Zinc in PDB 3pw3: Crystal Structure of A Cysteine Protease (BDI_2249) From Parabacteroides Distasonis Atcc 8503 at 2.23 A Resolution

The structure of Crystal Structure of A Cysteine Protease (BDI_2249) From Parabacteroides Distasonis Atcc 8503 at 2.23 A Resolution, PDB code: 3pw3 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)	29.97 / 2.23
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.592, 137.810, 223.165, 90.00, 90.00, 90.00
R / Rfree (%)	15.9 / 18.1

The structure of Crystal Structure of A Cysteine Protease (BDI_2249) From Parabacteroides Distasonis Atcc 8503 at 2.23 A Resolution also contains other interesting chemical elements:

Potassium	(K)	10 atoms
Chlorine	(Cl)	14 atoms

The binding sites of Zinc atom in the Crystal Structure of A Cysteine Protease (BDI_2249) From Parabacteroides Distasonis Atcc 8503 at 2.23 A Resolution (pdb code 3pw3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of A Cysteine Protease (BDI_2249) From Parabacteroides Distasonis Atcc 8503 at 2.23 A Resolution, PDB code: 3pw3:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of A Cysteine Protease (BDI_2249) From Parabacteroides Distasonis Atcc 8503 at 2.23 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 Cysteine Protease (BDI_2249) From Parabacteroides Distasonis Atcc 8503 at 2.23 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn406 b:28.8 occ:1.00 ND1 A:HIS340 1.8 32.1 1.0 OD2 C:ASP298 2.2 43.3 1.0 O C:HOH2426 2.3 21.9 0.5 SG A:CYS56 2.3 28.2 1.0 OD1 C:ASP298 2.6 45.0 1.0 CE1 A:HIS340 2.7 31.2 1.0 CG C:ASP298 2.7 49.8 1.0 CG A:HIS340 3.0 35.2 1.0 CB A:CYS56 3.2 24.1 1.0 CB A:HIS340 3.6 27.3 1.0 O C:HOH1977 3.7 53.1 1.0 NE1 C:TRP302 3.9 65.1 1.0 NE2 A:HIS340 3.9 31.3 1.0 O A:ASP339 3.9 24.8 0.5 CA A:HIS340 3.9 27.0 1.0 CD2 A:HIS340 4.0 35.6 1.0 NE2 A:GLN50 4.2 25.2 1.0 CB C:ASP298 4.3 53.5 1.0 OE1 A:GLN50 4.4 26.5 1.0 CD1 C:TRP302 4.5 59.9 1.0 CA A:CYS56 4.5 23.4 1.0 N A:GLY341 4.6 22.1 1.0 N A:CYS56 4.7 21.4 1.0 CD A:GLN50 4.8 26.6 1.0 O A:HOH1269 4.8 39.9 1.0 C A:HIS340 4.8 25.8 1.0 C A:ASP339 4.8 27.7 0.5 CE2 C:TRP302 4.9 67.3 1.0 N A:HIS340 5.0 30.4 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of A Cysteine Protease (BDI_2249) From Parabacteroides Distasonis Atcc 8503 at 2.23 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 Cysteine Protease (BDI_2249) From Parabacteroides Distasonis Atcc 8503 at 2.23 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn406 