Zinc in PDB 4df9: Crystal Structure of A Putative Peptidase (BF3526) From Bacteroides Fragilis Nctc 9343 at 2.17 A Resolution

The structure of Crystal Structure of A Putative Peptidase (BF3526) From Bacteroides Fragilis Nctc 9343 at 2.17 A Resolution, PDB code: 4df9 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)	48.73 / 2.17
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	238.730, 92.820, 173.890, 90.00, 125.26, 90.00
R / Rfree (%)	15.6 / 18.8

The structure of Crystal Structure of A Putative Peptidase (BF3526) From Bacteroides Fragilis Nctc 9343 at 2.17 A Resolution also contains other interesting chemical elements:

Chlorine	(Cl)	15 atoms
Sodium	(Na)	6 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of A Putative Peptidase (BF3526) From Bacteroides Fragilis Nctc 9343 at 2.17 A Resolution (pdb code 4df9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Crystal Structure of A Putative Peptidase (BF3526) From Bacteroides Fragilis Nctc 9343 at 2.17 A Resolution, PDB code: 4df9:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in the Crystal Structure of A Putative Peptidase (BF3526) From Bacteroides Fragilis Nctc 9343 at 2.17 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of A Putative Peptidase (BF3526) From Bacteroides Fragilis Nctc 9343 at 2.17 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:40.2 occ:0.50 OD1 A:ASP322 1.9 34.5 1.0 NE2 A:HIS311 2.1 29.8 1.0 O A:HOH683 2.1 37.6 1.0 NE2 A:HIS315 2.1 31.3 1.0 CG A:ASP322 2.7 36.0 1.0 OD2 A:ASP322 2.9 37.7 1.0 CD2 A:HIS311 2.9 29.8 1.0 CD2 A:HIS315 3.0 31.6 1.0 CE1 A:HIS315 3.1 31.1 1.0 CE1 A:HIS311 3.1 29.3 1.0 CG A:HIS311 4.1 28.0 1.0 CE2 A:TYR324 4.1 31.5 1.0 CB A:ASP322 4.2 30.1 1.0 CG A:HIS315 4.2 30.2 1.0 OE1 A:GLU312 4.2 49.7 1.0 ND1 A:HIS315 4.2 31.5 1.0 ND1 A:HIS311 4.2 29.7 1.0 OH A:TYR324 4.2 41.3 1.0 O A:HOH648 4.5 43.2 1.0 CE A:MSE400 4.5 21.6 1.0 CZ A:TYR324 4.7 37.1 1.0 O13 A:2PE504 4.7 62.1 1.0 CA A:ASP322 4.8 28.9 1.0 CD A:GLU312 4.9 55.6 1.0 OE2 A:GLU312 5.0 56.7 1.0

Zinc binding site 2 out of 12 in the Crystal Structure of A Putative Peptidase (BF3526) From Bacteroides Fragilis Nctc 9343 at 2.17 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of A Putative Peptidase (BF3526) From Bacteroides Fragilis Nctc 9343 at 2.17 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:31.1 occ:1.00 OE2 A:GLU323 2.1 32.8 1.0 SG A:CYS412 2.2 31.5 1.0 SG A:CYS409 2.3 33.9 1.0 SG A:CYS398 2.3 32.4 1.0 CD A:GLU323 3.0 50.3 1.0 OE1 A:GLU323 3.3 36.8 1.0 CB A:CYS412 3.3 29.0 1.0 CB A:CYS409 3.4 30.4 1.0 CB A:CYS398 3.4 29.5 1.0 N A:CYS409 3.7 30.9 1.0 CA A:CYS409 4.1 30.6 1.0 N A:CYS412 4.2 30.4 1.0 CA A:CYS412 4.3 30.0 1.0 CG A:GLU323 4.3 30.5 1.0 ND2 A:ASN345 4.4 28.9 1.0 CB A:MSE400 4.4 24.6 1.0 CG A:MSE400 4.5 24.9 1.0 CB A:ASN345 4.5 30.5 1.0 CD A:PRO394 4.6 28.4 1.0 O A:CYS409 4.7 33.6 1.0 C A:CYS409 4.8 35.4 1.0 CG A:PRO394 4.8 32.5 1.0 CA A:CYS398 4.8 30.3 1.0 C A:PHE408 4.9 33.8 1.0 CG A:ASN345 5.0 38.8 1.0

