Iodine in PDB 3ks7: Crystal Structure of Putative Peptide:N-Glycosidase F (Pngase F) (YP_210507.1) From Bacteroides Fragilis Nctc 9343 at 2.30 A Resolution

The structure of Crystal Structure of Putative Peptide:N-Glycosidase F (Pngase F) (YP_210507.1) From Bacteroides Fragilis Nctc 9343 at 2.30 A Resolution, PDB code: 3ks7 was solved by Joint Center For Structural Genomics (Jcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.88 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	106.057, 119.221, 154.314, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 23.7

The structure of Crystal Structure of Putative Peptide:N-Glycosidase F (Pngase F) (YP_210507.1) From Bacteroides Fragilis Nctc 9343 at 2.30 A Resolution also contains other interesting chemical elements:

Chlorine

(Cl)

10 atoms

The binding sites of Iodine atom in the Crystal Structure of Putative Peptide:N-Glycosidase F (Pngase F) (YP_210507.1) From Bacteroides Fragilis Nctc 9343 at 2.30 A Resolution (pdb code 3ks7). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 7 binding sites of Iodine where determined in the Crystal Structure of Putative Peptide:N-Glycosidase F (Pngase F) (YP_210507.1) From Bacteroides Fragilis Nctc 9343 at 2.30 A Resolution, PDB code: 3ks7:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7;

Iodine binding site 1 out of 7 in the Crystal Structure of Putative Peptide:N-Glycosidase F (Pngase F) (YP_210507.1) From Bacteroides Fragilis Nctc 9343 at 2.30 A Resolution


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 Putative Peptide:N-Glycosidase F (Pngase F) (YP_210507.1) From Bacteroides Fragilis Nctc 9343 at 2.30 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:I4 b:36.2 occ:0.50 N B:VAL330 3.7 25.1 1.0 CA A:TYR339 3.8 28.9 1.0 N A:TYR339 4.0 28.8 1.0 C A:TYR339 4.1 29.1 1.0 CG1 A:ILE340 4.1 30.0 1.0 CB B:VAL330 4.2 25.1 1.0 N A:ILE340 4.2 29.3 1.0 CA B:GLY329 4.2 24.4 1.0 O B:VAL330 4.3 25.7 1.0 C A:SER338 4.3 28.4 1.0 CG2 B:VAL330 4.3 24.7 1.0 O A:SER338 4.3 28.6 1.0 C B:GLY329 4.4 24.8 1.0 CA B:VAL330 4.5 25.2 1.0 O B:THR328 4.6 23.3 1.0 CB A:SER338 4.7 28.0 1.0 O A:TYR339 4.7 29.4 1.0 CD1 A:ILE340 4.8 30.1 1.0 C B:VAL330 4.9 25.8 1.0

Iodine binding site 2 out of 7 in the Crystal Structure of Putative Peptide:N-Glycosidase F (Pngase F) (YP_210507.1) From Bacteroides Fragilis Nctc 9343 at 2.30 A Resolution


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 Putative Peptide:N-Glycosidase F (Pngase F) (YP_210507.1) From Bacteroides Fragilis Nctc 9343 at 2.30 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:I6 b:45.6 occ:0.33 N A:ASN41 3.4 22.5 1.0 O A:HOH440 3.7 26.8 1.0 CE1 A:HIS63 3.8 23.9 1.0 CG1 A:VAL40 4.0 22.7 1.0 CA A:VAL40 4.0 23.4 1.0 CB A:ASN41 4.0 22.8 1.0 NE2 A:HIS63 4.1 23.9 1.0 C A:VAL40 4.2 23.0 1.0 CA A:ASN41 4.3 22.6 1.0 OH A:TYR49 4.3 26.1 1.0 O A:ASN39 4.5 25.3 1.0 CB A:VAL40 4.5 23.4 1.0 O A:ASN41 4.6 22.4 1.0 C A:ASN41 4.9 21.9 1.0

Iodine binding site 3 out of 7 in the Crystal Structure of Putative Peptide:N-Glycosidase F (Pngase F) (YP_210507.1) From Bacteroides Fragilis Nctc 9343 at 2.30 A Resolution


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 Putative Peptide:N-Glycosidase F (Pngase F) (YP_210507.1) From Bacteroides Fragilis Nctc 9343 at 2.30 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:I1 b:36.8 occ:0.50 OG B:SER338 3.6 29.9 1.0 N A:VAL330 3.7 24.6 1.0 CA B:TYR339 3.9 28.6 1.0 CG1 B:ILE340 4.0 29.8 1.0 C B:TYR339 4.0 28.6 1.0 N B:TYR339 4.1 28.4 1.0 CA A:GLY329 4.2 24.0 1.0 N B:ILE340 4.2 29.0 1.0 CB A:VAL330 4.3 24.9 1.0 O A:VAL330 4.3 26.1 1.0 C B:SER338 4.4 28.2 1.0 C A:GLY329 4.4 24.1 1.0 CA A:VAL330 4.5 24.9 1.0 O B:SER338 4.5 28.6 1.0 O B:TYR339 4.5 28.2 1.0 O A:THR328 4.6 23.6 1.0 CG2 A:VAL330 4.6 23.8 1.0 CB B:SER338 4.7 28.3 1.0 CD1 B:ILE340 4.8 30.1 1.0 C A:VAL330 4.9 25.6 1.0

