Iodine in PDB 3luz: Crystal Structure of Extragenic Suppressor Protein Suhb From Bartonella Henselae, Via Combined Iodide Sad Molecular Replacement

The structure of Crystal Structure of Extragenic Suppressor Protein Suhb From Bartonella Henselae, Via Combined Iodide Sad Molecular Replacement, PDB code: 3luz 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)	29.04 / 2.05
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	48.540, 81.280, 58.760, 90.00, 98.78, 90.00
R / Rfree (%)	21.7 / 26.2

The structure of Crystal Structure of Extragenic Suppressor Protein Suhb From Bartonella Henselae, Via Combined Iodide Sad Molecular Replacement also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of Extragenic Suppressor Protein Suhb From Bartonella Henselae, Via Combined Iodide Sad Molecular Replacement (pdb code 3luz). 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 Extragenic Suppressor Protein Suhb From Bartonella Henselae, Via Combined Iodide Sad Molecular Replacement, PDB code: 3luz:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 13 in the Crystal Structure of Extragenic Suppressor Protein Suhb From Bartonella Henselae, Via Combined Iodide Sad Molecular Replacement


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 Extragenic Suppressor Protein Suhb From Bartonella Henselae, Via Combined Iodide Sad Molecular Replacement within 5.0Å range: probe atom residue distance (Å) B Occ A:I265 b:56.2 occ:0.94 N A:LYS63 3.7 66.6 1.0 CD A:PRO62 3.8 69.5 1.0 CE1 A:PHE64 3.8 60.7 1.0 C A:ARG61 3.9 65.9 1.0 CA A:ARG61 3.9 65.2 1.0 N A:PRO62 4.0 68.0 1.0 CB A:LYS63 4.0 66.9 1.0 CD1 A:PHE64 4.0 60.5 1.0 CD A:ARG61 4.2 64.8 1.0 CB A:ARG61 4.3 62.9 1.0 CA A:LYS63 4.4 65.8 1.0 O A:ARG61 4.5 64.9 1.0 O A:HOH307 4.6 58.0 1.0 C A:PRO62 4.8 67.9 1.0 N A:PHE64 4.8 61.9 1.0 CZ A:PHE64 4.8 57.8 1.0 C A:LYS63 4.9 63.8 1.0 CA A:PRO62 4.9 68.6 1.0 CG A:ARG61 4.9 63.0 1.0

Iodine binding site 2 out of 13 in the Crystal Structure of Extragenic Suppressor Protein Suhb From Bartonella Henselae, Via Combined Iodide Sad Molecular Replacement


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 Extragenic Suppressor Protein Suhb From Bartonella Henselae, Via Combined Iodide Sad Molecular Replacement within 5.0Å range: probe atom residue distance (Å) B Occ A:I266 b:59.3 occ:0.54 O A:HOH308 3.2 61.1 1.0 O A:HOH281 3.7 56.1 1.0 CB A:VAL6 3.8 56.6 1.0 CZ A:PHE64 3.8 57.8 1.0 NE A:ARG61 3.9 65.6 1.0 CG2 A:VAL6 3.9 55.4 1.0 O A:HOH307 3.9 58.0 1.0 CE2 A:PHE64 4.1 56.8 1.0 CG1 A:VAL6 4.2 55.5 1.0 O A:HOH310 4.2 73.7 1.0 NH2 A:ARG61 4.4 68.9 1.0 CD2 A:LEU107 4.5 42.1 1.0 CZ A:ARG61 4.7 67.2 1.0 CD A:ARG61 4.8 64.8 1.0

Iodine binding site 3 out of 13 in the Crystal Structure of Extragenic Suppressor Protein Suhb From Bartonella Henselae, Via Combined Iodide Sad Molecular Replacement


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 Extragenic Suppressor Protein Suhb From Bartonella Henselae, Via Combined Iodide Sad Molecular Replacement within 5.0Å range: probe atom residue distance (Å) B Occ A:I267 b:45.3 occ:0.55 O A:HOH338 3.0 68.2 1.0 I A:IOD272 3.2 60.2 0.4 NH2 A:ARG131 3.3 48.8 1.0 NH1 A:ARG223 3.6 42.3 1.0 CA A:LEU220 3.9 36.1 1.0 CD A:ARG223 4.0 41.1 1.0 CG2 A:ILE219 4.1 39.8 1.0 CB A:LEU220 4.1 35.8 1.0 O A:HOH336 4.2 66.6 1.0 CD1 A:LEU220 4.2 41.5 1.0 N A:LEU220 4.2 36.0 1.0 CB A:ILE113 4.2 41.9 1.0 O A:ILE113 4.4 43.5 1.0 CZ A:ARG131 4.5 53.5 1.0 C A:ILE219 4.6 35.4 1.0 CZ A:ARG223 4.6 42.6 1.0 CG1 A:ILE113 4.8 41.6 1.0 NE A:ARG223 4.8 39.0 1.0 O A:ILE219 4.8 36.1 1.0 CG A:LEU220 4.8 37.3 1.0 CG2 A:ILE113 4.9 42.1 1.0

