Zinc in PDB 7tm9: Crystal Structure of Bacterial Alkaline Phosphatase From Klebsiella Pneumoniae

The structure of Crystal Structure of Bacterial Alkaline Phosphatase From Klebsiella Pneumoniae, PDB code: 7tm9 was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.09 / 1.95
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	71.95, 240.6, 101.479, 90, 105.13, 90
R / Rfree (%)	17.2 / 21.1

The structure of Crystal Structure of Bacterial Alkaline Phosphatase From Klebsiella Pneumoniae also contains other interesting chemical elements:

Magnesium

(Mg)

8 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Bacterial Alkaline Phosphatase From Klebsiella Pneumoniae (pdb code 7tm9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 16 binding sites of Zinc where determined in the Crystal Structure of Bacterial Alkaline Phosphatase From Klebsiella Pneumoniae, PDB code: 7tm9:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 16 in the Crystal Structure of Bacterial Alkaline Phosphatase From Klebsiella Pneumoniae


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 Bacterial Alkaline Phosphatase From Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:40.0 occ:1.00 O1P A:SEP117 1.8 27.7 1.0 OD2 A:ASP342 2.1 29.4 1.0 NE2 A:HIS346 2.2 22.5 1.0 NE2 A:HIS427 2.2 16.1 1.0 CG A:ASP342 2.7 20.4 1.0 OD1 A:ASP342 2.7 18.7 1.0 CD2 A:HIS346 3.1 26.2 1.0 CE1 A:HIS427 3.2 13.0 1.0 CD2 A:HIS427 3.2 18.7 1.0 P A:SEP117 3.2 25.8 1.0 CE1 A:HIS346 3.3 19.6 1.0 O2P A:SEP117 3.8 18.0 1.0 NE2 A:HIS387 3.9 22.9 1.0 ZN A:ZN502 4.0 34.7 1.0 O3P A:SEP117 4.0 25.2 1.0 CE1 A:HIS385 4.1 12.1 1.0 CB A:ASP342 4.1 20.2 1.0 NE2 A:HIS385 4.2 13.7 1.0 O A:HOH839 4.2 28.5 1.0 CG A:HIS346 4.2 22.2 1.0 ND1 A:HIS427 4.3 15.1 1.0 ND1 A:HIS346 4.3 23.0 1.0 CG A:HIS427 4.3 14.3 1.0 OG A:SEP117 4.3 23.9 1.0 O A:HOH630 4.4 17.4 1.0 CD2 A:HIS387 4.5 21.4 1.0 OD1 A:ASP66 4.5 13.8 1.0 O A:HOH959 4.7 27.2 1.0 O A:ASP342 4.9 15.5 1.0 C A:ASP342 4.9 15.9 1.0 CA A:ASP342 5.0 13.8 1.0 CE1 A:HIS387 5.0 24.0 1.0

Zinc binding site 2 out of 16 in the Crystal Structure of Bacterial Alkaline Phosphatase From Klebsiella Pneumoniae


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 Bacterial Alkaline Phosphatase From Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:34.7 occ:1.00 OG A:SEP117 2.0 23.9 1.0 OD1 A:ASP66 2.2 13.8 1.0 OD2 A:ASP384 2.2 10.6 1.0 NE2 A:HIS385 2.3 13.7 1.0 O1P A:SEP117 2.6 27.7 1.0 OD2 A:ASP66 2.8 9.3 1.0 CG A:ASP66 2.8 13.8 1.0 P A:SEP117 2.9 25.8 1.0 CD2 A:HIS385 3.1 10.4 1.0 CG A:ASP384 3.2 7.4 1.0 CB A:SEP117 3.2 14.0 1.0 CE1 A:HIS385 3.2 12.1 1.0 OD1 A:ASP384 3.4 7.3 1.0 OD2 A:ASP342 3.5 29.4 1.0 CA A:SEP117 3.6 12.2 1.0 O3P A:SEP117 4.0 25.2 1.0 CG A:ASP342 4.0 20.4 1.0 ZN A:ZN501 4.0 40.0 1.0 O2P A:SEP117 4.0 18.0 1.0 N A:SEP117 4.1 6.4 1.0 CE1 A:HIS427 4.2 13.0 1.0 CB A:ASP66 4.3 9.3 1.0 CG A:HIS385 4.3 10.6 1.0 ND1 A:HIS385 4.3 11.2 1.0 O A:HOH649 4.3 8.8 1.0 O A:HOH641 4.4 10.3 1.0 NE2 A:HIS427 4.5 16.1 1.0 OD1 A:ASP342 4.5 18.7 1.0 CB A:ASP342 4.5 20.2 1.0 CB A:ASP384 4.5 8.8 1.0 N A:GLY67 4.5 13.1 1.0 MG A:MG503 4.6 14.0 1.0 CA A:ASP66 4.7 10.8 1.0 C A:ASP66 4.8 14.6 1.0 O A:HOH630 4.9 17.4 1.0 C A:ASP116 4.9 7.8 1.0

