Iodine in PDB 4s2m: Crystal Structure of Oxa-163 Complexed with Iodide in the Active Site

All present enzymatic activity of Crystal Structure of Oxa-163 Complexed with Iodide in the Active Site:
3.5.2.6;

The structure of Crystal Structure of Oxa-163 Complexed with Iodide in the Active Site, PDB code: 4s2m was solved by V.Stojanoski, L.Hu, T.G.Palzkill, B.Prasad, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	59.80 / 2.87
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	67.630, 68.410, 70.223, 62.20, 68.00, 71.58
R / Rfree (%)	20.1 / 25.6

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of Oxa-163 Complexed with Iodide in the Active Site (pdb code 4s2m). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 20 binding sites of Iodine where determined in the Crystal Structure of Oxa-163 Complexed with Iodide in the Active Site, PDB code: 4s2m:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 20 in the Crystal Structure of Oxa-163 Complexed with Iodide in the Active Site


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 Oxa-163 Complexed with Iodide in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:I301 b:57.1 occ:1.00 NE1 A:TRP157 3.6 36.1 1.0 CG A:LYS73 4.1 42.1 1.0 O A:HOH403 4.1 38.7 1.0 CG2 A:VAL120 4.1 36.3 1.0 CD2 A:TYR123 4.2 46.9 1.0 CA A:SER70 4.3 33.0 1.0 CB A:TYR123 4.4 41.8 1.0 CA A:VAL120 4.4 34.8 1.0 CE A:LYS73 4.4 50.8 1.0 CD1 A:TRP157 4.4 37.2 1.0 CE2 A:TRP157 4.5 36.0 1.0 CG A:TYR123 4.5 43.2 1.0 CG1 A:VAL120 4.6 36.0 1.0 CB A:VAL120 4.6 35.7 1.0 CD A:LYS73 4.7 45.9 1.0 OG A:SER118 4.7 42.4 1.0 O A:ALA69 4.7 33.7 1.0 O A:SER70 4.7 34.9 1.0 CZ2 A:TRP157 4.8 36.8 1.0 CB A:SER70 5.0 34.1 1.0 C A:SER70 5.0 31.7 1.0

Iodine binding site 2 out of 20 in the Crystal Structure of Oxa-163 Complexed with Iodide in the Active Site


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 Oxa-163 Complexed with Iodide in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:I302 b:55.0 occ:1.00 NH1 A:ARG206 3.3 22.3 1.0 NH1 D:ARG206 3.3 34.7 1.0 NH2 A:ARG206 3.6 23.5 1.0 NH2 D:ARG206 3.8 33.2 1.0 CZ A:ARG206 3.9 22.9 1.0 CZ D:ARG206 4.0 34.9 1.0 CA D:GLN193 4.2 28.9 1.0 CA A:GLN193 4.2 31.5 1.0 CG D:GLN193 4.4 29.1 1.0 CB D:GLN193 4.5 29.2 1.0 CG A:GLN193 4.5 34.3 1.0 CB A:GLN193 4.5 33.3 1.0 CD2 D:LEU196 4.6 37.6 1.0 CD2 A:LEU196 4.7 33.5 1.0 O D:GLN193 4.8 27.5 1.0 O A:GLN193 4.9 31.3 1.0 CD D:GLN193 5.0 31.0 1.0

Iodine binding site 3 out of 20 in the Crystal Structure of Oxa-163 Complexed with Iodide in the Active Site


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 Oxa-163 Complexed with Iodide in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:I303 b:48.2 occ:1.00 CA A:ARG186 3.6 34.8 1.0 CB A:ARG186 3.7 34.9 1.0 CA D:ARG186 3.8 33.3 1.0 CB D:ARG186 3.9 33.2 1.0 CD D:ARG189 4.0 42.9 1.0 CD A:ARG189 4.0 38.7 1.0 N A:ARG186 4.1 36.4 1.0 CG A:ARG186 4.1 33.5 1.0 N D:ARG186 4.3 35.8 1.0 CG D:ARG186 4.4 32.7 1.0 NE D:ARG189 4.4 43.9 1.0 NE A:ARG189 4.5 39.6 1.0 CD A:ARG186 4.6 33.8 1.0 OE1 D:GLU185 4.6 46.4 1.0 CG A:ARG189 4.8 37.5 1.0 CG D:GLU185 4.8 42.6 1.0 CG A:GLU185 4.8 38.6 1.0 CG D:ARG189 4.8 41.6 1.0 C A:GLU185 4.8 37.2 1.0 CD D:ARG186 4.8 34.0 1.0 C A:ARG186 4.9 34.9 1.0 CB A:ARG189 4.9 36.2 1.0 C D:GLU185 5.0 39.1 1.0

