Iodine in PDB 8a56: Coenzyme A-Persulfide Reductase (Coapr) From Enterococcus Faecalis

The structure of Coenzyme A-Persulfide Reductase (Coapr) From Enterococcus Faecalis, PDB code: 8a56 was solved by S.S.Costa, B.J.Walsh, D.P.Giedroc, J.A.Brito, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.25 / 2.05
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	139.797, 194.809, 91.46, 90, 90, 90
R / Rfree (%)	18.6 / 23.4

The binding sites of Iodine atom in the Coenzyme A-Persulfide Reductase (Coapr) From Enterococcus Faecalis (pdb code 8a56). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 6 binding sites of Iodine where determined in the Coenzyme A-Persulfide Reductase (Coapr) From Enterococcus Faecalis, PDB code: 8a56:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6;

Iodine binding site 1 out of 6 in the Coenzyme A-Persulfide Reductase (Coapr) From Enterococcus Faecalis


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Coenzyme A-Persulfide Reductase (Coapr) From Enterococcus Faecalis within 5.0Å range: probe atom residue distance (Å) B Occ A:I603 b:60.3 occ:0.59 HG22 A:ILE390 3.1 37.8 1.0 HD11 A:LEU332 3.3 44.4 1.0 HG2 A:GLN372 3.3 48.2 1.0 HE21 A:GLN372 3.4 63.7 1.0 HA2 A:GLY391 3.4 33.2 1.0 HB2 A:ASP370 3.7 48.6 1.0 O A:HOH730 3.7 30.4 1.0 HG3 A:GLN372 3.8 48.2 1.0 O A:HOH712 3.9 46.9 1.0 CG A:GLN372 4.0 39.9 1.0 CG2 A:ILE390 4.0 31.2 1.0 HB3 A:ASP370 4.2 48.6 1.0 CD1 A:LEU332 4.2 36.7 1.0 HD1 A:PHE194 4.2 36.1 1.0 NE2 A:GLN372 4.2 52.8 1.0 HD21 A:LEU332 4.3 60.2 1.0 CA A:GLY391 4.3 27.4 1.0 HG21 A:ILE390 4.3 37.8 1.0 O A:ASP370 4.3 31.7 1.0 CB A:ASP370 4.4 40.2 1.0 HD12 A:LEU332 4.4 44.4 1.0 O A:ILE390 4.4 31.7 1.0 HG23 A:ILE390 4.4 37.8 1.0 CD1 A:PHE194 4.5 29.8 1.0 HB3 A:PHE194 4.6 40.0 1.0 C A:ILE390 4.6 29.0 1.0 N A:GLY391 4.6 28.6 1.0 CD A:GLN372 4.6 49.9 1.0 HD13 A:LEU332 4.7 44.4 1.0 C A:ASP370 4.7 33.9 1.0 HA3 A:GLY391 4.7 33.2 1.0 HB A:ILE390 4.7 38.3 1.0 HE1 A:PHE194 4.8 35.8 1.0 HE22 A:GLN372 4.9 63.7 1.0 CE1 A:PHE194 4.9 29.6 1.0 H A:GLN372 4.9 33.1 1.0 H A:ALA392 4.9 35.0 1.0 HA A:LEU371 4.9 36.3 1.0 CB A:ILE390 5.0 31.7 1.0

Iodine binding site 2 out of 6 in the Coenzyme A-Persulfide Reductase (Coapr) From Enterococcus Faecalis