Zinc binding site 3 out of 16 in the Crystal Structure of Bacterial Alkaline Phosphatase From Klebsiella Pneumoniae


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 Bacterial Alkaline Phosphatase From Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:37.4 occ:1.00 O3P B:SEP117 1.8 24.6 1.0 NE2 B:HIS346 2.3 23.0 1.0 NE2 B:HIS427 2.3 15.2 1.0 OD1 B:ASP342 2.3 17.6 1.0 OD2 B:ASP342 2.5 13.4 1.0 CG B:ASP342 2.7 18.1 1.0 CD2 B:HIS346 2.8 24.9 1.0 P B:SEP117 3.2 26.7 1.0 CD2 B:HIS427 3.2 13.7 1.0 CE1 B:HIS427 3.3 13.2 1.0 CE1 B:HIS346 3.4 22.6 1.0 O1P B:SEP117 3.8 18.1 1.0 O2P B:SEP117 3.9 15.3 1.0 NE2 B:HIS387 3.9 17.1 1.0 CG B:HIS346 4.1 24.9 1.0 CE1 B:HIS385 4.2 13.3 1.0 CB B:ASP342 4.2 12.7 1.0 NE2 B:HIS385 4.2 11.5 1.0 ZN B:ZN502 4.2 32.9 1.0 O B:HOH988 4.2 14.4 1.0 ND1 B:HIS427 4.3 11.1 1.0 CG B:HIS427 4.3 11.6 1.0 OG B:SEP117 4.3 27.2 1.0 ND1 B:HIS346 4.4 22.5 1.0 CD2 B:HIS387 4.5 13.7 1.0 O B:HOH1247 4.5 27.9 1.0 OD1 B:ASP66 4.6 11.8 1.0 O B:ASP342 4.7 11.8 1.0 C B:ASP342 4.9 14.5 1.0 CE1 B:HIS387 4.9 17.4 1.0

Zinc binding site 4 out of 16 in the Crystal Structure of Bacterial Alkaline Phosphatase From Klebsiella Pneumoniae


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 Bacterial Alkaline Phosphatase From Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:32.9 occ:1.00 OG B:SEP117 2.0 27.2 1.0 OD2 B:ASP384 2.1 10.6 1.0 OD1 B:ASP66 2.1 11.8 1.0 NE2 B:HIS385 2.3 11.5 1.0 O3P B:SEP117 2.7 24.6 1.0 CG B:ASP66 2.8 9.4 1.0 OD2 B:ASP66 2.8 9.8 1.0 P B:SEP117 3.0 26.7 1.0 CG B:ASP384 3.0 11.8 1.0 CD2 B:HIS385 3.0 11.5 1.0 CB B:SEP117 3.2 11.0 1.0 CE1 B:HIS385 3.3 13.3 1.0 OD1 B:ASP384 3.3 7.3 1.0 CA B:SEP117 3.6 9.1 1.0 OD1 B:ASP342 4.0 17.6 1.0 O1P B:SEP117 4.1 18.1 1.0 N B:SEP117 4.1 8.3 1.0 O2P B:SEP117 4.1 15.3 1.0 CG B:ASP342 4.1 18.1 1.0 CG B:HIS385 4.2 12.3 1.0 O B:HOH1092 4.2 6.9 1.0 CB B:ASP66 4.2 9.6 1.0 ZN B:ZN501 4.2 37.4 1.0 ND1 B:HIS385 4.3 13.7 1.0 CB B:ASP384 4.3 5.7 1.0 O B:HOH1122 4.4 9.1 1.0 CE1 B:HIS427 4.4 13.2 1.0 MG B:MG503 4.5 10.7 1.0 N B:GLY67 4.5 8.4 1.0 OD2 B:ASP342 4.5 13.4 1.0 CB B:ASP342 4.6 12.7 1.0 NE2 B:HIS427 4.6 15.2 1.0 CA B:ASP66 4.7 10.7 1.0 C B:ASP66 4.9 7.6 1.0 O B:HOH988 4.9 14.4 1.0 C B:ASP116 4.9 7.8 1.0 OG1 B:THR170 4.9 4.2 1.0 O B:HOH1069 5.0 6.7 1.0 C B:SEP117 5.0 7.9 1.0

