Zinc in PDB 7kwd: Crystal Structure of Thermus Thermophilus Alkaline Phosphatase

The structure of Crystal Structure of Thermus Thermophilus Alkaline Phosphatase, PDB code: 7kwd was solved by G.Gallo, C.Coelho, B.Borges, N.Negri, F.Maiello, L.Hardy, M.Wurtele, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.26 / 2.10
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	163.175, 163.175, 163.175, 90, 90, 90
R / Rfree (%)	16.3 / 20.1

The structure of Crystal Structure of Thermus Thermophilus Alkaline Phosphatase also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Thermus Thermophilus Alkaline Phosphatase (pdb code 7kwd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Thermus Thermophilus Alkaline Phosphatase, PDB code: 7kwd:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Thermus Thermophilus Alkaline Phosphatase


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 Thermus Thermophilus Alkaline Phosphatase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn603 b:37.0 occ:1.00 OG A:SER95 2.1 36.7 1.0 OD2 A:ASP317 2.2 27.0 1.0 OD1 A:ASP47 2.2 21.9 1.0 NE2 A:HIS318 2.2 26.8 1.0 OD2 A:ASP47 2.7 25.0 1.0 CG A:ASP47 2.7 25.4 1.0 O41 A:TLA601 2.9 43.5 1.0 CG A:ASP317 3.0 22.1 1.0 CD2 A:HIS318 3.1 29.1 1.0 OD1 A:ASP317 3.1 20.1 1.0 CE1 A:HIS318 3.2 23.4 1.0 HD2 A:HIS318 3.2 35.0 1.0 HA A:SER95 3.3 39.0 1.0 CB A:SER95 3.3 38.8 1.0 HE1 A:HIS318 3.4 28.1 1.0 C4 A:TLA601 3.7 40.0 1.0 CA A:SER95 3.8 32.5 1.0 O4 A:TLA601 3.8 43.9 1.0 HB3 A:SER95 3.9 46.6 1.0 HB2 A:SER95 3.9 46.6 1.0 H A:GLY48 3.9 24.5 1.0 O A:HOH717 4.1 23.1 1.0 O A:HOH705 4.1 33.9 1.0 HA A:ASP47 4.1 25.8 1.0 CB A:ASP47 4.1 21.5 1.0 HE1 A:HIS433 4.2 30.6 1.0 CG A:HIS318 4.2 27.9 1.0 ND1 A:HIS318 4.2 21.4 1.0 HB2 A:ASP275 4.2 28.3 1.0 N A:SER95 4.3 30.5 1.0 N A:GLY48 4.3 20.4 1.0 HG1 A:THR148 4.3 26.1 1.0 CB A:ASP317 4.4 22.4 1.0 MG A:MG602 4.4 33.8 1.0 CG A:ASP275 4.4 25.3 1.0 H A:SER95 4.5 36.6 1.0 HB2 A:ASP317 4.5 26.9 1.0 OD2 A:ASP275 4.5 24.3 1.0 OD1 A:ASP275 4.5 20.6 1.0 CA A:ASP47 4.5 21.5 1.0 CE1 A:HIS433 4.5 25.5 1.0 HB3 A:ASP47 4.6 25.9 1.0 HB2 A:ASP47 4.7 25.9 1.0 OG1 A:THR148 4.7 21.7 1.0 C A:ASP47 4.7 22.8 1.0 CB A:ASP275 4.8 23.6 1.0 HB3 A:ASP317 4.8 26.9 1.0 O3 A:TLA601 4.8 53.6 1.0 NE2 A:HIS433 4.8 23.4 1.0 O A:HOH727 4.8 25.0 1.0 HA2 A:GLY48 4.8 29.2 1.0 HB3 A:ALA98 4.8 28.6 1.0 ZN A:ZN604 4.9 30.3 1.0 C3 A:TLA601 4.9 54.6 1.0 O A:HOH712 5.0 36.3 1.0 HB3 A:ASP275 5.0 28.3 1.0 HD1 A:HIS318 5.0 25.7 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Thermus Thermophilus Alkaline Phosphatase


