Zinc in PDB 3e38: Crystal Structure of A Two-Domain Protein Containing Predicted Php- Like Metal-Dependent Phosphoesterase (BVU_3505) From Bacteroides Vulgatus Atcc 8482 at 2.20 A Resolution

The structure of Crystal Structure of A Two-Domain Protein Containing Predicted Php- Like Metal-Dependent Phosphoesterase (BVU_3505) From Bacteroides Vulgatus Atcc 8482 at 2.20 A Resolution, PDB code: 3e38 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)	29.60 / 2.20
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	95.680, 117.820, 79.560, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 22.5

The structure of Crystal Structure of A Two-Domain Protein Containing Predicted Php- Like Metal-Dependent Phosphoesterase (BVU_3505) From Bacteroides Vulgatus Atcc 8482 at 2.20 A Resolution also contains other interesting chemical elements:

Arsenic

(As)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of A Two-Domain Protein Containing Predicted Php- Like Metal-Dependent Phosphoesterase (BVU_3505) From Bacteroides Vulgatus Atcc 8482 at 2.20 A Resolution (pdb code 3e38). 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 Two-Domain Protein Containing Predicted Php- Like Metal-Dependent Phosphoesterase (BVU_3505) From Bacteroides Vulgatus Atcc 8482 at 2.20 A Resolution, PDB code: 3e38:
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 Two-Domain Protein Containing Predicted Php- Like Metal-Dependent Phosphoesterase (BVU_3505) From Bacteroides Vulgatus Atcc 8482 at 2.20 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 Two-Domain Protein Containing Predicted Php- Like Metal-Dependent Phosphoesterase (BVU_3505) From Bacteroides Vulgatus Atcc 8482 at 2.20 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1 b:35.0 occ:1.00 O2 A:CAC7 2.1 52.9 1.0 O A:HOH378 2.1 24.0 1.0 NE2 A:HIS157 2.2 27.0 1.0 OE2 A:GLU113 2.2 29.3 1.0 ND1 A:HIS122 2.3 27.4 1.0 CE1 A:HIS157 3.1 33.9 1.0 CE1 A:HIS122 3.2 29.7 1.0 CD A:GLU113 3.2 32.8 1.0 AS A:CAC7 3.2 54.6 1.0 CD2 A:HIS157 3.2 24.7 1.0 O1 A:CAC7 3.3 47.6 1.0 CG A:HIS122 3.3 31.8 1.0 OE1 A:GLU113 3.5 34.1 1.0 ZN A:ZN2 3.6 30.5 1.0 CB A:HIS122 3.6 32.4 1.0 C1 A:CAC7 4.1 28.6 1.0 CE1 A:HIS76 4.1 31.9 1.0 OD2 A:ASP214 4.2 32.5 1.0 ND1 A:HIS157 4.3 24.7 1.0 NE2 A:HIS122 4.3 31.3 1.0 CG A:HIS157 4.3 28.0 1.0 CD2 A:HIS122 4.4 26.8 1.0 CG A:GLU113 4.4 27.9 1.0 NE2 A:HIS44 4.4 29.0 1.0 ND2 A:ASN156 4.5 37.1 1.0 CE1 A:HIS44 4.5 32.5 1.0 C2 A:CAC7 4.7 30.8 1.0 CB A:ASN156 4.8 31.4 1.0 ND1 A:HIS76 4.8 24.8 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of A Two-Domain Protein Containing Predicted Php- Like Metal-Dependent Phosphoesterase (BVU_3505) From Bacteroides Vulgatus Atcc 8482 at 2.20 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 Two-Domain Protein Containing Predicted Php- Like Metal-Dependent Phosphoesterase (BVU_3505) From Bacteroides Vulgatus Atcc 