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Coenzyme A-Persulfide Reductase (Coapr) From Enterococcus Faecalis within 5.0Å range: probe atom residue distance (Å) B Occ A:I604 b:67.5 occ:0.51 HE A:ARG69 2.5 62.4 1.0 HH21 A:ARG69 2.8 67.8 1.0 HB2 A:ARG69 3.0 48.0 1.0 HB3 B:ASN489 3.1 78.2 1.0 HH12 B:ARG513 3.3 82.1 1.0 NE A:ARG69 3.4 51.7 1.0 HD23 B:LEU488 3.4 51.7 1.0 O B:HOH728 3.5 30.8 1.0 HA B:ASN489 3.5 60.8 1.0 NH2 A:ARG69 3.5 56.2 1.0 HB3 B:LEU488 3.6 47.7 1.0 HG B:LEU488 3.8 53.0 1.0 H B:ASN489 3.8 60.6 1.0 HA A:ARG69 3.9 53.9 1.0 CB B:ASN489 3.9 64.9 1.0 CB A:ARG69 3.9 39.7 1.0 N B:ASN489 3.9 50.3 1.0 NH1 B:ARG513 3.9 68.1 1.0 HH11 B:ARG513 3.9 82.1 1.0 CA B:ASN489 3.9 50.4 1.0 CZ A:ARG69 3.9 56.9 1.0 HG3 A:ARG69 4.1 55.0 1.0 CD2 B:LEU488 4.2 42.8 1.0 HH22 A:ARG69 4.3 67.8 1.0 CA A:ARG69 4.3 44.6 1.0 CG B:LEU488 4.3 43.9 1.0 HB3 A:ALA68 4.3 45.9 1.0 HB2 B:ASN489 4.3 78.2 1.0 CG A:ARG69 4.4 45.5 1.0 CB B:LEU488 4.4 39.5 1.0 CD A:ARG69 4.4 44.7 1.0 N A:ARG69 4.5 47.8 1.0 C B:LEU488 4.5 40.5 1.0 HB1 A:ALA68 4.5 45.9 1.0 HD21 B:LEU488 4.6 51.7 1.0 HB3 A:ARG69 4.6 48.0 1.0 H A:ARG69 4.6 57.7 1.0 HD21 B:ASN471 4.6 106.0 1.0 HB1 A:ALA65 4.7 82.2 1.0 HD22 B:ASN489 4.8 94.4 1.0 CB A:ALA68 4.9 37.9 1.0 O A:ALA65 4.9 52.0 1.0 HD22 B:LEU488 4.9 51.7 1.0 HD2 A:ARG69 5.0 54.0 1.0 C A:ALA68 5.0 43.3 1.0 CG B:ASN489 5.0 77.5 1.0

Iodine binding site 3 out of 6 in the Coenzyme A-Persulfide Reductase (Coapr) From Enterococcus Faecalis


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Coenzyme A-Persulfide Reductase (Coapr) From Enterococcus Faecalis within 5.0Å range: probe atom residue distance (Å) B Occ A:I606 b:113.1 occ:1.00 HA A:SER238 3.0 48.9 1.0 H A:GLY240 3.1 39.0 1.0 HB2 A:SER238 3.3 45.5 1.0 HD12 A:ILE159 3.6 44.5 1.0 HG13 A:VAL241 3.6 44.7 1.0 CA A:SER238 3.6 40.5 1.0 HB A:ILE159 3.8 51.2 1.0 CB A:SER238 3.8 37.7 1.0 HA2 A:GLY240 3.8 37.5 1.0 HG21 A:ILE159 3.9 45.8 1.0 N A:GLY240 3.9 32.2 1.0 C A:SER238 3.9 35.0 1.0 HB3 A:SER238 4.0 45.5 1.0 HG12 A:VAL241 4.2 44.7 1.0 CA A:GLY240 4.2 30.9 1.0 CG1 A:VAL241 4.3 37.0 1.0 HG22 A:ILE159 4.3 45.8 1.0 N A:VAL239 4.3 37.0 1.0 HE A:ARG132 4.3 48.7 1.0 H A:VAL239 4.3 44.8 1.0 O A:SER238 4.3 37.8 1.0 CG2 A:ILE159 4.4 37.9 1.0 C A:GLY240 4.4 38.0 1.0 CD1 A:ILE159 4.4 36.8 1.0 O A:GLY240 4.4 39.1 1.0 HG11 A:VAL241 4.5 44.7 1.0 CB A:ILE159 4.5 42.4 1.0 HD13 A:ILE159 4.5 44.5 1.0 O A:HOH773 4.5 32.2 1.0 HD2 A:ARG132 4.7 55.3 1.0 O A:LEU237 4.8 34.4 1.0 N A:SER238 5.0 46.8 1.0 C A:VAL239 5.0 30.0 1.0

