Iodine in PDB 3qd5: Crystal Structure of A Putative Ribose-5-Phosphate Isomerase From Coccidioides Immitis Solved By Combined Iodide Ion Sad and Mr

All present enzymatic activity of Crystal Structure of A Putative Ribose-5-Phosphate Isomerase From Coccidioides Immitis Solved By Combined Iodide Ion Sad and Mr:
5.3.1.6;

The structure of Crystal Structure of A Putative Ribose-5-Phosphate Isomerase From Coccidioides Immitis Solved By Combined Iodide Ion Sad and Mr, PDB code: 3qd5 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)	50.00 / 1.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	103.150, 49.890, 61.970, 90.00, 108.62, 90.00
R / Rfree (%)	16.4 / 20.5

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 29;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of A Putative Ribose-5-Phosphate Isomerase From Coccidioides Immitis Solved By Combined Iodide Ion Sad and Mr (pdb code 3qd5). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 29 binding sites of Iodine where determined in the Crystal Structure of A Putative Ribose-5-Phosphate Isomerase From Coccidioides Immitis Solved By Combined Iodide Ion Sad and Mr, PDB code: 3qd5:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 29 in the Crystal Structure of A Putative Ribose-5-Phosphate Isomerase From Coccidioides Immitis Solved By Combined Iodide Ion Sad and Mr


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 A Putative Ribose-5-Phosphate Isomerase From Coccidioides Immitis Solved By Combined Iodide Ion Sad and Mr within 5.0Å range: probe atom residue distance (Å) B Occ A:I165 b:35.0 occ:0.26 O A:HOH241 3.1 26.3 1.0 I A:IOD166 3.4 54.1 0.6 OG1 A:THR4 3.7 28.9 1.0 CG A:PRO34 4.0 24.8 1.0 CG A:LEU35 4.0 18.1 1.0 CD A:PRO5 4.2 22.9 1.0 CD2 A:LEU35 4.2 18.5 1.0 O A:HOH248 4.3 38.1 1.0 CD1 A:LEU35 4.4 19.2 1.0 CB A:THR4 4.5 26.3 1.0 CB A:PRO34 4.7 24.0 1.0 CA A:THR4 4.8 26.3 1.0 O A:ALA3 4.9 31.8 1.0 CD A:PRO34 4.9 23.9 1.0

Iodine binding site 2 out of 29 in the Crystal Structure of A Putative Ribose-5-Phosphate Isomerase From Coccidioides Immitis Solved By Combined Iodide Ion Sad and Mr


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 A Putative Ribose-5-Phosphate Isomerase From Coccidioides Immitis Solved By Combined Iodide Ion Sad and Mr within 5.0Å range: probe atom residue distance (Å) B Occ A:I166 b:54.1 occ:0.55 I A:IOD165 3.4 35.0 0.3 CD1 A:LEU35 3.9 19.2 1.0 CD A:PRO5 4.0 22.9 1.0 CD2 A:LEU35 4.1 18.5 1.0 CG A:LEU6 4.2 20.8 1.0 CG A:PRO5 4.2 24.2 1.0 CG A:LEU35 4.4 18.1 1.0 CD1 A:LEU6 4.5 22.7 1.0 CB A:PRO5 4.5 21.6 1.0 CB A:LEU6 4.6 18.0 1.0 N A:LEU6 4.6 17.7 1.0 OG1 A:THR4 4.7 28.9 1.0 O A:HOH215 4.7 14.6 1.0 O A:HOH248 4.8 38.1 1.0 N A:PRO5 4.8 22.6 1.0

Iodine binding site 3 out of 29 in the Crystal Structure of A Putative Ribose-5-Phosphate Isomerase From Coccidioides Immitis Solved By Combined Iodide Ion Sad and Mr


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 A Putative Ribose-5-Phosphate Isomerase From Coccidioides Immitis Solved By Combined Iodide Ion Sad and Mr within 5.0Å range: probe atom residue distance (Å) B Occ A:I167 b:36.7 occ:1.00 I A:IOD168 3.2 41.5 0.3 CB A:ARG138 4.2 10.7 1.0 CG A:ARG138 4.2 9.4 1.0 CD A:PRO7 4.5 16.0 1.0 CD A:ARG138 4.9 10.6 1.0 NH2 A:ARG138 4.9 11.5 1.0 CG A:PRO7 5.0 15.9 1.0

Iodine binding site 4 out of 29 in the Crystal Structure of A Putative Ribose-5-Phosphate Isomerase From Coccidioides Immitis Solved By Combined Iodide Ion Sad and Mr