Iodine binding site 4 out of 20 in the Crystal Structure of Oxa-163 Complexed with Iodide in the Active Site


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 Oxa-163 Complexed with Iodide in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:I304 b:0.5 occ:1.00 CD A:LYS51 3.2 70.8 1.0 ND2 A:ASN48 3.3 32.7 1.0 NZ A:LYS51 3.4 73.2 1.0 CE A:LYS51 3.5 76.2 1.0 CZ A:PHE55 3.8 47.5 1.0 CE1 A:PHE55 4.2 45.4 1.0 CH2 A:TRP233 4.2 34.7 1.0 CG A:ASN48 4.3 32.8 1.0 CG A:LYS51 4.4 63.4 1.0 CB A:ASN48 4.5 32.5 1.0 CB A:LYS51 4.5 55.4 1.0 CZ2 A:TRP233 4.6 33.1 1.0 CE2 A:PHE55 4.8 48.0 1.0

Iodine binding site 5 out of 20 in the Crystal Structure of Oxa-163 Complexed with Iodide in the Active Site


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 Oxa-163 Complexed with Iodide in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:I305 b:97.2 occ:1.00 OD1 A:ASN32 3.6 56.6 1.0 N A:GLY42 3.9 50.5 1.0 CG A:ASN32 4.0 53.1 1.0 O A:GLY42 4.0 44.2 1.0 CA A:GLN41 4.0 61.6 1.0 CB A:PHE35 4.1 57.5 1.0 CG A:GLN41 4.2 70.7 1.0 CB A:ASN32 4.3 51.8 1.0 CG A:PHE35 4.3 53.8 1.0 O A:SER40 4.4 66.7 1.0 CD2 A:PHE35 4.4 52.2 1.0 ND2 A:ASN57 4.4 53.7 1.0 CB A:GLN41 4.4 64.2 1.0 C A:GLN41 4.5 56.8 1.0 CA A:ASN32 4.5 50.4 1.0 O A:ASN32 4.6 49.0 1.0 OE1 A:GLN41 4.7 76.1 1.0 ND2 A:ASN32 4.8 54.0 1.0 C A:GLY42 4.9 47.3 1.0 CA A:GLY42 5.0 50.0 1.0 CD A:GLN41 5.0 75.5 1.0

Iodine binding site 6 out of 20 in the Crystal Structure of Oxa-163 Complexed with Iodide in the Active Site


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 Oxa-163 Complexed with Iodide in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:I306 b:73.3 occ:1.00 N A:LEU67 3.7 38.9 1.0 CD1 A:PHE66 4.0 40.1 1.0 CA A:PHE66 4.1 38.3 1.0 CG A:LEU67 4.1 43.4 1.0 CG1 A:ILE219 4.2 69.7 1.0 CB A:PHE66 4.3 36.8 1.0 NE A:ARG163 4.3 50.4 1.0 CD1 A:LEU67 4.3 43.5 1.0 C A:PHE66 4.4 38.5 1.0 CB A:LEU67 4.4 41.7 1.0 CD1 A:ILE219 4.5 67.8 1.0 CZ A:ARG163 4.6 48.4 1.0 CA A:LEU67 4.6 40.4 1.0 CG A:PHE66 4.6 37.8 1.0 CD A:ARG163 4.6 48.1 1.0 NH2 A:ARG163 4.8 49.8 1.0 CE1 A:PHE66 5.0 41.8 1.0

Iodine binding site 7 out of 20 in the Crystal Structure of Oxa-163 Complexed with Iodide in the Active Site


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 Oxa-163 Complexed with Iodide in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:I307 b:71.0 occ:1.00 CE A:LYS180 3.3 55.3 1.0 CG A:LYS180 3.8 52.7 1.0 CD2 A:HIS178 3.9 40.5 1.0 NH2 A:ARG174 4.0 35.9 1.0 CD A:LYS180 4.2 55.6 1.0 N A:LYS175 4.2 32.8 1.0 CA A:LYS175 4.2 34.6 1.0 C A:ARG174 4.2 33.6 1.0 CZ A:ARG174 4.3 35.6 1.0 O A:ARG174 4.3 34.4 1.0 CB A:ARG174 4.3 34.1 1.0 NH1 A:ARG174 4.3 37.4 1.0 CG A:LYS175 4.4 38.6 1.0 NZ A:LYS180 4.5 57.4 1.0 CG A:HIS178 4.6 40.1 1.0 CB A:HIS178 4.8 39.2 1.0 NE2 A:HIS178 4.8 41.6 1.0 CB A:LYS175 4.9 37.1 1.0 CA A:ARG174 4.9 33.3 1.0

