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Chlorine 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

Protein crystallography data

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

Other elements in 3ks7:

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:

Iodine (I) 7 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 10 binding sites of Chlorine 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 Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 10 in 3ks7

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Chlorine binding site 1 out of 10 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 Chlorine with other atoms in the Cl 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:Cl9

b:58.2
occ:1.00
 CA A:GLU134 3.6 32.8 1.0
CB A:GLU134 3.8 32.8 1.0
C A:GLU134 4.0 32.4 1.0
N A:LYS135 4.2 31.7 1.0
CG A:GLU134 4.3 33.4 1.0
CB A:SER130 4.4 38.2 1.0
O A:GLU134 4.5 32.4 1.0
O A:SER130 4.7 38.1 1.0
N A:GLU134 5.0 33.3 1.0

Chlorine binding site 2 out of 10 in 3ks7

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Chlorine binding site 2 out of 10 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 Chlorine with other atoms in the Cl 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:Cl11

b:40.7
occ:1.00
 NH2 A:ARG97 3.0 42.5 1.0
N A:GLY329 3.9 23.8 1.0
CA A:GLY329 4.1 24.0 1.0
CB A:SER356 4.1 21.5 1.0
CZ A:ARG97 4.2 41.9 1.0
OG A:SER356 4.3 21.5 1.0
CE1 A:PHE158 4.3 20.6 1.0
CZ3 A:TRP98 4.5 34.9 1.0
CZ A:PHE158 4.5 19.4 1.0
NH1 A:ARG97 4.6 43.1 1.0

Chlorine binding site 3 out of 10 in 3ks7

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Chlorine binding site 3 out of 10 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 Chlorine with other atoms in the Cl 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
A:Cl12

b:42.1
occ:1.00
 N A:ARG97 3.4 25.0 1.0
CG A:ARG97 3.4 30.9 1.0
CB A:ARG97 3.9 26.6 1.0
CA A:ASP96 4.0 23.3 1.0
O A:GLY95 4.0 22.4 1.0
CG2 A:THR213 4.1 21.1 1.0
CD1 A:TRP98 4.2 31.2 1.0
C A:ASP96 4.2 24.1 1.0
NE1 A:TRP98 4.2 32.8 1.0
CA A:ARG97 4.3 26.3 1.0
OD1 A:ASP96 4.3 23.5 1.0
CD A:ARG97 4.7 35.8 1.0
CG A:ASP96 4.7 23.3 1.0
C A:GLY95 4.9 22.3 1.0
N A:ASP96 4.9 22.6 1.0
CB A:ASP96 5.0 23.4 1.0

Chlorine binding site 4 out of 10 in 3ks7

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Chlorine binding site 4 out of 10 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 Chlorine with other atoms in the Cl 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:Cl8

b:36.6
occ:1.00
 CB B:ARG97 3.5 27.5 1.0
N B:ARG97 3.5 25.5 1.0
O B:GLY95 4.0 22.2 1.0
CG2 B:THR213 4.1 20.1 1.0
CA B:ARG97 4.2 26.7 1.0
NE B:ARG97 4.2 39.5 1.0
CA B:ASP96 4.2 23.5 1.0
CD1 B:TRP98 4.3 31.2 1.0
NE1 B:TRP98 4.3 32.0 1.0
OD1 B:ASP96 4.3 22.8 1.0
C B:ASP96 4.4 24.4 1.0
CD B:ARG97 4.6 36.7 1.0
CG B:ARG97 4.6 32.2 1.0
CG B:ASP96 4.9 23.0 1.0
C B:GLY95 4.9 22.5 1.0
OH B:TYR163 4.9 28.9 1.0

Chlorine binding site 5 out of 10 in 3ks7

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Chlorine binding site 5 out of 10 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 Chlorine with other atoms in the Cl 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
B:Cl14

b:48.9
occ:1.00
 CA B:GLU134 3.9 33.0 1.0
CB B:GLU134 3.9 33.2 1.0
C B:GLU134 4.1 32.5 1.0
N B:LYS135 4.3 31.8 1.0
CB B:SER130 4.3 38.3 1.0
CG B:GLU134 4.5 33.9 1.0
O B:SER130 4.7 38.4 1.0
O B:GLU134 4.7 32.5 1.0

