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Iodine binding site 8 out of 8 in the X-Ray Structure of Toxin/Anti-Toxin Complex From Mesorhizobium Opportunistum


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of X-Ray Structure of Toxin/Anti-Toxin Complex From Mesorhizobium Opportunistum within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I207

b:45.7
occ:0.35
 NE D:ARG101 3.3 30.2 1.0
CG D:ARG101 3.6 24.1 1.0
CD D:ARG101 3.7 36.2 1.0
O D:ASN100 3.8 12.5 1.0
NH1 B:ARG101 3.8 24.7 1.0
O A:HOH263 3.9 19.0 1.0
O D:HOH372 3.9 42.7 1.0
CB D:ASN100 4.0 11.3 1.0
C D:ASN100 4.2 12.4 1.0
NH2 B:ARG101 4.3 21.9 1.0
CZ D:ARG101 4.4 24.0 1.0
CZ B:ARG101 4.5 22.9 1.0
NH2 D:ARG101 4.5 35.6 1.0
CA D:ASN100 4.6 11.9 1.0
O B:HOH402 4.7 35.4 1.0
CB D:ARG101 4.7 19.3 1.0
CD1 A:LEU48 4.8 17.6 1.0
N D:ARG101 4.8 13.3 1.0
CG D:ASN100 4.9 13.7 1.0
OD1 D:ASN100 5.0 17.4 1.0

Reference:

C.D.Aakre, J.Herrou, T.N.Phung, B.S.Perchuk, S.Crosson, M.T.Laub. Evolving New Protein-Protein Interaction Specificity Through Promiscuous Intermediates. Cell V. 163 594 2015.
ISSN: ISSN 1097-4172
PubMed: 26478181
DOI: 10.1016/J.CELL.2015.09.055
Page generated: Sun Dec 13 19:38:34 2020

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