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 Thermus Thermophilus Alkaline Phosphatase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn604 b:30.3 occ:1.00 H2 A:TLA601 1.6 55.9 1.0 OD2 A:ASP275 2.0 24.3 1.0 NE2 A:HIS433 2.2 23.4 1.0 NE2 A:HIS279 2.2 25.9 1.0 O41 A:TLA601 2.4 43.5 1.0 C2 A:TLA601 2.6 46.6 1.0 CG A:ASP275 2.6 25.3 1.0 OD1 A:ASP275 2.7 20.6 1.0 C4 A:TLA601 3.0 40.0 1.0 CD2 A:HIS279 3.1 20.1 1.0 CD2 A:HIS433 3.1 24.8 1.0 HD2 A:HIS279 3.1 24.1 1.0 CE1 A:HIS433 3.2 25.5 1.0 C3 A:TLA601 3.2 54.6 1.0 CE1 A:HIS279 3.3 25.4 1.0 HD2 A:HIS433 3.3 29.8 1.0 HE1 A:HIS433 3.4 30.6 1.0 O1 A:TLA601 3.4 62.5 1.0 C1 A:TLA601 3.5 62.9 1.0 HE1 A:HIS279 3.5 30.5 1.0 O2 A:TLA601 3.6 54.3 1.0 HE1 A:HIS318 3.6 28.1 1.0 O3 A:TLA601 3.8 53.6 1.0 O A:HOH712 4.1 36.3 1.0 O4 A:TLA601 4.1 43.9 1.0 CB A:ASP275 4.1 23.6 1.0 H3 A:TLA601 4.2 65.5 1.0 HG21 A:THR320 4.2 30.3 1.0 CG A:HIS279 4.3 23.7 1.0 ND1 A:HIS433 4.3 28.2 1.0 CG A:HIS433 4.3 24.1 1.0 HD2 A:HIS276 4.3 32.8 1.0 CE1 A:HIS318 4.3 23.4 1.0 ND1 A:HIS279 4.3 27.6 1.0 HB3 A:ASP275 4.3 28.3 1.0 HA A:TLA601 4.4 65.2 1.0 HE2 B:TYR332 4.5 30.1 1.0 HB2 A:ASP275 4.5 28.3 1.0 HB A:TLA601 4.5 64.3 1.0 OG1 A:THR320 4.6 22.0 1.0 NE2 A:HIS318 4.7 26.8 1.0 O11 A:TLA601 4.7 60.5 1.0 ZN A:ZN603 4.9 37.0 1.0 HG23 A:THR320 4.9 30.3 1.0 CG2 A:THR320 5.0 25.3 1.0 OD1 A:ASP47 5.0 21.9 1.0 HG1 A:THR320 5.0 26.5 1.0 C A:ASP275 5.0 22.7 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Thermus Thermophilus Alkaline Phosphatase


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 Thermus Thermophilus Alkaline Phosphatase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn603 b:38.5 occ:1.00 OG B:SER95 1.9 44.2 1.0 OD2 B:ASP317 2.2 26.9 1.0 NE2 B:HIS318 2.3 27.9 1.0 OD1 B:ASP47 2.3 26.7 1.0 O4 B:TLA601 2.7 41.3 1.0 OD2 B:ASP47 2.8 28.7 1.0 CG B:ASP47 2.8 24.5 1.0 CG B:ASP317 3.0 29.1 1.0 CD2 B:HIS318 3.1 24.6 1.0 OD1 B:ASP317 3.1 22.7 1.0 HA B:SER95 3.1 40.9 1.0 HD2 B:HIS318 3.2 29.5 1.0 CB B:SER95 3.2 39.4 1.0 CE1 B:HIS318 3.2 27.9 1.0 HE1 B:HIS318 3.5 33.5 1.0 CA B:SER95 3.6 34.1 1.0 HB2 B:SER95 3.7 47.3 1.0 HB3 B:SER95 3.8 47.3 1.0 H B:GLY48 3.9 28.6 1.0 C4 B:TLA601 3.9 42.3 1.0 O B:HOH720 4.0 37.8 1.0 O B:HOH763 4.0 23.6 1.0 HA B:ASP47 4.1 29.0 1.0 N B:SER95 4.2 35.5 1.0 CB B:ASP47 4.2 25.4 1.0 CG B:HIS318 4.2 26.0 1.0 ND1 B:HIS318 4.2 23.8 1.0 H B:SER95 4.3 42.6 1.0 HB2 B:ASP275 4.3 28.9 1.0 N B:GLY48 4.3 23.8 1.0 O3 B:TLA601 4.3 45.8 1.0 HE1 B:HIS433 4.3 33.7 1.0 CB B:ASP317 4.4 19.3 1.0 MG B:MG602 4.4 34.5 1.0 HB2 B:ASP317 4.5 23.1 1.0 O41 B:TLA601 4.5 51.6 1.0 CG B:ASP275 4.5 24.1 1.0 CA B:ASP47 4.6 24.1 1.0 OD1 B:ASP275 4.6 30.2 1.0 CE1 B:HIS433 4.6 28.1 1.0 OD2 B:ASP275 4.7 27.5 1.0 HB2 B:ASP47 4.7 30.5 1.0 HB3 B:ASP47 4.7 30.5 1.0 NE2 B:HIS433 4.7 23.3 1.0 OG1 B:THR148 4.7 27.2 1.0 C B:ASP47 4.8 25.2 1.0 HA2 B:GLY48 4.8 29.9 1.0 HB3 B:ALA98 4.8 33.2 1.0 HB3 B:ASP317 4.8 23.1 1.0 ZN B:ZN604 4.8 33.4 1.0 CB B:ASP275 4.9 24.1 1.0 C3 B:TLA601 4.9 57.8 1.0 O B:HOH726 4.9 28.9 1.0 C B:GLU94 4.9 34.6 1.0 C B:SER95 4.9 30.3 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Thermus Thermophilus Alkaline Phosphatase