b:33.9 occ:1.00 ND1 B:HIS340 1.7 30.9 0.5 ND1 B:HIS340 2.0 27.6 0.5 OXT B:ACT441 2.0 35.7 1.0 SG B:CYS56 2.3 30.2 1.0 CE1 B:HIS340 2.6 31.3 0.5 C B:ACT441 2.7 49.4 1.0 O B:ACT441 2.8 60.8 1.0 CG B:HIS340 2.8 32.4 0.5 CE1 B:HIS340 2.9 29.0 0.5 CG B:HIS340 2.9 30.0 0.5 CL B:CL417 3.2 70.6 0.5 CB B:CYS56 3.2 27.0 1.0 CB B:HIS340 3.3 29.8 0.5 CB B:HIS340 3.4 31.4 0.5 CL B:CL417 3.6 60.1 0.5 NE2 B:HIS340 3.8 33.7 0.5 CA B:HIS340 3.8 30.8 0.5 CD2 B:HIS340 3.9 32.7 0.5 CA B:HIS340 3.9 30.3 0.5 NE2 B:HIS340 3.9 30.9 0.5 CD2 B:HIS340 4.0 30.9 0.5 CH3 B:ACT441 4.0 71.0 1.0 NE2 B:GLN50 4.3 23.9 1.0 O B:HOH1868 4.3 53.7 1.0 N B:GLY341 4.5 26.4 1.0 CA B:CYS56 4.5 25.6 1.0 OE1 B:GLN50 4.6 26.1 1.0 C B:HIS340 4.7 29.6 1.0 N B:CYS56 4.7 22.0 1.0 CD B:GLN50 4.9 26.3 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of A Cysteine Protease (BDI_2249) From Parabacteroides Distasonis Atcc 8503 at 2.23 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 Cysteine Protease (BDI_2249) From Parabacteroides Distasonis Atcc 8503 at 2.23 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn406 b:45.4 occ:1.00 ND1 C:HIS340 1.9 49.5 1.0 OD2 E:ASP298 2.2 74.2 1.0 SG C:CYS56 2.3 43.3 1.0 OD1 E:ASP298 2.6 77.4 1.0 CE1 C:HIS340 2.7 52.3 1.0 CG E:ASP298 2.8 80.4 1.0 CL E:CL419 2.9 86.2 1.0 CG C:HIS340 3.1 51.9 1.0 CB C:CYS56 3.2 37.5 1.0 CB C:HIS340 3.6 49.2 1.0 NE2 C:HIS340 3.9 49.4 1.0 CA C:HIS340 4.0 48.4 1.0 CD2 C:HIS340 4.1 52.1 1.0 NE2 C:GLN50 4.2 41.7 1.0 CB E:ASP298 4.3 86.5 1.0 NE1 E:TRP302 4.3 0.6 1.0 OE1 C:GLN50 4.5 47.8 1.0 CA C:CYS56 4.5 38.1 1.0 N C:GLY341 4.6 43.8 1.0 N C:CYS56 4.7 37.4 1.0 CD C:GLN50 4.8 41.2 1.0 C C:HIS340 4.8 46.4 1.0 CD1 E:TRP302 4.9 0.7 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of A Cysteine Protease (BDI_2249) From Parabacteroides Distasonis Atcc 8503 at 2.23 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 Cysteine Protease (BDI_2249) From Parabacteroides Distasonis Atcc 8503 at 2.23 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn406 b:37.7 occ:1.00 ND1 D:HIS340 1.9 44.5 1.0 SG D:CYS56 2.3 41.4 1.0 OD2 B:ASP298 2.3 58.2 1.0 OD1 B:ASP298 2.5 62.2 1.0 CL B:CL422 2.6 73.0 1.0 CE1 D:HIS340 2.7 45.9 1.0 CG B:ASP298 2.8 64.5 1.0 CG D:HIS340 3.0 45.9 1.0 CB D:CYS56 3.2 34.0 1.0 CB D:HIS340 3.6 41.2 1.0 NE2 D:HIS340 3.9 43.0 1.0 CA D:HIS340 4.0 43.2 1.0 NE1 B:TRP302 4.0 98.8 1.0 CD2 D:HIS340 4.1 48.6 1.0 NE2 D:GLN50 4.2 