8482 at 2.20 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2 b:30.5 occ:1.00 O A:HOH378 1.8 24.0 1.0 O1 A:CAC7 1.9 47.6 1.0 NE2 A:HIS46 2.0 22.9 1.0 OE1 A:GLU113 2.3 34.1 1.0 NE2 A:HIS44 2.3 29.0 1.0 OD1 A:ASP214 2.4 30.4 1.0 CE1 A:HIS46 2.8 27.8 1.0 CG A:ASP214 3.1 29.1 1.0 CD2 A:HIS46 3.1 21.6 1.0 CD2 A:HIS44 3.1 34.4 1.0 CD A:GLU113 3.2 32.8 1.0 OD2 A:ASP214 3.2 32.5 1.0 CE1 A:HIS44 3.4 32.5 1.0 OE2 A:GLU113 3.5 29.3 1.0 AS A:CAC7 3.5 54.6 1.0 ZN A:ZN1 3.6 35.0 1.0 CE1 A:HIS76 3.9 31.9 1.0 ND1 A:HIS46 4.0 25.6 1.0 CE1 A:HIS216 4.0 32.7 1.0 NE2 A:HIS76 4.1 23.2 1.0 ZN A:ZN3 4.2 27.2 1.0 CG A:HIS46 4.2 20.6 1.0 O2 A:CAC7 4.2 52.9 1.0 C1 A:CAC7 4.2 28.6 1.0 CG A:HIS44 4.3 28.9 1.0 ND1 A:HIS44 4.4 32.4 1.0 NE2 A:HIS216 4.4 32.9 1.0 CB A:ASP214 4.5 30.0 1.0 CG A:GLU113 4.5 27.9 1.0 ND1 A:HIS76 4.8 24.8 1.0 CB A:GLU113 4.9 30.2 1.0 CA A:ASP214 4.9 27.6 1.0 C2 A:CAC7 5.0 30.8 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of A Two-Domain Protein Containing Predicted Php- Like Metal-Dependent Phosphoesterase (BVU_3505) From Bacteroides Vulgatus Atcc 8482 at 2.20 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 Two-Domain Protein Containing Predicted Php- Like Metal-Dependent Phosphoesterase (BVU_3505) From Bacteroides Vulgatus Atcc 8482 at 2.20 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn3 b:27.2 occ:1.00 NE2 A:HIS216 2.1 32.9 1.0 OD2 A:ASP51 2.1 37.1 1.0 NE2 A:HIS76 2.1 23.2 1.0 C2 A:CAC7 2.1 30.8 1.0 OD1 A:ASP51 2.5 21.4 1.0 CG A:ASP51 2.6 28.8 1.0 O1 A:CAC7 2.6 47.6 1.0 AS A:CAC7 2.8 54.6 1.0 CE1 A:HIS76 2.9 31.9 1.0 CD2 A:HIS216 3.0 31.6 1.0 CE1 A:HIS216 3.1 32.7 1.0 CD2 A:HIS76 3.2 32.5 1.0 CE1 A:HIS46 3.9 27.8 1.0 NE2 A:HIS46 3.9 22.9 1.0 CB A:ASP51 4.1 27.4 1.0 ND1 A:HIS76 4.1 24.8 1.0 ND1 A:HIS46 4.2 25.6 1.0 ZN A:ZN2 4.2 30.5 1.0 CG A:HIS216 4.2 26.8 1.0 ND1 A:HIS216 4.2 27.0 1.0 CD2 A:HIS46 4.2 21.6 1.0 O2 A:CAC7 4.2 52.9 1.0 C1 A:CAC7 4.2 28.6 1.0 CG A:HIS76 4.3 28.4 1.0 CG A:HIS46 4.3 20.6 1.0 O A:HOH378 4.8 24.0 1.0 CD2 A:TYR79 4.8 31.5 1.0 OE1 A:GLU113 4.8 34.1 1.0 OD1 A:ASP214 4.9 30.4 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of A Two-Domain Protein Containing Predicted Php- Like Metal-Dependent Phosphoesterase (BVU_3505) From Bacteroides Vulgatus Atcc 8482 at 2.20 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 Two-Domain Protein Containing Predicted Php- Like Metal-Dependent Phosphoesterase (BVU_3505) From Bacteroides Vulgatus Atcc 8482 at 2.20 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn4 b:40.7 occ:1.00 O B:HOH403 1.8 32.7 1.0 O2 B:CAC8 1.9 49.8 1.0 OE2 B:GLU113 2.2 25.4 1.0 NE2 B:HIS157 2.2 26.7 1.0 ND1 B:HIS122 2.3 33.2 1.0 CE1 B:HIS157 3.0 29.3 1.0 CD B:GLU113 3.2 32.4 1.0 CE1 B:HIS122 3.2 28.2 1.0 AS B:CAC8 3.2 61.7 1.0 CG B:HIS122 3.3 29.0 1.0 CD2 B:HIS157 3.3 28.7 1.0 O1 B:CAC8 3.5 37.2 1.0 OE1 B:GLU113 3.5 30.5 1.0 ZN B:ZN5 