Zinc binding site 5 out of 16 in the Crystal Structure of Bacterial Alkaline Phosphatase From Klebsiella Pneumoniae


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 Bacterial Alkaline Phosphatase From Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:42.9 occ:1.00 O1P C:SEP117 1.8 29.0 1.0 OD2 C:ASP342 2.3 22.4 1.0 NE2 C:HIS346 2.3 22.8 1.0 NE2 C:HIS427 2.3 16.5 1.0 OD1 C:ASP342 2.5 16.7 1.0 CG C:ASP342 2.7 22.1 1.0 CD2 C:HIS346 2.9 26.2 1.0 P C:SEP117 3.1 20.8 1.0 CE1 C:HIS427 3.3 16.7 1.0 CD2 C:HIS427 3.3 14.7 1.0 CE1 C:HIS346 3.5 24.4 1.0 O2P C:SEP117 3.7 16.4 1.0 NE2 C:HIS387 3.8 21.4 1.0 O3P C:SEP117 4.0 21.1 1.0 O C:HOH610 4.0 19.4 1.0 CE1 C:HIS385 4.1 14.4 1.0 NE2 C:HIS385 4.1 17.0 1.0 CB C:ASP342 4.1 26.3 1.0 CG C:HIS346 4.2 23.9 1.0 OG C:SEP117 4.2 31.0 1.0 ZN C:ZN502 4.3 39.1 1.0 ND1 C:HIS427 4.4 18.5 1.0 ND1 C:HIS346 4.4 26.4 1.0 CG C:HIS427 4.4 19.8 1.0 OD1 C:ASP66 4.5 22.4 1.0 CD2 C:HIS387 4.6 16.8 1.0 O C:ASP342 4.7 19.1 1.0 CE1 C:HIS387 4.7 20.3 1.0 C C:ASP342 4.8 24.8 1.0 O C:HOH986 4.9 32.4 1.0 CA C:ASP342 5.0 20.1 1.0

Zinc binding site 6 out of 16 in the Crystal Structure of Bacterial Alkaline Phosphatase From Klebsiella Pneumoniae


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 Bacterial Alkaline Phosphatase From Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn502 b:39.1 occ:1.00 OG C:SEP117 2.0 31.0 1.0 OD2 C:ASP384 2.0 12.3 1.0 OD1 C:ASP66 2.1 22.4 1.0 NE2 C:HIS385 2.3 17.0 1.0 OD2 C:ASP66 2.7 10.6 1.0 CG C:ASP66 2.7 18.8 1.0 O1P C:SEP117 2.8 29.0 1.0 CD2 C:HIS385 2.9 11.6 1.0 CG C:ASP384 2.9 13.2 1.0 CB C:SEP117 3.0 14.0 1.0 P C:SEP117 3.1 20.8 1.0 OD1 C:ASP384 3.3 5.9 1.0 CE1 C:HIS385 3.4 14.4 1.0 CA C:SEP117 3.6 11.5 1.0 OD2 C:ASP342 3.7 22.4 1.0 O3P C:SEP117 4.0 21.1 1.0 CG C:ASP342 4.1 22.1 1.0 N C:SEP117 4.1 9.5 1.0 CG C:HIS385 4.1 14.3 1.0 O C:HOH658 4.2 6.0 1.0 CB C:ASP66 4.2 11.0 1.0 O2P C:SEP117 4.2 16.4 1.0 CB C:ASP384 4.2 5.2 1.0 ZN C:ZN501 4.3 42.9 1.0 ND1 C:HIS385 4.3 12.1 1.0 O C:HOH706 4.4 8.7 1.0 CE1 C:HIS427 4.4 16.7 1.0 MG C:MG503 4.4 8.2 1.0 OD1 C:ASP342 4.5 16.7 1.0 N C:GLY67 4.5 13.4 1.0 CB C:ASP342 4.6 26.3 1.0 NE2 C:HIS427 4.6 16.5 1.0 CA C:ASP66 4.6 10.9 1.0 O C:HOH610 4.7 19.4 1.0 C C:ASP66 4.9 11.8 1.0 C C:ASP116 4.9 7.4 1.0 C C:SEP117 4.9 9.3 1.0 OG1 C:THR170 4.9 7.6 1.0