Zinc binding site 3 out of 12 in the Crystal Structure of A Putative Peptidase (BF3526) From Bacteroides Fragilis Nctc 9343 at 2.17 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of A Putative Peptidase (BF3526) From Bacteroides Fragilis Nctc 9343 at 2.17 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:45.6 occ:0.50 OD1 B:ASP322 2.2 32.3 1.0 NE2 B:HIS311 2.3 26.7 1.0 NE2 B:HIS315 2.4 29.7 1.0 CG B:ASP322 2.8 30.4 1.0 OD2 B:ASP322 2.8 36.1 1.0 CD2 B:HIS311 3.2 26.7 1.0 CD2 B:HIS315 3.3 28.8 1.0 O B:HOH887 3.3 57.0 1.0 CE1 B:HIS315 3.4 29.3 1.0 CE1 B:HIS311 3.5 26.8 1.0 OH B:TYR324 3.9 43.2 1.0 CE2 B:TYR324 4.0 30.3 1.0 OE1 B:GLU312 4.1 26.2 1.0 CB B:ASP322 4.3 25.4 1.0 CG B:HIS311 4.4 25.1 1.0 CZ B:TYR324 4.5 38.3 1.0 CG B:HIS315 4.5 28.4 1.0 ND1 B:HIS315 4.5 29.8 1.0 ND1 B:HIS311 4.5 26.6 1.0 C12 B:2PE504 4.7 38.9 1.0 C14 B:2PE504 4.7 41.3 1.0 OE2 B:GLU312 4.7 38.6 1.0 CD B:GLU312 4.8 34.2 1.0 O B:HOH745 4.8 41.8 1.0 CE B:MSE400 5.0 18.3 1.0

Zinc binding site 4 out of 12 in the Crystal Structure of A Putative Peptidase (BF3526) From Bacteroides Fragilis Nctc 9343 at 2.17 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of A Putative Peptidase (BF3526) From Bacteroides Fragilis Nctc 9343 at 2.17 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn503 b:25.3 occ:1.00 OE2 B:GLU323 2.0 22.9 1.0 SG B:CYS412 2.3 26.5 1.0 SG B:CYS409 2.3 25.5 1.0 SG B:CYS398 2.4 26.9 1.0 CD B:GLU323 3.0 30.7 1.0 OE1 B:GLU323 3.3 25.5 1.0 CB B:CYS412 3.4 23.3 1.0 CB B:CYS398 3.4 23.9 1.0 CB B:CYS409 3.4 22.0 1.0 N B:CYS409 3.8 22.6 1.0 CA B:CYS409 4.1 21.9 1.0 N B:CYS412 4.2 24.6 1.0 CG B:GLU323 4.3 22.4 1.0 ND2 B:ASN345 4.3 19.6 1.0 CA B:CYS412 4.3 23.8 1.0 CB B:MSE400 4.4 18.4 1.0 CB B:ASN345 4.4 23.7 1.0 CG B:MSE400 4.5 19.9 1.0 CD B:PRO394 4.6 20.5 1.0 CG B:PRO394 4.7 24.4 1.0 CA B:CYS398 4.8 24.9 1.0 C B:CYS409 4.8 26.5 1.0 O B:CYS409 4.8 24.7 1.0 C B:PHE408 4.9 25.4 1.0 CG B:ASN345 4.9 26.4 1.0

Zinc binding site 5 out of 12 in the Crystal Structure of A Putative Peptidase (BF3526) From Bacteroides Fragilis Nctc 9343 at 2.17 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of A Putative Peptidase (BF3526) From Bacteroides Fragilis Nctc 9343 at 2.17 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn502 b:45.0 occ:0.50 OD1 C:ASP322 1.9 36.2 1.0 NE2 C:HIS311 2.0 25.4 1.0 O C:HOH950 2.0 38.6 1.0 NE2 C:HIS315 2.2 25.1 1.0 CG C:ASP322 2.7 34.5 1.0 CD2 C:HIS311 2.9 24.3 1.0 OD2 C:ASP322 2.9 37.6 1.0 CD2 C:HIS315 3.1 25.4 1.0 CE1 C:HIS311 3.1 25.1 1.0 CE1 C:HIS315 3.3 24.6 1.0 CE2 C:TYR324 4.0 31.4 1.0 CG C:HIS311 4.1 23.7 1.0 ND1 C:HIS311 4.1 25.9 1.0 CB C:ASP322 4.2 27.7 1.0 OH C:TYR324 4.2 43.2 1.0 CG C:HIS315 4.3 24.9 1.0 O C:HOH917 4.3 65.7 1.0 OE1 C:GLU312 4.3 39.4 1.0 ND1 C:HIS315 4.4 25.6 1.0 CE C:MSE400 4.6 17.6 1.0 CZ C:TYR324 4.6 39.1 1.0 C12 C:2PE504 4.6 47.5 1.0 CA C:ASP322 4.7 26.4 1.0 CD C:GLU312 5.0 40.7 1.0