32.0 1.0 CB B:ASP298 4.3 74.9 1.0 OE1 D:GLN50 4.5 34.7 1.0 CA D:CYS56 4.5 33.6 1.0 CD1 B:TRP302 4.6 96.4 1.0 N D:GLY341 4.6 37.1 1.0 N D:CYS56 4.7 31.8 1.0 CD D:GLN50 4.8 38.0 1.0 C D:HIS340 4.8 36.2 1.0 O D:HOH1396 4.9 45.3 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of A Cysteine Protease (BDI_2249) From Parabacteroides Distasonis Atcc 8503 at 2.23 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 Cysteine Protease (BDI_2249) From Parabacteroides Distasonis Atcc 8503 at 2.23 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn406 b:39.1 occ:1.00 ND1 E:HIS340 1.8 33.1 0.5 ND1 E:HIS340 1.9 30.6 0.5 O E:HOH590 2.2 27.2 1.0 SG E:CYS56 2.3 36.1 1.0 CE1 E:HIS340 2.7 35.7 0.5 CE1 E:HIS340 2.8 32.0 0.5 CG E:HIS340 2.9 36.0 0.5 CG E:HIS340 2.9 32.5 0.5 CB E:CYS56 3.2 32.8 1.0 CL E:CL420 3.3 65.6 0.5 CB E:HIS340 3.3 32.0 0.5 CB E:HIS340 3.4 34.0 0.5 CL E:CL420 3.7 69.0 0.5 NE2 E:HIS340 3.8 37.2 0.5 CA E:HIS340 3.8 34.1 0.5 CA E:HIS340 3.9 33.3 0.5 NE2 E:HIS340 3.9 33.5 0.5 CD2 E:HIS340 3.9 37.4 0.5 CD2 E:HIS340 4.0 33.5 0.5 NE2 E:GLN50 4.4 30.2 1.0 N E:GLY341 4.5 31.6 1.0 O E:HOH2053 4.5 55.9 1.0 CA E:CYS56 4.6 28.9 1.0 OE1 E:GLN50 4.6 36.3 1.0 C E:HIS340 4.7 36.0 1.0 N E:CYS56 4.7 28.4 1.0 CD E:GLN50 5.0 36.1 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of A Cysteine Protease (BDI_2249) From Parabacteroides Distasonis Atcc 8503 at 2.23 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 Cysteine Protease (BDI_2249) From Parabacteroides Distasonis Atcc 8503 at 2.23 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn406 b:37.4 occ:1.00 ND1 F:HIS340 1.8 31.3 0.5 ND1 F:HIS340 2.0 36.6 0.5 OXT F:ACT442 2.2 46.4 1.0 SG F:CYS56 2.3 36.9 1.0 O F:ACT442 2.4 69.4 1.0 CE1 F:HIS340 2.7 33.8 0.5 C F:ACT442 2.7 59.0 1.0 CL F:CL418 2.7 65.8 0.5 CG F:HIS340 2.9 35.4 0.5 CG F:HIS340 2.9 40.9 0.5 CE1 F:HIS340 2.9 39.0 0.5 CB F:CYS56 3.2 34.5 1.0 CB F:HIS340 3.3 38.2 0.5 CL F:CL418 3.3 68.3 0.5 CB F:HIS340 3.5 34.7 0.5 NE2 F:HIS340 3.8 36.9 0.5 CA F:HIS340 3.9 35.5 0.5 CA F:HIS340 3.9 37.2 0.5 CD2 F:HIS340 4.0 38.2 0.5 NE2 F:HIS340 4.0 41.7 0.5 CD2 F:HIS340 4.1 43.5 0.5 CH3 F:ACT442 4.2 72.2 1.0 NE2 F:GLN50 4.3 34.5 1.0 OE1 F:GLN50 4.5 36.9 1.0 CA F:CYS56 4.5 30.0 1.0 N F:GLY341 4.5 32.0 1.0 O F:HOH1921 4.6 53.2 1.0 N F:CYS56 4.7 27.9 1.0 C F:HIS340 4.7 36.5 1.0 CD F:GLN50 4.9 33.4 1.0 O F:HOH2042 4.9 57.7 1.0

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