Iodine binding site 8 out of 20 in the Crystal Structure of Oxa-163 Complexed with Iodide in the Active Site


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 Oxa-163 Complexed with Iodide in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ B:I301 b:57.3 occ:1.00 NH1 C:ARG206 3.3 24.9 1.0 NH1 B:ARG206 3.3 39.3 1.0 NH2 C:ARG206 3.6 25.9 1.0 NH2 B:ARG206 3.7 41.7 1.0 CZ C:ARG206 3.9 25.0 1.0 CZ B:ARG206 4.0 40.1 1.0 CA B:GLN193 4.2 29.4 1.0 CA C:GLN193 4.3 32.9 1.0 CG C:GLN193 4.4 35.0 1.0 CG B:GLN193 4.4 33.3 1.0 CB B:GLN193 4.5 30.4 1.0 CB C:GLN193 4.5 33.5 1.0 CD2 B:LEU196 4.6 31.6 1.0 CD2 C:LEU196 4.7 27.8 1.0 O B:GLN193 4.9 26.7 1.0 O C:GLN193 4.9 31.3 1.0

Iodine binding site 9 out of 20 in the Crystal Structure of Oxa-163 Complexed with Iodide in the Active Site


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 Oxa-163 Complexed with Iodide in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ B:I302 b:48.4 occ:1.00 O B:HOH402 3.5 27.1 1.0 NE1 B:TRP157 3.6 46.2 1.0 CG B:LYS73 3.8 52.3 1.0 CD B:LYS73 4.0 57.4 1.0 CD2 B:TYR123 4.0 56.6 1.0 CB B:TYR123 4.2 47.6 1.0 CG2 B:VAL120 4.2 44.5 1.0 CG B:TYR123 4.3 51.1 1.0 CA B:VAL120 4.4 42.1 1.0 CD1 B:TRP157 4.4 47.5 1.0 CE2 B:TRP157 4.5 47.1 1.0 CA B:SER70 4.5 45.5 1.0 CB B:VAL120 4.7 45.1 1.0 O B:SER70 4.7 41.7 1.0 O B:ALA69 4.7 49.4 1.0 CG1 B:VAL120 4.7 45.8 1.0 CZ2 B:TRP157 4.7 48.5 1.0 CE2 B:TYR123 4.8 55.5 1.0 OG B:SER118 4.9 50.3 1.0 N B:VAL120 5.0 41.3 1.0

Iodine binding site 10 out of 20 in the Crystal Structure of Oxa-163 Complexed with Iodide in the Active Site


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 Oxa-163 Complexed with Iodide in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ B:I303 b:0.9 occ:1.00 N B:LEU67 3.6 52.1 1.0 CG B:LEU67 3.8 52.3 1.0 CD1 B:LEU67 3.9 52.4 1.0 CB B:LEU67 4.1 52.3 1.0 CG1 B:ILE219 4.1 87.3 1.0 NE B:ARG163 4.2 51.5 1.0 CA B:PHE66 4.2 56.0 1.0 CD1 B:PHE66 4.3 60.4 1.0 CD1 B:ILE219 4.3 92.0 1.0 C B:PHE66 4.4 52.4 1.0 CB B:PHE66 4.4 55.2 1.0 CZ B:ARG163 4.4 53.2 1.0 CA B:LEU67 4.4 53.1 1.0 NH2 B:ARG163 4.6 55.9 1.0 CD B:ARG163 4.6 51.5 1.0 CG B:PHE66 4.8 59.2 1.0

V.Stojanoski, D.C.Chow, B.Fryszczyn, L.Hu, P.Nordmann, L.Poirel, B.Sankaran, B.V.Prasad, T.Palzkill. Structural Basis For Different Substrate Profiles of Two Closely Related Class D Beta-Lactamases and Their Inhibition By Halogens. Biochemistry V. 54 3370 2015.
ISSN: ISSN 0006-2960
PubMed: 25938261
DOI: 10.1021/ACS.BIOCHEM.5B00298