Zinc binding site 6 out of 12 in the Crystal Structure of A Putative Peptidase (BF3526) From Bacteroides Fragilis Nctc 9343 at 2.17 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of A Putative Peptidase (BF3526) From Bacteroides Fragilis Nctc 9343 at 2.17 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn503 b:24.3 occ:1.00 OE2 C:GLU323 2.1 24.9 1.0 SG C:CYS412 2.2 24.2 1.0 SG C:CYS409 2.3 26.2 1.0 SG C:CYS398 2.4 24.3 1.0 CD C:GLU323 3.0 38.3 1.0 OE1 C:GLU323 3.2 30.8 1.0 CB C:CYS412 3.3 21.5 1.0 CB C:CYS409 3.4 22.6 1.0 CB C:CYS398 3.4 22.9 1.0 N C:CYS409 3.8 23.3 1.0 CA C:CYS409 4.1 22.9 1.0 N C:CYS412 4.2 25.2 1.0 CA C:CYS412 4.3 22.6 1.0 ND2 C:ASN345 4.3 22.5 1.0 CG C:GLU323 4.3 30.2 1.0 CB C:MSE400 4.4 19.2 1.0 CB C:ASN345 4.5 26.1 1.0 CG C:MSE400 4.5 19.2 1.0 CD C:PRO394 4.6 24.1 1.0 O C:CYS409 4.7 28.0 1.0 CG C:PRO394 4.8 27.8 1.0 C C:CYS409 4.8 27.6 1.0 CA C:CYS398 4.8 24.2 1.0 C C:PHE408 4.9 28.2 1.0 CG C:ASN345 4.9 33.3 1.0

Zinc binding site 7 out of 12 in the Crystal Structure of A Putative Peptidase (BF3526) From Bacteroides Fragilis Nctc 9343 at 2.17 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of A Putative Peptidase (BF3526) From Bacteroides Fragilis Nctc 9343 at 2.17 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn502 b:41.6 occ:0.50 OD1 D:ASP322 2.1 26.3 1.0 NE2 D:HIS315 2.2 26.4 1.0 NE2 D:HIS311 2.2 24.0 1.0 O D:HOH826 2.6 54.3 1.0 CG D:ASP322 2.8 26.1 1.0 OD2 D:ASP322 2.9 29.6 1.0 CD2 D:HIS311 3.0 24.7 1.0 CD2 D:HIS315 3.1 26.9 1.0 CE1 D:HIS315 3.2 26.1 1.0 CE1 D:HIS311 3.4 23.5 1.0 C1 D:GOL515 3.8 67.9 1.0 O1 D:GOL515 4.0 68.9 1.0 OE1 D:GLU312 4.0 43.7 1.0 CE2 D:TYR324 4.1 23.3 1.0 OH D:TYR324 4.1 32.8 1.0 CG D:HIS311 4.3 24.1 1.0 CB D:ASP322 4.3 24.6 1.0 CG D:HIS315 4.3 26.3 1.0 ND1 D:HIS315 4.4 27.6 1.0 ND1 D:HIS311 4.4 24.8 1.0 CZ D:TYR324 4.6 29.0 1.0 C12 D:2PE504 4.6 46.9 1.0 CD D:GLU312 4.7 39.4 1.0 CE D:MSE400 4.8 14.5 1.0 OE2 D:GLU312 4.8 39.1 1.0 CA D:ASP322 4.9 23.2 1.0