Zinc binding site 7 out of 16 in the Crystal Structure of Bacterial Alkaline Phosphatase From Klebsiella Pneumoniae


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 Bacterial Alkaline Phosphatase From Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn501 b:42.4 occ:1.00 O2P D:SEP117 1.8 31.9 1.0 NE2 D:HIS346 2.2 27.9 1.0 NE2 D:HIS427 2.3 18.5 1.0 OD2 D:ASP342 2.3 19.5 1.0 OD1 D:ASP342 2.5 20.8 1.0 CG D:ASP342 2.6 23.3 1.0 CD2 D:HIS346 3.0 19.1 1.0 CD2 D:HIS427 3.2 15.2 1.0 P D:SEP117 3.2 28.0 1.0 CE1 D:HIS427 3.3 19.1 1.0 CE1 D:HIS346 3.3 25.9 1.0 O1P D:SEP117 3.8 17.9 1.0 NE2 D:HIS387 3.8 19.7 1.0 O3P D:SEP117 3.9 14.3 1.0 CB D:ASP342 4.1 22.7 1.0 CE1 D:HIS385 4.1 14.5 1.0 ZN D:ZN502 4.1 33.3 1.0 NE2 D:HIS385 4.2 12.5 1.0 CG D:HIS346 4.2 22.2 1.0 O D:HOH662 4.2 16.3 1.0 OG D:SEP117 4.3 22.4 1.0 ND1 D:HIS346 4.3 24.4 1.0 ND1 D:HIS427 4.4 13.7 1.0 CG D:HIS427 4.4 18.5 1.0 CD2 D:HIS387 4.5 14.9 1.0 OD1 D:ASP66 4.5 10.6 1.0 O D:HOH963 4.6 25.8 1.0 O D:HOH999 4.7 34.0 1.0 O D:ASP342 4.8 15.8 1.0 CE1 D:HIS387 4.8 21.2 1.0 C D:ASP342 4.9 18.2 1.0 CA D:ASP342 5.0 15.1 1.0

Zinc binding site 8 out of 16 in the Crystal Structure of Bacterial Alkaline Phosphatase From Klebsiella Pneumoniae


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 Bacterial Alkaline Phosphatase From Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn502 b:33.3 occ:1.00 OG D:SEP117 1.9 22.4 1.0 OD2 D:ASP384 2.2 8.3 1.0 OD1 D:ASP66 2.2 10.6 1.0 NE2 D:HIS385 2.3 12.5 1.0 O2P D:SEP117 2.6 31.9 1.0 OD2 D:ASP66 2.8 10.5 1.0 CG D:ASP66 2.8 15.3 1.0 P D:SEP117 2.9 28.0 1.0 CD2 D:HIS385 3.0 8.5 1.0 CB D:SEP117 3.0 10.5 1.0 CG D:ASP384 3.1 8.4 1.0 CE1 D:HIS385 3.4 14.5 1.0 OD1 D:ASP384 3.4 8.9 1.0 CA D:SEP117 3.6 10.9 1.0 O3P D:SEP117 3.8 14.3 1.0 OD2 D:ASP342 4.0 19.5 1.0 N D:SEP117 4.0 11.0 1.0 O1P D:SEP117 4.1 17.9 1.0 ZN D:ZN501 4.1 42.4 1.0 CG D:ASP342 4.1 23.3 1.0 O D:HOH711 4.2 8.8 1.0 CG D:HIS385 4.2 10.3 1.0 CB D:ASP66 4.3 10.9 1.0 O D:HOH647 4.3 9.3 1.0 CE1 D:HIS427 4.3 19.1 1.0 ND1 D:HIS385 4.3 8.6 1.0 CB D:ASP384 4.4 6.8 1.0 NE2 D:HIS427 4.4 18.5 1.0 OD1 D:ASP342 4.5 20.8 1.0 N D:GLY67 4.5 8.5 1.0 CB D:ASP342 4.6 22.7 1.0 MG D:MG503 4.6 8.3 1.0 CA D:ASP66 4.8 8.3 1.0 C D:ASP116 4.9 9.3 1.0 C D:ASP66 4.9 9.7 1.0 OG1 D:THR170 5.0 7.3 1.0 O D:HOH662 5.0 16.3 1.0 C D:SEP117 5.0 7.8 1.0

