Iodine in PDB 8dc1: Structural and Biochemical Characterization of L. Interrogans LSA45 Reveals A Penicillin-Binding Protein with Esterase Activity

The structure of Structural and Biochemical Characterization of L. Interrogans LSA45 Reveals A Penicillin-Binding Protein with Esterase Activity, PDB code: 8dc1 was solved by J.C.Santos, A.L.T.O.Nascimento, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.17 / 1.62
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	44.141, 74.862, 113.47, 90, 90, 90
R / Rfree (%)	18.5 / 21.1

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Iodine atom in the Structural and Biochemical Characterization of L. Interrogans LSA45 Reveals A Penicillin-Binding Protein with Esterase Activity (pdb code 8dc1). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 15 binding sites of Iodine where determined in the Structural and Biochemical Characterization of L. Interrogans LSA45 Reveals A Penicillin-Binding Protein with Esterase Activity, PDB code: 8dc1:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 15 in the Structural and Biochemical Characterization of L. Interrogans LSA45 Reveals A Penicillin-Binding Protein with Esterase Activity


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Structural and Biochemical Characterization of L. Interrogans LSA45 Reveals A Penicillin-Binding Protein with Esterase Activity within 5.0Å range: probe atom residue distance (Å) B Occ A:I402 b:63.1 occ:1.00 CB A:ASN360 3.6 36.1 1.0 CD2 A:LEU363 3.7 20.7 1.0 CA A:ASN360 3.8 25.2 1.0 O A:HOH658 3.9 36.5 1.0 CG1 A:ILE359 4.0 25.7 1.0 N A:ASN360 4.0 26.9 1.0 CE A:MET329 4.1 22.7 1.0 O A:HOH540 4.2 33.7 1.0 O A:HOH648 4.3 37.0 1.0 CD1 A:ILE359 4.3 23.4 1.0 C A:ILE359 4.6 26.4 1.0 CE1 A:PHE337 4.7 18.8 1.0 CB A:LEU363 4.8 19.3 1.0 ND2 A:ASN331 4.8 20.5 1.0 SD A:MET329 4.9 16.3 1.0 CG A:LEU363 4.9 19.1 1.0 CZ A:PHE337 4.9 21.7 1.0 O A:ILE359 4.9 22.5 1.0 CG A:ASN360 5.0 54.2 1.0

Iodine binding site 2 out of 15 in the Structural and Biochemical Characterization of L. Interrogans LSA45 Reveals A Penicillin-Binding Protein with Esterase Activity


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Structural and Biochemical Characterization of L. Interrogans LSA45 Reveals A Penicillin-Binding Protein with Esterase Activity within 5.0Å range: probe atom residue distance (Å) B Occ A:I403 b:64.6 occ:1.00 O A:GLU242 3.8 25.2 1.0 O A:HOH663 3.9 22.8 1.0 CB A:GLU242 4.4 14.3 1.0 C A:GLU242 4.6 16.0 1.0 OH A:TYR254 4.7 13.1 1.0 OE2 A:GLU242 4.8 18.4 1.0 CA A:GLU242 4.9 13.8 1.0

Iodine binding site 3 out of 15 in the Structural and Biochemical Characterization of L. Interrogans LSA45 Reveals A Penicillin-Binding Protein with Esterase Activity


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Structural and Biochemical Characterization of L. Interrogans LSA45 Reveals A Penicillin-Binding Protein with Esterase Activity within 5.0Å range: probe atom residue distance (Å) B Occ A:I404 b:31.3 occ:1.00 NH2 A:ARG193 3.6 23.6 1.0 O A:HOH533 3.6 16.5 1.0 OG A:SER122 3.9 13.6 1.0 CB A:PHE268 4.0 9.8 1.0 O A:HOH635 4.0 28.4 1.0 NH1 A:ARG193 4.2 20.0 1.0 ND2 A:ASN219 4.2 14.6 1.0 NZ A:LYS333 4.2 47.9 1.0 CE A:LYS333 4.2 49.3 1.0 NZ A:LYS125 4.3 10.0 1.0 CZ A:ARG193 4.3 19.1 1.0 O A:GLY267 4.4 9.7 1.0 CD1 A:PHE268 4.5 12.1 1.0 OD1 A:ASN219 4.5 11.8 1.0 CG A:PHE268 4.5 11.8 1.0 CD A:LYS333 4.5 38.5 1.0 N A:SER122 4.5 10.8 1.0 CB A:TYR121 4.6 14.8 1.0 CG A:ASN219 4.8 11.4 1.0 C A:TYR121 4.9 12.7 1.0 CA A:TYR121 4.9 13.0 1.0 CG A:LYS333 4.9 25.9 1.0 O A:HOH706 5.0 23.0 1.0

Iodine binding site 4 out of 15 in the Structural and Biochemical Characterization of L. Interrogans LSA45 Reveals A Penicillin-Binding Protein with Esterase Activity