Iodine binding site 4 out of 6 in the Coenzyme A-Persulfide Reductase (Coapr) From Enterococcus Faecalis


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Coenzyme A-Persulfide Reductase (Coapr) From Enterococcus Faecalis within 5.0Å range: probe atom residue distance (Å) B Occ B:I604 b:53.2 occ:0.59 HE21 B:GLN372 2.5 70.4 1.0 HG2 B:GLN372 3.0 52.9 1.0 HG22 B:ILE390 3.4 40.4 1.0 NE2 B:GLN372 3.4 58.4 1.0 HA2 B:GLY391 3.4 28.7 1.0 O B:HOH705 3.5 28.2 1.0 HG3 B:GLN372 3.5 52.9 1.0 HD11 B:LEU332 3.5 49.5 1.0 HB2 B:ASP370 3.6 47.5 1.0 CG B:GLN372 3.6 43.8 1.0 HE22 B:GLN372 4.0 70.4 1.0 CD B:GLN372 4.0 45.7 1.0 HB3 B:ASP370 4.0 47.5 1.0 O B:ASP370 4.1 29.3 1.0 CB B:ASP370 4.2 39.3 1.0 O B:ILE390 4.3 28.1 1.0 CG2 B:ILE390 4.3 33.4 1.0 CA B:GLY391 4.3 23.6 1.0 CD1 B:LEU332 4.4 41.0 1.0 HD1 B:PHE194 4.4 29.7 1.0 C B:ASP370 4.5 26.5 1.0 HD12 B:LEU332 4.5 49.5 1.0 HG21 B:ILE390 4.6 40.4 1.0 C B:ILE390 4.6 20.3 1.0 N B:GLY391 4.6 26.4 1.0 HB B:ILE390 4.7 30.7 1.0 HA B:LEU371 4.7 34.3 1.0 HA3 B:GLY391 4.7 28.7 1.0 H B:GLN372 4.7 31.2 1.0 CD1 B:PHE194 4.7 24.5 1.0 HD21 B:LEU332 4.8 49.8 1.0 HG23 B:ILE390 4.8 40.4 1.0 H B:ALA392 4.9 33.8 1.0 HD13 B:LEU332 4.9 49.5 1.0 HB3 B:PHE194 4.9 36.1 1.0 N B:LEU371 4.9 30.4 1.0 N B:GLN372 5.0 25.7 1.0 CA B:ASP370 5.0 35.4 1.0 HE1 B:PHE194 5.0 46.4 1.0

Iodine binding site 5 out of 6 in the Coenzyme A-Persulfide Reductase (Coapr) From Enterococcus Faecalis