Iodine binding site 4 out of 13 in the Crystal Structure of Extragenic Suppressor Protein Suhb From Bartonella Henselae, Via Combined Iodide Sad Molecular Replacement


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 Extragenic Suppressor Protein Suhb From Bartonella Henselae, Via Combined Iodide Sad Molecular Replacement within 5.0Å range: probe atom residue distance (Å) B Occ A:I268 b:48.3 occ:0.26 N A:ALA146 3.4 47.7 1.0 CA A:SER145 4.0 43.5 1.0 CB A:SER145 4.0 43.4 1.0 CB A:ALA146 4.1 52.5 1.0 C A:SER145 4.2 45.7 1.0 CA A:ALA146 4.2 51.0 1.0 NH1 A:ARG147 4.2 56.9 1.0 CZ A:ARG147 4.5 59.0 1.0 N A:ARG147 4.5 50.8 1.0 CG A:ARG147 4.6 53.3 1.0 C A:ALA146 4.7 52.0 1.0 NH2 A:ARG147 4.7 59.9 1.0 OG A:SER145 4.8 43.1 1.0 O A:HOH302 4.9 49.7 1.0

Iodine binding site 5 out of 13 in the Crystal Structure of Extragenic Suppressor Protein Suhb From Bartonella Henselae, Via Combined Iodide Sad Molecular Replacement


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 Extragenic Suppressor Protein Suhb From Bartonella Henselae, Via Combined Iodide Sad Molecular Replacement within 5.0Å range: probe atom residue distance (Å) B Occ A:I269 b:67.0 occ:0.29 O A:HOH296 3.4 56.7 1.0 CB A:ASN248 3.8 44.5 1.0 O A:SER145 4.0 44.7 1.0 CG A:ASN248 4.1 45.5 1.0 ND2 A:ASN248 4.2 47.0 1.0 CA A:ALA146 4.3 51.0 1.0 ND1 A:HIS250 4.4 63.1 1.0 OD1 A:ASN248 4.6 43.8 1.0 CE1 A:HIS250 4.6 65.0 1.0 CG2 A:VAL144 4.8 42.2 1.0 CG A:GLU249 4.8 57.7 1.0 OE2 A:GLU249 4.9 65.3 1.0 C A:SER145 4.9 45.7 1.0 CB A:ALA146 4.9 52.5 1.0

Iodine binding site 6 out of 13 in the Crystal Structure of Extragenic Suppressor Protein Suhb From Bartonella Henselae, Via Combined Iodide Sad Molecular Replacement


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 Extragenic Suppressor Protein Suhb From Bartonella Henselae, Via Combined Iodide Sad Molecular Replacement within 5.0Å range: probe atom residue distance (Å) B Occ A:I270 b:53.2 occ:0.30 O B:HOH296 3.3 45.3 1.0 CG A:MET178 3.4 57.1 1.0 O A:HOH342 3.7 60.4 1.0 CG1 A:ILE184 3.8 42.8 1.0 N A:ILE184 4.0 39.3 1.0 CB B:MET159 4.1 68.4 1.0 CA A:GLY183 4.1 42.1 1.0 O A:MET178 4.2 56.7 1.0 CB A:ILE184 4.4 39.2 1.0 C A:GLY183 4.4 40.0 1.0 CA A:MET178 4.4 55.4 1.0 CB A:MET178 4.5 56.1 1.0 SD A:MET178 4.5 60.0 0.7 O A:SER182 4.6 45.7 1.0 CG2 A:VAL181 4.6 28.6 1.0 CE A:MET178 4.7 57.0 1.0 N A:GLY183 4.8 44.3 1.0 C A:MET178 4.8 56.8 1.0 CA A:ILE184 4.8 38.2 1.0 O A:VAL181 4.9 49.4 1.0 CA B:MET159 4.9 66.7 1.0 C A:SER182 5.0 46.0 1.0

Iodine binding site 7 out of 13 in the Crystal Structure of Extragenic Suppressor Protein Suhb From Bartonella Henselae, Via Combined Iodide Sad Molecular Replacement