Chlorine binding site 6 out of 10 in 3ks7

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Chlorine binding site 6 out of 10 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 Chlorine with other atoms in the Cl 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
B:Cl16

b:48.3
occ:1.00
 N B:ASP168 3.4 42.6 1.0
ND2 B:ASN167 3.5 40.1 1.0
CA D:ASP304 3.9 25.5 1.0
C D:ASP304 3.9 25.8 1.0
CG B:ASN167 3.9 40.5 1.0
CB B:ASP168 3.9 44.2 1.0
CA B:ASN167 3.9 39.7 1.0
O D:ASP304 4.1 25.8 1.0
C B:ASN167 4.2 41.0 1.0
CA B:ASP168 4.3 44.0 1.0
OG1 D:THR386 4.3 23.8 1.0
N D:GLY305 4.3 26.5 1.0
OD1 D:ASP304 4.4 26.3 1.0
CB D:THR386 4.4 24.0 1.0
CB B:ASN167 4.4 39.9 1.0
OD1 B:ASN167 4.4 42.2 1.0
CB D:ASP304 4.5 25.6 1.0
O D:HOH459 4.8 20.0 1.0
CG D:ASP304 4.9 26.1 1.0
O B:ASN166 4.9 35.6 1.0
N D:ASP304 5.0 24.9 1.0

Chlorine binding site 7 out of 10 in 3ks7

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Chlorine binding site 7 out of 10 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 Chlorine with other atoms in the Cl 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
C:Cl10

b:35.1
occ:1.00
 OG1 C:THR268 3.3 25.5 1.0
CA C:PHE267 3.7 25.5 1.0
O C:ASP266 3.8 25.9 1.0
C C:PHE267 3.8 25.6 1.0
N C:PHE267 3.9 25.7 1.0
C C:ASP266 3.9 25.9 1.0
N C:THR268 3.9 25.9 1.0
O C:HOH503 4.1 15.6 1.0
CE C:LYS384 4.2 29.0 1.0
CB C:ASP266 4.2 26.1 1.0
CB C:THR268 4.4 26.1 1.0
O C:PHE267 4.4 25.1 1.0
CA C:THR268 4.7 26.0 1.0
CA C:ASP266 4.8 25.9 1.0
CG C:LYS384 5.0 26.8 1.0

Chlorine binding site 8 out of 10 in 3ks7

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Chlorine binding site 8 out of 10 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 Chlorine with other atoms in the Cl binding site number 8 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:Cl13

b:41.5
occ:1.00
 N C:ARG97 3.3 25.6 1.0
CB C:ARG97 3.5 27.5 1.0
O C:GLY95 3.9 23.2 1.0
CA C:ARG97 4.1 26.6 1.0
CA C:ASP96 4.1 23.9 1.0
CG2 C:THR213 4.1 20.8 1.0
CD1 C:TRP98 4.2 31.1 1.0
C C:ASP96 4.2 24.6 1.0
NE1 C:TRP98 4.3 32.1 1.0
OD1 C:ASP96 4.4 23.3 1.0
CG C:ARG97 4.8 31.2 1.0
C C:GLY95 4.8 23.1 1.0
CD C:ARG97 4.9 35.8 1.0
CG C:ASP96 4.9 23.7 1.0
N C:ASP96 4.9 23.4 1.0

Chlorine binding site 9 out of 10 in 3ks7

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Chlorine binding site 9 out of 10 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 Chlorine with other atoms in the Cl binding site number 9 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:Cl15

b:50.0
occ:1.00
 N C:GLY329 3.8 24.5 1.0
O C:HOH518 3.8 23.0 1.0
NH2 C:ARG97 3.8 42.6 1.0
CA C:GLY329 3.9 24.9 1.0
CB C:SER356 4.0 21.4 1.0
OG C:SER356 4.1 21.6 1.0
CE1 C:PHE158 4.5 20.0 1.0
CZ C:PHE158 4.6 19.2 1.0
CZ3 C:TRP98 4.6 34.5 1.0
NH1 C:ARG97 4.7 42.7 1.0
CZ C:ARG97 4.7 41.8 1.0
C C:GLY329 4.9 24.9 1.0

Chlorine binding site 10 out of 10 in 3ks7

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Chlorine binding site 10 out of 10 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 Chlorine with other atoms in the Cl binding site number 10 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:Cl17

b:49.7
occ:1.00
 N D:ARG97 3.2 24.0 1.0
CB D:ARG97 3.7 24.5 1.0
CG2 D:THR213 3.9 19.3 1.0
CA D:ASP96 3.9 23.3 1.0
O D:GLY95 4.0 22.9 1.0
C D:ASP96 4.1 23.6 1.0
CA D:ARG97 4.1 24.3 1.0
CD1 D:TRP98 4.2 29.7 1.0
OD1 D:ASP96 4.3 23.0 1.0
NE1 D:TRP98 4.3 31.1 1.0
O1 D:EDO416 4.4 58.8 1.0
CG D:ASP96 4.6 23.6 1.0
C D:GLY95 4.8 22.7 1.0
N D:ASP96 4.8 23.1 1.0
OH D:TYR163 4.8 29.0 1.0
CB D:ASP96 4.9 23.5 1.0
CB D:THR213 4.9 21.0 1.0
N D:TRP98 5.0 24.5 1.0

Reference:

Joint Center For Structural Genomics (Jcsg), Joint Center For Structural Genomics (Jcsg). N/A N/A.
Page generated: Fri Jul 11 07:04:27 2025

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