Iodine binding site 4 out of 7 in the Crystal Structure of Putative Peptide:N-Glycosidase F (Pngase F) (YP_210507.1) From Bacteroides Fragilis Nctc 9343 at 2.30 A Resolution


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 Putative Peptide:N-Glycosidase F (Pngase F) (YP_210507.1) From Bacteroides Fragilis Nctc 9343 at 2.30 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:I5 b:45.4 occ:0.33 N B:GLY329 3.8 24.0 1.0 CA B:GLY329 3.8 24.4 1.0 CB B:SER356 4.0 21.0 1.0 OG B:SER356 4.2 20.0 1.0 O B:HOH544 4.2 26.6 1.0 CZ3 B:TRP98 4.4 35.6 1.0 CE1 B:PHE158 4.4 21.3 1.0 CZ B:PHE158 4.6 21.0 1.0 C B:GLY329 4.8 24.8 1.0 CH2 B:TRP98 4.8 35.9 1.0

Iodine binding site 5 out of 7 in the Crystal Structure of Putative Peptide:N-Glycosidase F (Pngase F) (YP_210507.1) From Bacteroides Fragilis Nctc 9343 at 2.30 A Resolution


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 Putative Peptide:N-Glycosidase F (Pngase F) (YP_210507.1) From Bacteroides Fragilis Nctc 9343 at 2.30 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:I2 b:35.2 occ:0.50 N D:VAL330 3.8 25.0 1.0 CA C:TYR339 3.9 29.1 1.0 N C:TYR339 4.1 28.7 1.0 O C:SER338 4.1 28.4 1.0 C C:TYR339 4.1 29.2 1.0 C C:SER338 4.2 28.4 1.0 OG C:SER338 4.3 28.3 1.0 CB D:VAL330 4.3 24.9 1.0 N C:ILE340 4.4 29.5 1.0 O D:VAL330 4.4 26.0 1.0 CA D:GLY329 4.4 24.5 1.0 CG1 C:ILE340 4.5 30.0 1.0 C D:GLY329 4.5 24.8 1.0 CA D:VAL330 4.6 25.0 1.0 CG2 D:VAL330 4.7 24.4 1.0 O C:TYR339 4.7 29.6 1.0 O D:THR328 4.7 23.4 1.0 CB C:SER338 4.8 28.0 1.0 C D:VAL330 4.9 25.8 1.0

Iodine binding site 6 out of 7 in the Crystal Structure of Putative Peptide:N-Glycosidase F (Pngase F) (YP_210507.1) From Bacteroides Fragilis Nctc 9343 at 2.30 A Resolution


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 Putative Peptide:N-Glycosidase F (Pngase F) (YP_210507.1) From Bacteroides Fragilis Nctc 9343 at 2.30 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ D:I3 b:33.8 occ:0.50 OG D:SER338 3.6 28.8 1.0 N C:VAL330 3.7 24.9 1.0 CA D:TYR339 3.9 28.5 1.0 N D:TYR339 4.0 28.2 1.0 C D:TYR339 4.1 28.6 1.0 C D:SER338 4.2 27.9 1.0 CB C:VAL330 4.2 25.0 1.0 O D:SER338 4.3 27.9 1.0 O C:VAL330 4.3 25.6 1.0 CG1 D:ILE340 4.3 29.8 1.0 CA C:GLY329 4.3 24.9 1.0 O D:TYR339 4.4 28.5 1.0 C C:GLY329 4.5 24.9 1.0 CA C:VAL330 4.5 25.1 1.0 N D:ILE340 4.5 29.0 1.0 O C:THR328 4.5 23.4 1.0 CB D:SER338 4.6 27.9 1.0 CG2 C:VAL330 4.7 24.6 1.0 C C:VAL330 4.9 25.7 1.0 CD1 D:ILE340 5.0 30.0 1.0

Iodine binding site 7 out of 7 in the Crystal Structure of Putative Peptide:N-Glycosidase F (Pngase F) (YP_210507.1) From Bacteroides Fragilis Nctc 9343 at 2.30 A Resolution


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 Putative Peptide:N-Glycosidase F (Pngase F) (YP_210507.1) From Bacteroides Fragilis Nctc 9343 at 2.30 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ D:I7 b:44.7 occ:0.33 N D:GLY329 3.7 23.9 1.0 CA D:GLY329 3.9 24.5 1.0 O D:HOH485 3.9 23.6 1.0 CB D:SER356 4.0 20.5 1.0 CE1 D:PHE158 4.2 20.6 1.0 OG D:SER356 4.2 19.6 1.0 CZ D:PHE158 4.3 20.1 1.0 CZ3 D:TRP98 4.5 34.8 1.0 C D:GLY329 4.9 24.8 1.0 C D:THR328 4.9 23.4 1.0

Joint Center For Structural Genomics (Jcsg), Joint Center For Structural Genomics (Jcsg). N/A N/A.