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 Thermus Thermophilus Alkaline Phosphatase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn604 b:33.4 occ:1.00 H2 B:TLA601 1.6 67.7 1.0 OD2 B:ASP275 2.1 27.5 1.0 NE2 B:HIS433 2.2 23.3 1.0 NE2 B:HIS279 2.2 26.1 1.0 C2 B:TLA601 2.6 56.4 1.0 OD1 B:ASP275 2.7 30.2 1.0 CG B:ASP275 2.7 24.1 1.0 O4 B:TLA601 3.0 41.3 1.0 CD2 B:HIS279 3.0 25.8 1.0 HD2 B:HIS279 3.0 31.0 1.0 C4 B:TLA601 3.1 42.3 1.0 CD2 B:HIS433 3.1 27.4 1.0 CE1 B:HIS433 3.1 28.1 1.0 O2 B:TLA601 3.2 59.3 1.0 C3 B:TLA601 3.2 57.8 1.0 HD2 B:HIS433 3.3 32.9 1.0 CE1 B:HIS279 3.3 29.4 1.0 HE1 B:HIS433 3.3 33.7 1.0 HA B:TLA601 3.3 71.2 1.0 O3 B:TLA601 3.5 45.8 1.0 HE1 B:HIS318 3.6 33.5 1.0 HE1 B:HIS279 3.6 35.4 1.0 C1 B:TLA601 3.8 70.8 1.0 HB B:TLA601 3.8 54.9 1.0 O41 B:TLA601 3.8 51.6 1.0 O11 B:TLA601 4.0 60.2 1.0 CB B:ASP275 4.2 24.1 1.0 H3 B:TLA601 4.2 69.4 1.0 CG B:HIS279 4.2 29.8 1.0 HD2 B:HIS276 4.2 39.3 1.0 ND1 B:HIS433 4.3 29.1 1.0 CG B:HIS433 4.3 21.1 1.0 CE1 B:HIS318 4.3 27.9 1.0 HG1 B:THR320 4.3 32.8 1.0 ND1 B:HIS279 4.3 28.9 1.0 HG21 B:THR320 4.3 28.8 1.0 HB3 B:ASP275 4.4 28.9 1.0 HB2 B:ASP275 4.6 28.9 1.0 OG1 B:THR320 4.6 27.3 1.0 HE2 A:TYR332 4.6 36.6 1.0 NE2 B:HIS318 4.7 27.9 1.0 ZN B:ZN603 4.8 38.5 1.0 O1 B:TLA601 4.9 68.0 1.0 OD1 B:ASP47 4.9 26.7 1.0

B.Borges, G.Gallo, C.Coelho, N.Negri, F.Maiello, L.Hardy, M.Wurtele. Dynamic Cross Correlation Analysis of Thermus Thermophilus Alkaline Phosphatase and Determinants of Thermostability. Biochim Biophys Acta Gen 29895 2021SUBJ.
ISSN: ISSN 1872-8006
PubMed: 33781823
DOI: 10.1016/J.BBAGEN.2021.129895