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Structural and Biochemical Characterization of L. Interrogans LSA45 Reveals A Penicillin-Binding Protein with Esterase Activity within 5.0Å range: probe atom residue distance (Å) B Occ A:I405 b:70.0 occ:1.00 N A:LYS291 3.3 32.0 1.0 CG A:LYS291 3.6 46.3 1.0 CA A:LYS291 3.8 37.7 1.0 CG2 A:ILE282 4.0 16.9 1.0 CB A:LYS291 4.3 31.1 1.0 C A:TYR290 4.3 22.7 1.0 CD1 A:TYR290 4.4 20.6 1.0 CA A:TYR290 4.5 19.5 1.0 CE1 A:TYR290 4.5 21.2 1.0 NZ A:LYS291 4.7 45.7 1.0 ND2 A:ASN286 4.8 20.5 1.0 CG A:TYR290 4.8 18.8 1.0 CD A:LYS291 4.8 51.4 1.0

Iodine binding site 5 out of 15 in the Structural and Biochemical Characterization of L. Interrogans LSA45 Reveals A Penicillin-Binding Protein with Esterase Activity


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Structural and Biochemical Characterization of L. Interrogans LSA45 Reveals A Penicillin-Binding Protein with Esterase Activity within 5.0Å range: probe atom residue distance (Å) B Occ A:I406 b:28.8 occ:1.00 O A:HOH621 3.2 26.5 1.0 CD1 A:TYR121 4.0 20.0 1.0 CE1 A:TYR121 4.0 19.2 1.0 O A:HOH610 4.0 16.5 1.0 N A:GLY269 4.0 11.1 1.0 CD2 A:PHE268 4.0 11.7 1.0 CA A:GLY269 4.2 11.2 1.0 CB A:PHE268 4.3 9.8 1.0 NH1 A:ARG193 4.6 20.0 1.0 CG A:PHE268 4.6 11.8 1.0 C A:PHE268 4.9 11.7 1.0 CE2 A:PHE268 5.0 15.8 1.0

Iodine binding site 6 out of 15 in the Structural and Biochemical Characterization of L. Interrogans LSA45 Reveals A Penicillin-Binding Protein with Esterase Activity


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Structural and Biochemical Characterization of L. Interrogans LSA45 Reveals A Penicillin-Binding Protein with Esterase Activity within 5.0Å range: probe atom residue distance (Å) B Occ A:I407 b:32.1 occ:1.00 O A:HOH579 3.5 24.1 1.0 ND2 A:ASN286 3.6 20.5 1.0 CA A:GLY101 3.7 23.1 1.0 N A:GLY101 4.0 21.6 1.0 NH2 A:ARG345 4.2 44.6 1.0 CG2 A:ILE282 4.3 16.9 1.0 CD2 A:LEU98 4.4 25.4 1.0 CD2 A:LEU285 4.4 15.2 1.0 CG1 A:ILE282 4.5 17.7 1.0 CG A:ASN286 4.5 22.1 1.0 OD1 A:ASN286 4.6 29.5 1.0 C A:ASP100 4.9 23.5 1.0 CB A:ILE282 5.0 16.0 1.0 CD1 A:ILE282 5.0 21.2 1.0

Iodine binding site 7 out of 15 in the Structural and Biochemical Characterization of L. Interrogans LSA45 Reveals A Penicillin-Binding Protein with Esterase Activity


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Structural and Biochemical Characterization of L. Interrogans LSA45 Reveals A Penicillin-Binding Protein with Esterase Activity within 5.0Å range: probe atom residue distance (Å) B Occ A:I408 b:26.4 occ:1.00 O A:HOH501 3.5 21.1 1.0 N A:LEU237 3.6 10.4 1.0 N A:GLN264 3.8 10.1 1.0 O A:GLN264 3.9 12.3 1.0 CG A:LEU237 3.9 11.6 1.0 CB A:THR236 3.9 16.3 1.0 CA A:THR236 3.9 13.0 1.0 CB A:ARG263 4.0 12.9 1.0 CA A:ARG263 4.0 14.7 1.0 CD1 A:LEU237 4.1 11.8 1.0 CG A:ARG263 4.1 20.5 1.0 CB A:LEU237 4.2 9.8 1.0 C A:THR236 4.3 11.4 1.0 C A:ARG263 4.4 10.1 1.0 OE1 A:GLU230 4.4 32.5 1.0 CG2 A:THR236 4.4 18.3 1.0 CD A:ARG263 4.4 21.1 1.0 OE1 A:GLN264 4.5 11.8 1.0 NE2 A:GLN223 4.5 10.7 1.0 CA A:LEU237 4.5 11.4 1.0 CA A:GLN264 4.6 10.0 1.0 C A:GLN264 4.7 12.4 1.0 CB A:ALA226 4.7 9.2 1.0 CB A:GLN264 4.8 11.1 1.0 NE A:ARG263 4.9 28.6 1.0 CB A:GLU230 4.9 12.5 1.0 O A:ALA226 5.0 10.1 1.0