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 Extragenic Suppressor Protein Suhb From Bartonella Henselae, Via Combined Iodide Sad Molecular Replacement within 5.0Å range: probe atom residue distance (Å) B Occ A:I271 b:64.0 occ:0.44 NH1 A:ARG186 2.9 32.2 0.5 CZ A:ARG186 3.5 39.6 0.5 CG2 A:ILE184 3.9 38.8 1.0 CD2 B:LEU174 3.9 77.4 1.0 CE A:MET178 3.9 57.0 1.0 NH2 A:ARG186 4.1 38.6 0.5 NE A:ARG186 4.2 39.2 0.5 CD2 A:LEU174 4.3 58.0 1.0 CB A:ILE184 4.4 39.2 1.0 CD1 A:LEU174 4.5 54.8 1.0 CB B:ARG186 4.5 43.9 1.0 CG B:ARG186 4.7 49.8 1.0 CG A:LEU174 4.8 58.2 1.0 CD1 B:LEU174 4.9 72.6 1.0 CG B:LEU174 5.0 76.1 1.0

Iodine binding site 8 out of 13 in the Crystal Structure of Extragenic Suppressor Protein Suhb From Bartonella Henselae, Via Combined Iodide Sad Molecular Replacement


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 Extragenic Suppressor Protein Suhb From Bartonella Henselae, Via Combined Iodide Sad Molecular Replacement within 5.0Å range: probe atom residue distance (Å) B Occ A:I272 b:60.2 occ:0.42 I A:IOD267 3.2 45.3 0.6 NH2 A:ARG131 3.3 48.8 1.0 N A:ILE113 3.5 44.5 1.0 O A:HOH336 3.9 66.6 1.0 CA A:LYS112 4.0 48.5 1.0 CB A:ILE113 4.1 41.9 1.0 CG1 A:ILE113 4.1 41.6 1.0 C A:LYS112 4.3 46.4 1.0 CB A:LYS112 4.3 49.3 1.0 CG A:LYS112 4.3 52.3 1.0 CA A:ILE113 4.3 43.1 1.0 O A:HOH298 4.4 66.2 1.0 CZ A:ARG131 4.5 53.5 1.0 O A:ILE113 4.5 43.5 1.0 NH1 A:ARG223 4.5 42.3 1.0 O A:GLY111 4.6 51.3 1.0 O A:HOH338 4.9 68.2 1.0 C A:ILE113 4.9 42.7 1.0

Iodine binding site 9 out of 13 in the Crystal Structure of Extragenic Suppressor Protein Suhb From Bartonella Henselae, Via Combined Iodide Sad Molecular Replacement


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 Extragenic Suppressor Protein Suhb From Bartonella Henselae, Via Combined Iodide Sad Molecular Replacement within 5.0Å range: probe atom residue distance (Å) B Occ B:I265 b:56.4 occ:0.39 CZ B:PHE64 3.6 79.4 1.0 NE B:ARG61 3.8 87.8 1.0 CE2 B:PHE64 3.9 76.5 1.0 CB B:VAL6 3.9 73.3 1.0 CG2 B:VAL6 4.1 72.5 1.0 CG1 B:VAL6 4.1 71.1 1.0 CD2 B:LEU107 4.3 55.3 1.0 CD B:ARG61 4.5 88.1 1.0 NH2 B:ARG61 4.7 87.7 1.0 CZ B:ARG61 4.8 88.7 1.0 CE1 B:PHE64 4.9 82.4 1.0

Iodine binding site 10 out of 13 in the Crystal Structure of Extragenic Suppressor Protein Suhb From Bartonella Henselae, Via Combined Iodide Sad Molecular Replacement


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 Extragenic Suppressor Protein Suhb From Bartonella Henselae, Via Combined Iodide Sad Molecular Replacement within 5.0Å range: probe atom residue distance (Å) B Occ B:I266 b:69.5 occ:0.77 N B:LYS63 3.5 95.8 1.0 CB B:LYS63 3.6 96.8 1.0 CA B:ARG61 3.8 91.3 1.0 C B:ARG61 3.8 92.7 1.0 N B:PRO62 3.9 96.6 1.0 CD B:PRO62 3.9 99.8 1.0 CE1 B:PHE64 4.0 82.4 1.0 CB B:ARG61 4.0 87.4 1.0 CD1 B:PHE64 4.0 82.6 1.0 CA B:LYS63 4.1 95.4 1.0 CD B:ARG61 4.3 88.1 1.0 O B:ARG61 4.3 91.0 1.0 C B:PRO62 4.6 97.4 1.0 N B:PHE64 4.7 87.2 1.0 CA B:PRO62 4.7 98.2 1.0 C B:LYS63 4.8 91.3 1.0 CG B:ARG61 4.8 85.8 1.0 CZ B:PHE64 4.9 79.4 1.0

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 Genomics V. 12 83 2011.
PubMed: 21359836
DOI: 10.1007/S10969-011-9101-7