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 A Putative Ribose-5-Phosphate Isomerase From Coccidioides Immitis Solved By Combined Iodide Ion Sad and Mr within 5.0Å range: probe atom residue distance (Å) B Occ A:I168 b:41.5 occ:0.33 NH2 A:ARG138 3.1 11.5 1.0 I A:IOD167 3.2 36.7 1.0 O A:HOH232 3.7 27.2 1.0 CD A:ARG138 3.9 10.6 1.0 CG A:PRO7 4.2 15.9 1.0 CD A:PRO7 4.3 16.0 1.0 CZ A:ARG138 4.3 11.2 1.0 CB A:PRO7 4.3 15.2 1.0 CG A:ARG138 4.3 9.4 1.0 NE A:ARG138 4.6 11.8 1.0 CB A:ARG138 4.7 10.7 1.0 O A:PRO7 5.0 13.3 1.0

Iodine binding site 5 out of 29 in the Crystal Structure of A Putative Ribose-5-Phosphate Isomerase From Coccidioides Immitis Solved By Combined Iodide Ion Sad and Mr


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 A Putative Ribose-5-Phosphate Isomerase From Coccidioides Immitis Solved By Combined Iodide Ion Sad and Mr within 5.0Å range: probe atom residue distance (Å) B Occ A:I169 b:29.8 occ:0.39 O A:HOH195 2.6 26.2 1.0 OD A:CSO76 2.7 16.6 0.3 OD A:CSO76 2.9 12.3 0.7 N A:GLY81 3.4 13.2 1.0 OG1 A:THR78 3.4 17.6 1.0 SG A:CSO76 3.8 21.4 0.6 CA A:GLY81 3.8 13.3 1.0 OD1 B:ASN110 3.9 17.9 1.0 ND2 B:ASN110 3.9 13.8 1.0 SG A:CSO76 4.1 20.0 0.2 O A:HOH204 4.2 28.3 1.0 CG B:ASN110 4.3 15.1 1.0 CE2 A:TYR53 4.4 22.3 1.0 N A:LEU80 4.5 14.3 1.0 C A:LEU80 4.5 13.1 1.0 CD2 A:TYR53 4.5 22.1 1.0 CB A:LEU80 4.5 14.2 1.0 CZ A:TYR53 4.7 22.9 1.0 CA A:LEU80 4.7 13.4 1.0 CB A:THR78 4.8 17.9 1.0 N A:THR78 4.8 17.9 1.0 CG A:TYR53 4.9 21.6 1.0 CB B:SER109 4.9 13.3 1.0 CB A:CSO76 4.9 19.5 0.3 CB A:CSO76 5.0 19.6 0.3

Iodine binding site 6 out of 29 in the Crystal Structure of A Putative Ribose-5-Phosphate Isomerase From Coccidioides Immitis Solved By Combined Iodide Ion Sad and Mr


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 A Putative Ribose-5-Phosphate Isomerase From Coccidioides Immitis Solved By Combined Iodide Ion Sad and Mr within 5.0Å range: probe atom residue distance (Å) B Occ A:I170 b:34.1 occ:0.60 I A:IOD171 2.3 37.6 0.3 O A:HOH278 3.9 40.1 1.0 CZ B:PHE101 3.9 17.8 1.0 CA A:GLY77 3.9 19.7 1.0 CE2 B:PHE101 4.0 13.6 1.0 CG B:ARG105 4.3 15.1 1.0 CG2 A:THR78 4.3 19.2 1.0 C A:GLY77 4.4 19.6 1.0 O A:HOH204 4.6 28.3 1.0 NE B:ARG105 4.6 26.3 1.0 N A:THR78 4.6 17.9 1.0 CD B:ARG105 4.7 22.2 1.0 N A:GLY77 4.9 20.0 1.0 O A:GLY77 5.0 18.1 1.0

Iodine binding site 7 out of 29 in the Crystal Structure of A Putative Ribose-5-Phosphate Isomerase From Coccidioides Immitis Solved By Combined Iodide Ion Sad and Mr


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 A Putative Ribose-5-Phosphate Isomerase From Coccidioides Immitis Solved By Combined Iodide Ion Sad and Mr within 5.0Å range: probe atom residue distance (Å) B Occ A:I171 b:37.6 occ:0.32 I A:IOD170 2.3 34.1 0.6 O A:HOH278 2.5 40.1 1.0 CA A:GLY77 2.6 19.7 1.0 C A:GLY77 3.3 19.6 1.0 CB A:ARG120 3.4 15.2 1.0 O A:GLY77 3.5 18.1 1.0 N A:GLY77 3.9 20.0 1.0 N A:THR78 4.2 17.9 1.0 CE2 B:PHE101 4.3 13.6 1.0 CB A:ALA18 4.4 28.4 1.0 CZ B:PHE101 4.5 17.8 1.0 O A:HOH204 4.6 28.3 1.0 CA A:ARG120 4.7 13.6 1.0 N A:ARG120 4.7 13.5 1.0 O A:HOH251 4.9 27.7 1.0 CG2 A:THR78 4.9 19.2 1.0 C A:CSO76 4.9 20.4 1.0

