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

Protein crystallography data

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

Other elements in 3pw3:

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

Zinc Binding Sites:

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 3pw3

Go back to Zinc Binding Sites List in 3pw3
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 3pw3

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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 3pw3

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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 3pw3

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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 3pw3

Go back to Zinc Binding Sites List in 3pw3
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 3pw3

Go back to Zinc Binding Sites List in 3pw3
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

Reference:

Joint Center For Structural Genomics (Jcsg), Joint Center For Structural Genomics (Jcsg). N/A N/A.
Page generated: Sat Oct 26 11:48:44 2024

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