Zinc in PDB 3kya: Crystal Structure of Putative Phosphatase (NP_812416.1) From Bacteroides Thetaiotaomicron Vpi-5482 at 1.77 A Resolution

The structure of Crystal Structure of Putative Phosphatase (NP_812416.1) From Bacteroides Thetaiotaomicron Vpi-5482 at 1.77 A Resolution, PDB code: 3kya 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)	29.26 / 1.77
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	94.830, 124.623, 98.389, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 19.8

The structure of Crystal Structure of Putative Phosphatase (NP_812416.1) From Bacteroides Thetaiotaomicron Vpi-5482 at 1.77 A Resolution also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Putative Phosphatase (NP_812416.1) From Bacteroides Thetaiotaomicron Vpi-5482 at 1.77 A Resolution (pdb code 3kya). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Crystal Structure of Putative Phosphatase (NP_812416.1) From Bacteroides Thetaiotaomicron Vpi-5482 at 1.77 A Resolution, PDB code: 3kya:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in the Crystal Structure of Putative Phosphatase (NP_812416.1) From Bacteroides Thetaiotaomicron Vpi-5482 at 1.77 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 Putative Phosphatase (NP_812416.1) From Bacteroides Thetaiotaomicron Vpi-5482 at 1.77 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn22 b:24.6 occ:1.00 OD1 A:ASP66 1.9 12.9 1.0 CG A:ASP66 3.0 12.2 1.0 OD2 A:ASP66 3.5 13.2 1.0 O A:THR65 3.8 13.1 1.0 CB A:ASP66 4.2 12.3 1.0 O A:HOH555 4.3 15.4 1.0 O A:HOH606 4.3 22.9 1.0 CA A:ASP66 4.4 12.5 1.0 C A:THR65 4.4 12.8 1.0 OG1 A:THR65 4.5 11.9 1.0 N A:ASP66 4.7 12.7 1.0 O A:HOH538 4.8 11.0 1.0

Zinc binding site 2 out of 9 in the Crystal Structure of Putative Phosphatase (NP_812416.1) From Bacteroides Thetaiotaomicron Vpi-5482 at 1.77 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 Putative Phosphatase (NP_812416.1) From Bacteroides Thetaiotaomicron Vpi-5482 at 1.77 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn519 b:24.8 occ:1.00 O A:HOH803 1.9 13.0 1.0 O A:HOH877 1.9 24.8 1.0 OD2 A:ASP190 2.0 13.2 1.0 NE2 A:HIS175 2.1 10.5 1.0 O A:HOH804 2.2 15.7 1.0 O A:HOH674 2.3 17.9 1.0 CG A:ASP190 3.1 13.0 1.0 CE1 A:HIS175 3.1 12.9 1.0 CD2 A:HIS175 3.1 13.4 1.0 OD1 A:ASP190 3.4 12.7 1.0 ND2 A:ASN193 3.8 19.8 0.5 O A:HOH653 4.0 21.0 1.0 O A:HOH618 4.0 18.2 1.0 ND1 A:HIS175 4.2 12.1 1.0 CG A:HIS175 4.3 11.8 1.0 CB A:ASP190 4.4 12.0 1.0 O A:HOH822 4.4 41.4 1.0 O A:HOH671 4.5 28.2 1.0 CG A:ASN193 4.8 17.4 0.5 ND2 A:ASN172 4.9 15.2 1.0