Zinc binding site 8 out of 12 in the Crystal Structure of A Putative Peptidase (BF3526) From Bacteroides Fragilis Nctc 9343 at 2.17 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of A Putative Peptidase (BF3526) From Bacteroides Fragilis Nctc 9343 at 2.17 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn503 b:23.9 occ:1.00 OE2 D:GLU323 2.0 23.0 1.0 SG D:CYS412 2.3 22.8 1.0 SG D:CYS409 2.3 23.5 1.0 SG D:CYS398 2.4 25.1 1.0 CD D:GLU323 3.0 29.3 1.0 OE1 D:GLU323 3.3 26.5 1.0 CB D:CYS412 3.3 19.9 1.0 CB D:CYS398 3.4 21.9 1.0 CB D:CYS409 3.4 20.5 1.0 N D:CYS409 3.8 21.6 1.0 CA D:CYS409 4.2 20.5 1.0 N D:CYS412 4.2 21.4 1.0 CA D:CYS412 4.3 20.7 1.0 CG D:GLU323 4.3 20.2 1.0 ND2 D:ASN345 4.3 20.3 1.0 CB D:MSE400 4.4 15.6 1.0 CB D:ASN345 4.4 21.8 1.0 CG D:MSE400 4.5 16.5 1.0 CD D:PRO394 4.6 24.3 1.0 CG D:PRO394 4.7 27.4 1.0 O D:CYS409 4.8 23.4 1.0 C D:CYS409 4.8 23.9 1.0 CA D:CYS398 4.8 22.7 1.0 CG D:ASN345 4.9 25.0 1.0 C D:PHE408 4.9 25.2 1.0

Zinc binding site 9 out of 12 in the Crystal Structure of A Putative Peptidase (BF3526) From Bacteroides Fragilis Nctc 9343 at 2.17 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of A Putative Peptidase (BF3526) From Bacteroides Fragilis Nctc 9343 at 2.17 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn502 b:36.0 occ:0.50 OD1 E:ASP322 1.9 43.3 1.0 O E:HOH857 2.1 40.3 1.0 NE2 E:HIS315 2.1 36.2 1.0 NE2 E:HIS311 2.2 35.7 1.0 CG E:ASP322 2.7 40.1 1.0 OD2 E:ASP322 2.8 37.2 1.0 CD2 E:HIS311 3.1 36.1 1.0 CE1 E:HIS315 3.1 35.7 1.0 CD2 E:HIS315 3.1 36.4 1.0 CE1 E:HIS311 3.2 36.4 1.0 CE2 E:TYR324 4.1 39.5 1.0 OH E:TYR324 4.1 54.0 1.0 CB E:ASP322 4.1 33.0 1.0 CG E:HIS311 4.3 36.6 1.0 ND1 E:HIS315 4.3 36.4 1.0 CG E:HIS315 4.3 34.5 1.0 OE1 E:GLU312 4.3 55.7 1.0 ND1 E:HIS311 4.3 38.4 1.0 O E:HOH756 4.3 45.4 1.0 CZ E:TYR324 4.6 48.2 1.0 CE E:MSE400 4.6 26.2 1.0 O10 E:2PE504 4.7 71.8 1.0 CA E:ASP322 4.8 31.9 1.0 C12 E:2PE504 4.9 73.4 1.0 CD E:GLU312 5.0 62.7 1.0

Zinc binding site 10 out of 12 in the Crystal Structure of A Putative Peptidase (BF3526) From Bacteroides Fragilis Nctc 9343 at 2.17 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of A Putative Peptidase (BF3526) From Bacteroides Fragilis Nctc 9343 at 2.17 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn503 b:39.0 occ:1.00 OE2 E:GLU323 2.0 32.7 1.0 SG E:CYS412 2.3 38.5 1.0 SG E:CYS409 2.3 37.9 1.0 SG E:CYS398 2.4 36.8 1.0 CD E:GLU323 3.0 38.0 1.0 OE1 E:GLU323 3.3 44.5 1.0 CB E:CYS412 3.3 35.4 1.0 CB E:CYS409 3.4 34.8 1.0 CB E:CYS398 3.4 33.6 1.0 N E:CYS409 3.8 36.1 1.0 CA E:CYS409 4.1 35.3 1.0 N E:CYS412 4.2 35.9 1.0 CA E:CYS412 4.3 34.9 1.0 ND2 E:ASN345 4.3 26.3 1.0 CG E:GLU323 4.3 35.5 1.0 CB E:MSE400 4.4 24.0 1.0 CB E:ASN345 4.4 31.5 1.0 CG E:MSE400 4.5 26.8 1.0 CD E:PRO394 4.6 35.0 1.0 CG E:PRO394 4.7 38.8 1.0 O E:CYS409 4.8 39.2 1.0 C E:CYS409 4.8 39.3 1.0 CA E:CYS398 4.8 35.2 1.0 C E:PHE408 4.9 41.5 1.0 CG E:ASN345 4.9 34.3 1.0

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