Zinc binding site 9 out of 16 in the Crystal Structure of Bacterial Alkaline Phosphatase From Klebsiella Pneumoniae


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 Bacterial Alkaline Phosphatase From Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn501 b:36.5 occ:1.00 O3P E:SEP117 1.9 25.9 1.0 OD2 E:ASP342 2.2 21.1 1.0 NE2 E:HIS346 2.3 23.5 1.0 NE2 E:HIS427 2.3 14.5 1.0 O E:HOH825 2.6 33.4 1.0 OD1 E:ASP342 2.6 13.4 1.0 CG E:ASP342 2.7 17.3 1.0 CD2 E:HIS346 3.0 25.0 1.0 CD2 E:HIS427 3.2 15.2 1.0 CE1 E:HIS427 3.3 17.8 1.0 P E:SEP117 3.3 25.8 1.0 CE1 E:HIS346 3.4 29.1 1.0 O1P E:SEP117 3.7 17.8 1.0 ZN E:ZN502 4.0 31.9 1.0 NE2 E:HIS387 4.0 19.0 1.0 O2P E:SEP117 4.0 21.1 1.0 CB E:ASP342 4.1 16.3 1.0 CE1 E:HIS385 4.1 11.8 1.0 NE2 E:HIS385 4.2 10.7 1.0 CG E:HIS346 4.3 23.9 1.0 O E:HOH877 4.3 31.0 1.0 O E:HOH604 4.3 20.1 1.0 O E:HOH891 4.4 28.1 1.0 CG E:HIS427 4.4 17.4 1.0 OG E:SEP117 4.4 15.4 1.0 ND1 E:HIS427 4.4 10.7 1.0 ND1 E:HIS346 4.4 29.2 1.0 CD2 E:HIS387 4.5 13.7 1.0 OD1 E:ASP66 4.6 8.2 1.0 O E:ASP342 4.9 17.9 1.0 C E:ASP342 5.0 18.4 1.0 CE1 E:HIS387 5.0 18.5 1.0

Zinc binding site 10 out of 16 in the Crystal Structure of Bacterial Alkaline Phosphatase From Klebsiella Pneumoniae


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 Bacterial Alkaline Phosphatase From Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn502 b:31.9 occ:1.00 OG E:SEP117 2.0 15.4 1.0 OD1 E:ASP66 2.1 8.2 1.0 OD2 E:ASP384 2.3 8.9 1.0 NE2 E:HIS385 2.3 10.7 1.0 O3P E:SEP117 2.6 25.9 1.0 CG E:ASP66 2.8 7.8 1.0 OD2 E:ASP66 2.9 6.8 1.0 P E:SEP117 2.9 25.8 1.0 CD2 E:HIS385 3.1 11.8 1.0 CG E:ASP384 3.2 8.9 1.0 CB E:SEP117 3.2 5.9 1.0 CE1 E:HIS385 3.2 11.8 1.0 OD1 E:ASP384 3.4 7.9 1.0 CA E:SEP117 3.7 10.4 1.0 OD2 E:ASP342 3.8 21.1 1.0 ZN E:ZN501 4.0 36.5 1.0 O1P E:SEP117 4.0 17.8 1.0 CG E:ASP342 4.0 17.3 1.0 O2P E:SEP117 4.0 21.1 1.0 N E:SEP117 4.1 6.2 1.0 ND1 E:HIS385 4.3 10.9 1.0 CB E:ASP66 4.3 8.6 1.0 CG E:HIS385 4.3 7.8 1.0 CE1 E:HIS427 4.3 17.8 1.0 O E:HOH713 4.4 5.6 1.0 NE2 E:HIS427 4.4 14.5 1.0 O E:HOH685 4.4 11.2 1.0 N E:GLY67 4.4 10.5 1.0 CB E:ASP342 4.5 16.3 1.0 CB E:ASP384 4.5 4.1 1.0 OD1 E:ASP342 4.5 13.4 1.0 MG E:MG503 4.5 7.2 1.0 CA E:ASP66 4.7 9.5 1.0 C E:ASP66 4.8 10.7 1.0 C E:ASP116 4.9 7.1 1.0 O E:HOH604 4.9 20.1 1.0

L.Liu, S.Lovell, K.P.Battaile, L.Tillery, R.Shek, J.K.Craig, L.K.Barrett, W.C.Van Voorhis. Crystal Structure of Bacterial Alkaline Phosphatase From Klebsiella Pneumoniae To Be Published.