Zinc binding site 3 out of 9 in the Crystal Structure of Putative Phosphatase (NP_812416.1) From Bacteroides Thetaiotaomicron Vpi-5482 at 1.77 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 Putative Phosphatase (NP_812416.1) From Bacteroides Thetaiotaomicron Vpi-5482 at 1.77 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn520 b:26.5 occ:0.50 O A:ACT17 1.9 34.2 1.0 OXT A:ACT18 2.0 54.2 1.0 O A:HOH764 2.0 19.7 1.0 ND1 A:HIS183 2.1 14.5 1.0 OXT A:ACT17 2.6 37.8 1.0 C A:ACT17 2.7 36.7 1.0 C A:ACT18 2.9 54.5 1.0 O A:ACT18 3.0 54.5 1.0 CE1 A:HIS183 3.0 13.9 1.0 CG A:HIS183 3.2 14.6 1.0 CB A:HIS183 3.6 14.5 1.0 CA A:HIS183 4.0 14.8 1.0 OD2 A:ASP162 4.1 17.1 1.0 CE2 A:TRP144 4.1 13.0 1.0 NE2 A:HIS183 4.2 13.8 1.0 CZ2 A:TRP144 4.2 13.0 1.0 CH3 A:ACT17 4.2 36.2 1.0 O A:GLY182 4.2 14.5 1.0 CD2 A:HIS183 4.3 14.2 1.0 CH3 A:ACT18 4.3 54.5 1.0 O A:HOH856 4.3 31.8 1.0 NE1 A:TRP144 4.4 14.9 1.0 CD2 A:TRP144 4.5 13.0 1.0 CH2 A:TRP144 4.6 13.0 1.0 CD1 A:TRP144 4.8 14.2 1.0 CE3 A:TRP144 4.9 13.3 1.0 N A:HIS183 4.9 14.6 1.0 CZ3 A:TRP144 4.9 12.5 1.0 CG A:TRP144 4.9 12.8 1.0 C A:GLY182 4.9 14.7 1.0 O A:HOH580 5.0 39.9 1.0

Zinc binding site 4 out of 9 in the Crystal Structure of Putative Phosphatase (NP_812416.1) From Bacteroides Thetaiotaomicron Vpi-5482 at 1.77 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 Putative Phosphatase (NP_812416.1) From Bacteroides Thetaiotaomicron Vpi-5482 at 1.77 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn521 b:88.8 occ:0.50 ZN A:ZN522 1.6 64.2 0.5 OE2 A:GLU390 2.6 18.8 0.5 O A:HOH677 2.6 39.0 1.0 CD A:GLU390 3.0 17.4 0.5 OE1 A:GLU390 3.1 19.6 0.5 OD2 A:ASP386 3.3 18.7 1.0 CG A:ASP386 4.1 17.5 1.0 OD1 A:ASP386 4.1 16.8 1.0 CG A:GLU390 4.2 17.5 0.5 CG A:GLU390 4.3 16.4 0.5 CB A:GLU390 4.3 16.4 0.5 OE1 A:GLU390 4.3 21.9 0.5 CB A:GLU390 4.4 16.0 0.5 CD A:GLU390 4.5 20.1 0.5 NH2 A:ARG384 4.5 27.9 1.0

Zinc binding site 5 out of 9 in the Crystal Structure of Putative Phosphatase (NP_812416.1) From Bacteroides Thetaiotaomicron Vpi-5482 at 1.77 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 Putative Phosphatase (NP_812416.1) From Bacteroides Thetaiotaomicron Vpi-5482 at 1.77 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn522 b:64.2 occ:0.50 ZN A:ZN521 1.6 88.8 0.5 OE2 A:GLU390 2.3 18.8 0.5 CD A:GLU390 3.1 17.4 0.5 OE1 A:GLU390 3.3 19.6 0.5 O A:HOH677 4.0 39.0 1.0 OD2 A:ASP386 4.2 18.7 1.0 OD1 A:ASP386 4.2 16.8 1.0 CG A:GLU390 4.3 17.5 0.5 CG A:GLU390 4.5 16.4 0.5 CG A:ASP386 4.6 17.5 1.0 CB A:GLU390 4.8 16.4 0.5 CB A:GLU390 4.9 16.0 0.5 CD A:GLU390 4.9 20.1 0.5