3.5 34.6 1.0 CB B:HIS122 3.6 30.2 1.0 C1 B:CAC8 4.0 33.6 1.0 CE1 B:HIS76 4.1 29.8 1.0 ND1 B:HIS157 4.2 30.4 1.0 OD2 B:ASP214 4.3 34.6 1.0 NE2 B:HIS122 4.3 33.6 1.0 CG B:GLU113 4.4 26.7 1.0 CD2 B:HIS122 4.4 35.5 1.0 CG B:HIS157 4.4 30.6 1.0 CE1 B:HIS44 4.4 32.3 1.0 NE2 B:HIS44 4.5 28.3 1.0 ND2 B:ASN156 4.6 28.3 1.0 CB B:ASN156 4.7 27.7 1.0 C2 B:CAC8 4.8 24.2 1.0 ND1 B:HIS76 4.9 28.2 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of A Two-Domain Protein Containing Predicted Php- Like Metal-Dependent Phosphoesterase (BVU_3505) From Bacteroides Vulgatus Atcc 8482 at 2.20 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 Two-Domain Protein Containing Predicted Php- Like Metal-Dependent Phosphoesterase (BVU_3505) From Bacteroides Vulgatus Atcc 8482 at 2.20 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn5 b:34.6 occ:1.00 O1 B:CAC8 1.9 37.2 1.0 O B:HOH403 2.1 32.7 1.0 NE2 B:HIS44 2.2 28.3 1.0 NE2 B:HIS46 2.2 14.6 1.0 OE1 B:GLU113 2.2 30.5 1.0 OD1 B:ASP214 2.5 34.8 1.0 CE1 B:HIS46 3.0 20.5 1.0 CD B:GLU113 3.0 32.4 1.0 CE1 B:HIS44 3.1 32.3 1.0 CD2 B:HIS44 3.2 31.6 1.0 OE2 B:GLU113 3.2 25.4 1.0 CG B:ASP214 3.2 32.4 1.0 CD2 B:HIS46 3.3 29.8 1.0 OD2 B:ASP214 3.4 34.6 1.0 AS B:CAC8 3.4 61.7 1.0 ZN B:ZN4 3.5 40.7 1.0 O2 B:CAC8 3.9 49.8 1.0 CE1 B:HIS76 4.0 29.8 1.0 C1 B:CAC8 4.1 33.6 1.0 NE2 B:HIS76 4.1 23.1 1.0 ZN B:ZN6 4.2 32.5 1.0 ND1 B:HIS46 4.2 24.6 1.0 CE1 B:HIS216 4.2 28.8 1.0 ND1 B:HIS44 4.2 39.0 1.0 CG B:HIS44 4.3 26.2 1.0 CG B:HIS46 4.4 20.3 1.0 CG B:GLU113 4.4 26.7 1.0 NE2 B:HIS216 4.6 32.0 1.0 CB B:ASP214 4.6 26.2 1.0 ND1 B:HIS76 4.8 28.2 1.0 CB B:GLU113 4.9 32.1 1.0 CA B:ASP214 4.9 28.8 1.0 NE2 B:HIS157 4.9 26.7 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of A Two-Domain Protein Containing Predicted Php- Like Metal-Dependent Phosphoesterase (BVU_3505) From Bacteroides Vulgatus Atcc 8482 at 2.20 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 Two-Domain Protein Containing Predicted Php- Like Metal-Dependent Phosphoesterase (BVU_3505) From Bacteroides Vulgatus Atcc 8482 at 2.20 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn6 b:32.5 occ:1.00 OD2 B:ASP51 1.8 23.9 1.0 NE2 B:HIS216 2.1 32.0 1.0 NE2 B:HIS76 2.1 23.1 1.0 C2 B:CAC8 2.4 24.2 1.0 O1 B:CAC8 2.5 37.2 1.0 CG B:ASP51 2.5 30.7 1.0 OD1 B:ASP51 2.5 23.0 1.0 AS B:CAC8 2.9 61.7 1.0 CD2 B:HIS216 3.1 34.3 1.0 CD2 B:HIS76 3.1 26.6 1.0 CE1 B:HIS216 3.1 28.8 1.0 CE1 B:HIS76 3.2 29.8 1.0 CE1 B:HIS46 3.9 20.5 1.0 NE2 B:HIS46 3.9 14.6 1.0 CB B:ASP51 4.0 31.7 1.0 ND1 B:HIS46 4.1 24.6 1.0 CD2 B:HIS46 4.2 29.8 1.0 ZN B:ZN5 4.2 34.6 1.0 ND1 B:HIS216 4.2 29.7 1.0 CG B:HIS216 4.2 25.3 1.0 CG B:HIS76 4.2 27.4 1.0 ND1 B:HIS76 4.3 28.2 1.0 O2 B:CAC8 4.3 49.8 1.0 C1 B:CAC8 4.3 33.6 1.0 CG B:HIS46 4.3 20.3 1.0 OE1 B:GLU113 4.6 30.5 1.0 CD2 B:TYR79 4.9 31.4 1.0 CA B:ASP51 5.0 31.7 1.0

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