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Coenzyme A-Persulfide Reductase (Coapr) From Enterococcus Faecalis within 5.0Å range: probe atom residue distance (Å) B Occ B:I605 b:79.7 occ:0.58 HE B:ARG69 2.5 54.3 1.0 HH21 B:ARG69 2.8 61.5 1.0 HB2 B:ARG69 3.0 50.2 1.0 HB3 A:ASN489 3.0 79.5 1.0 HH12 A:ARG513 3.3 79.1 1.0 O A:HOH722 3.3 49.6 1.0 NE B:ARG69 3.4 45.0 1.0 HD23 A:LEU488 3.4 45.8 1.0 HA A:ASN489 3.5 73.5 1.0 NH2 B:ARG69 3.6 51.0 1.0 HB3 A:LEU488 3.6 62.4 1.0 HH11 A:ARG513 3.7 79.1 1.0 NH1 A:ARG513 3.8 65.6 1.0 CB A:ASN489 3.8 65.9 1.0 HG A:LEU488 3.8 64.8 1.0 HA B:ARG69 3.8 48.3 1.0 CB B:ARG69 3.9 41.6 1.0 H A:ASN489 3.9 60.1 1.0 CA A:ASN489 3.9 60.9 1.0 N A:ASN489 3.9 49.8 1.0 CZ B:ARG69 3.9 54.2 1.0 HG3 B:ARG69 4.1 53.2 1.0 CD2 A:LEU488 4.2 37.9 1.0 CA B:ARG69 4.3 40.0 1.0 HB2 A:ASN489 4.3 79.5 1.0 HH22 B:ARG69 4.3 61.5 1.0 CG B:ARG69 4.3 44.1 1.0 CG A:LEU488 4.3 53.7 1.0 HB3 B:ALA68 4.4 57.0 1.0 CB A:LEU488 4.4 51.7 1.0 CD B:ARG69 4.4 42.0 1.0 N B:ARG69 4.5 42.2 1.0 C A:LEU488 4.5 41.2 1.0 H B:ARG69 4.6 51.0 1.0 HB3 B:ARG69 4.6 50.2 1.0 HB1 B:ALA68 4.6 57.0 1.0 HD21 A:LEU488 4.6 45.8 1.0 HD21 A:ASN471 4.7 108.5 1.0 HD22 A:ASN489 4.7 100.5 1.0 HB1 B:ALA65 4.8 80.3 1.0 O B:ALA65 4.9 59.1 1.0 HD2 B:ARG69 4.9 50.7 1.0 CB B:ALA68 4.9 47.2 1.0 CG A:ASN489 4.9 75.7 1.0 HD22 A:LEU488 5.0 45.8 1.0

Iodine binding site 6 out of 6 in the Coenzyme A-Persulfide Reductase (Coapr) From Enterococcus Faecalis


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Coenzyme A-Persulfide Reductase (Coapr) From Enterococcus Faecalis within 5.0Å range: probe atom residue distance (Å) B Occ B:I607 b:118.3 occ:1.00 H B:ALA212 2.9 55.8 1.0 OG B:SER211 3.1 83.0 1.0 HG B:SER211 3.4 99.9 1.0 HG21 B:ILE154 3.6 38.9 1.0 HB3 B:ALA212 3.7 48.1 1.0 HA B:SER211 3.7 57.5 1.0 HG23 B:ILE154 3.8 38.9 1.0 N B:ALA212 3.8 46.2 1.0 HG22 B:ILE154 3.8 38.9 1.0 HG11 B:VAL239 3.8 53.5 1.0 HD11 B:ILE119 3.8 69.0 1.0 HB2 B:LYS179 3.9 70.0 1.0 CG2 B:ILE154 3.9 32.1 1.0 CB B:SER211 4.1 48.3 1.0 HB2 B:SER211 4.2 58.3 1.0 CA B:SER211 4.3 47.7 1.0 HB3 B:PRO117 4.4 75.9 1.0 HG12 B:VAL239 4.4 53.5 1.0 HB2 B:PRO117 4.4 75.9 1.0 O B:ALA212 4.5 46.0 1.0 CB B:ALA212 4.5 39.8 1.0 CG1 B:VAL239 4.6 44.3 1.0 C B:SER211 4.6 50.6 1.0 HB2 B:ALA212 4.6 48.1 1.0 HD2 B:PRO118 4.6 83.5 1.0 CA B:ALA212 4.6 45.2 1.0 HD2 B:LYS179 4.7 98.7 1.0 CD1 B:ILE119 4.7 57.2 1.0 CB B:LYS179 4.8 58.1 1.0 HG12 B:ILE119 4.9 60.9 1.0 CB B:PRO117 4.9 63.0 1.0 HD13 B:ILE119 4.9 69.0 1.0 HB B:VAL239 4.9 53.4 1.0 HB3 B:SER211 4.9 58.3 1.0

B.J.C.Walsh, S.S.Costa, K.A.Edmonds, J.C.Trinidad, F.M.Issoglio, J.A.Brito, D.P.Giedroc. Metabolic and Structural Insights Into Hydrogen Sulfide Mis-Regulation in Enterococcus Faecalis. Antioxidants V. 11 2022.
ISSN: ESSN 2076-3921
PubMed: 36009332
DOI: 10.3390/ANTIOX11081607