Iodine binding site 8 out of 29 in the Crystal Structure of A Putative Ribose-5-Phosphate Isomerase From Coccidioides Immitis Solved By Combined Iodide Ion Sad and Mr


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 A Putative Ribose-5-Phosphate Isomerase From Coccidioides Immitis Solved By Combined Iodide Ion Sad and Mr within 5.0Å range: probe atom residue distance (Å) B Occ A:I172 b:42.1 occ:0.49 CD2 A:TYR22 4.0 18.9 1.0 O A:SER21 4.2 23.4 1.0 CE2 A:TYR22 4.2 17.4 1.0 O A:HOH210 4.3 29.6 1.0 CB A:ALA25 4.4 21.7 1.0 CB A:SER21 4.4 25.4 1.0 CG1 A:ILE124 4.4 13.4 1.0 C A:SER21 4.4 23.9 1.0 O A:HOH277 4.4 17.6 1.0 CB A:ILE124 4.4 13.1 1.0 CD1 A:ILE124 4.6 13.2 1.0 CG2 A:ILE124 4.7 14.7 1.0 N A:TYR22 4.7 22.9 1.0 OG A:SER21 4.8 29.5 1.0 CA A:TYR22 4.8 21.2 1.0

Iodine binding site 9 out of 29 in the Crystal Structure of A Putative Ribose-5-Phosphate Isomerase From Coccidioides Immitis Solved By Combined Iodide Ion Sad and Mr


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 A Putative Ribose-5-Phosphate Isomerase From Coccidioides Immitis Solved By Combined Iodide Ion Sad and Mr within 5.0Å range: probe atom residue distance (Å) B Occ A:I173 b:41.6 occ:0.40 NE2 A:HIS29 3.8 26.9 1.0 O A:HOH244 3.8 26.4 1.0 NH1 A:ARG129 3.9 21.3 0.4 O A:LYS128 4.0 12.0 1.0 CA A:GLY132 4.1 11.7 1.0 CA A:ARG129 4.2 11.7 0.6 CA A:ARG129 4.2 11.8 0.4 CE1 A:HIS29 4.2 26.1 1.0 O A:ARG129 4.3 10.4 1.0 O A:HOH247 4.4 30.2 1.0 C A:LYS128 4.7 12.0 1.0 C A:ARG129 4.7 11.2 1.0 N A:GLY132 4.8 11.1 1.0 CZ A:ARG129 4.8 19.8 0.4 N A:ARG129 4.8 11.8 1.0 C A:GLY132 4.8 11.7 1.0 CG A:ARG129 4.9 15.1 0.6

Iodine binding site 10 out of 29 in the Crystal Structure of A Putative Ribose-5-Phosphate Isomerase From Coccidioides Immitis Solved By Combined Iodide Ion Sad and Mr


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 A Putative Ribose-5-Phosphate Isomerase From Coccidioides Immitis Solved By Combined Iodide Ion Sad and Mr within 5.0Å range: probe atom residue distance (Å) B Occ A:I174 b:43.7 occ:0.51 O B:HOH194 3.3 34.6 1.0 O B:HOH279 3.3 24.6 1.0 CB A:ALA52 3.5 29.9 1.0 CB B:ALA151 3.7 22.2 1.0 N A:HIS55 3.9 19.3 1.0 CB A:HIS55 4.0 21.1 1.0 O A:HOH275 4.0 31.0 1.0 CD A:PRO54 4.2 20.5 1.0 CB A:PRO54 4.2 19.4 1.0 O A:ALA52 4.3 26.3 1.0 CG A:PRO54 4.3 19.6 1.0 CA A:ALA52 4.4 29.2 1.0 CA A:HIS55 4.5 19.7 1.0 N A:ALA52 4.5 32.3 1.0 C A:ALA52 4.5 27.3 1.0 N A:PRO54 4.8 19.6 1.0 C A:PRO54 4.8 19.0 1.0 CA A:PRO54 4.9 19.3 1.0

T.E.Edwards, A.B.Abramov, E.R.Smith, R.O.Baydo, J.T.Leonard, D.J.Leibly, K.B.Thompkins, M.C.Clifton, A.S.Gardberg, B.L.Staker, W.C.Van Voorhis, P.J.Myler, L.J.Stewart. Structural Characterization of A Ribose-5-Phosphate Isomerase B From the Pathogenic Fungus Coccidioides Immitis. Bmc Struct.Biol. V. 11 39 2011.
ISSN: ESSN 1472-6807
PubMed: 21995815
DOI: 10.1186/1472-6807-11-39