Zinc binding site 6 out of 9 in the Crystal Structure of Putative Phosphatase (NP_812416.1) From Bacteroides Thetaiotaomicron Vpi-5482 at 1.77 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 Putative Phosphatase (NP_812416.1) From Bacteroides Thetaiotaomicron Vpi-5482 at 1.77 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn523 b:25.2 occ:0.50 OXT A:ACT16 2.0 37.0 1.0 OXT A:ACT15 2.0 47.8 1.0 OD2 A:ASP362 2.0 14.2 1.0 O A:HOH768 2.1 15.7 1.0 CG A:ASP362 2.8 13.4 1.0 C A:ACT15 2.8 47.6 1.0 O A:ACT15 2.9 47.6 1.0 OD1 A:ASP362 2.9 13.3 1.0 C A:ACT16 3.2 38.6 1.0 O A:ACT16 3.8 39.9 1.0 CB A:ILE364 4.2 18.7 1.0 CB A:ASP362 4.3 13.9 1.0 CH3 A:ACT15 4.3 47.4 1.0 CH3 A:ACT16 4.3 38.9 1.0 CG A:LYS365 4.5 19.9 1.0 O A:HOH944 4.5 25.2 1.0 CD A:LYS365 4.5 19.2 1.0 CG1 A:ILE364 4.6 19.1 1.0 N A:LYS365 4.7 17.9 1.0 CG2 A:ILE364 4.9 19.1 1.0

Zinc binding site 7 out of 9 in the Crystal Structure of Putative Phosphatase (NP_812416.1) From Bacteroides Thetaiotaomicron Vpi-5482 at 1.77 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 Putative Phosphatase (NP_812416.1) From Bacteroides Thetaiotaomicron Vpi-5482 at 1.77 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn524 b:48.2 occ:0.50 OE2 A:GLU227 2.3 17.0 1.0 OE1 A:GLU227 2.9 15.0 1.0 CD A:GLU227 2.9 16.2 1.0 C1 A:EDO13 3.6 36.5 0.5 OD2 A:ASP224 4.0 18.5 1.0 O2 A:EDO13 4.0 35.6 0.5 O A:HOH771 4.1 18.2 1.0 CG A:GLU227 4.3 14.2 1.0 C1 A:EDO13 4.3 26.3 0.5 C2 A:EDO13 4.4 36.5 0.5 O A:HOH528 4.4 34.8 1.0 C2 A:EDO13 4.4 24.8 0.5 O1 A:EDO13 4.7 36.3 0.5 CG A:ASP224 4.9 16.4 1.0 CE A:LYS249 4.9 20.3 1.0

Zinc binding site 8 out of 9 in the Crystal Structure of Putative Phosphatase (NP_812416.1) From Bacteroides Thetaiotaomicron Vpi-5482 at 1.77 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 Putative Phosphatase (NP_812416.1) From Bacteroides Thetaiotaomicron Vpi-5482 at 1.77 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn525 b:56.6 occ:0.50 OE1 A:GLU241 2.4 20.6 1.0 OE2 A:GLU241 2.5 22.3 1.0 CD A:GLU241 2.8 19.6 1.0 CD1 A:ILE314 4.2 18.3 0.5 CG A:GLU241 4.2 18.4 1.0 ND2 A:ASN317 4.7 25.8 1.0 CE A:LYS316 4.7 24.3 1.0 NZ A:LYS316 4.8 25.1 1.0

Zinc binding site 9 out of 9 in the Crystal Structure of Putative Phosphatase (NP_812416.1) From Bacteroides Thetaiotaomicron Vpi-5482 at 1.77 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 Putative Phosphatase (NP_812416.1) From Bacteroides Thetaiotaomicron Vpi-5482 at 1.77 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn526 b:43.1 occ:0.50 O A:ACT16 2.0 39.9 1.0 C A:ACT16 2.8 38.6 1.0 CH3 A:ACT16 2.9 38.9 1.0 O A:HOH921 3.9 27.6 1.0 OXT A:ACT16 4.0 37.0 1.0 CG1 A:ILE364 4.1 19.1 1.0 CD1 A:ILE364 4.6 21.1 1.0

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