Iodine binding site 8 out of 15 in the Structural and Biochemical Characterization of L. Interrogans LSA45 Reveals A Penicillin-Binding Protein with Esterase Activity


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Structural and Biochemical Characterization of L. Interrogans LSA45 Reveals A Penicillin-Binding Protein with Esterase Activity within 5.0Å range: probe atom residue distance (Å) B Occ A:I409 b:44.0 occ:1.00 O A:ARG189 3.2 16.4 1.0 ND2 A:ASN219 3.3 14.6 1.0 NE1 A:TRP183 3.4 12.8 1.0 OE2 A:GLU190 3.8 31.7 1.0 C A:ARG189 3.8 14.2 1.0 O A:HOH647 3.9 14.2 1.0 CB A:ARG189 4.1 15.4 1.0 NH2 A:ARG193 4.1 23.6 1.0 CG2 A:ILE192 4.2 12.0 1.0 CE2 A:TRP183 4.2 12.5 1.0 CD A:GLU190 4.2 32.2 1.0 CG A:ARG189 4.2 19.0 1.0 CG A:ASN219 4.3 11.4 1.0 CB A:ASN219 4.3 10.0 1.0 CZ2 A:TRP183 4.3 14.2 1.0 N A:GLU190 4.3 15.7 1.0 CA A:GLU190 4.4 17.5 1.0 OE1 A:GLU190 4.4 29.0 1.0 CD1 A:TRP183 4.4 11.9 1.0 NE A:ARG193 4.5 18.4 1.0 CA A:ARG189 4.5 13.8 1.0 CD A:ARG189 4.6 24.6 1.0 CZ A:ARG193 4.7 19.1 1.0 O A:HOH706 4.8 23.0 1.0

Iodine binding site 9 out of 15 in the Structural and Biochemical Characterization of L. Interrogans LSA45 Reveals A Penicillin-Binding Protein with Esterase Activity


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Structural and Biochemical Characterization of L. Interrogans LSA45 Reveals A Penicillin-Binding Protein with Esterase Activity within 5.0Å range: probe atom residue distance (Å) B Occ A:I410 b:38.5 occ:1.00 O A:HOH701 2.8 30.3 1.0 O A:HOH634 3.6 24.5 1.0 N A:ASP197 3.7 15.0 1.0 O A:ASP197 4.0 14.7 1.0 CG1 A:VAL200 4.1 15.6 1.0 CB A:VAL200 4.1 13.9 1.0 CB A:ASP197 4.1 14.7 1.0 CB A:GLU196 4.2 21.7 1.0 N A:GLU196 4.2 17.7 1.0 CB A:ALA195 4.2 19.6 1.0 CA A:ASP197 4.3 14.6 1.0 CD1 A:ILE201 4.5 14.6 1.0 CA A:GLU196 4.5 19.0 1.0 C A:ASP197 4.6 13.8 1.0 CG2 A:VAL200 4.6 15.9 1.0 C A:GLU196 4.6 17.9 1.0 C A:ALA195 4.9 16.5 1.0 CG1 A:ILE201 5.0 13.7 1.0

Iodine binding site 10 out of 15 in the Structural and Biochemical Characterization of L. Interrogans LSA45 Reveals A Penicillin-Binding Protein with Esterase Activity


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Structural and Biochemical Characterization of L. Interrogans LSA45 Reveals A Penicillin-Binding Protein with Esterase Activity within 5.0Å range: probe atom residue distance (Å) B Occ A:I411 b:50.4 occ:1.00 NE A:ARG93 3.6 31.2 1.0 CB A:ALA109 3.8 38.4 1.0 CD A:ARG93 3.9 28.6 1.0 CA A:GLU91 3.9 30.3 1.0 CB A:GLU91 4.0 32.5 1.0 C A:GLU91 4.0 26.5 1.0 CG A:ARG93 4.2 23.9 1.0 N A:VAL92 4.3 26.6 1.0 O A:VAL92 4.4 24.6 1.0 O A:GLU91 4.5 28.9 1.0 C A:VAL92 4.5 24.7 1.0 N A:ARG93 4.6 20.2 1.0 CA A:ARG93 4.7 20.7 1.0 CZ A:ARG93 4.7 28.3 1.0 CG A:GLU91 4.7 63.4 1.0 NH2 A:ARG93 5.0 34.8 1.0

J.C.Santos, S.Handa, L.G.V.Fernandes, L.Bleicher, C.A.Gandin, M.De Oliveira-Neto, P.Ghosh, A.L.T.O.Nascimento. Structural and Biochemical Characterization of Leptospira Interrogans LSA45 Reveals A Penicillin-Binding Protein with Esterase Activity Process Biochem V. 125 141 2023.
ISSN: ESSN 1873-3298
DOI: 10.1016/J.PROCBIO.2022.12.010