Zinc in PDB 5tj3: Crystal Structure of Wild Type Alkaline Phosphatase Pafa to 1.7A Resolution

All present enzymatic activity of Crystal Structure of Wild Type Alkaline Phosphatase Pafa to 1.7A Resolution:
3.1.3.1;

The structure of Crystal Structure of Wild Type Alkaline Phosphatase Pafa to 1.7A Resolution, PDB code: 5tj3 was solved by A.Y.Lyubimov, F.Sunden, S.Ressl, D.Herschlag, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.99 / 1.70
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	113.797, 113.797, 71.442, 90.00, 90.00, 90.00
R / Rfree (%)	15.8 / 17.7

The binding sites of Zinc atom in the Crystal Structure of Wild Type Alkaline Phosphatase Pafa to 1.7A Resolution (pdb code 5tj3). 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 Wild Type Alkaline Phosphatase Pafa to 1.7A Resolution, PDB code: 5tj3:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Wild Type Alkaline Phosphatase Pafa to 1.7A 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 Wild Type Alkaline Phosphatase Pafa to 1.7A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:12.7 occ:1.00 OD1 A:ASP38 2.0 13.0 1.0 OD2 A:ASP352 2.0 10.9 1.0 OG1 A:TPO79 2.0 8.2 1.0 NE2 A:HIS353 2.1 11.5 1.0 CG A:ASP38 2.8 8.7 1.0 O3P A:TPO79 2.8 18.1 1.0 CG A:ASP352 2.9 7.2 1.0 P A:TPO79 3.0 16.7 1.0 OD2 A:ASP38 3.0 9.8 1.0 CD2 A:HIS353 3.0 8.0 1.0 CE1 A:HIS353 3.0 10.3 1.0 OD1 A:ASP352 3.2 5.2 1.0 CB A:TPO79 3.3 8.8 1.0 CA A:TPO79 3.6 9.3 1.0 OD1 A:ASP305 3.9 9.9 1.0 CG2 A:TPO79 3.9 9.0 1.0 O1P A:TPO79 3.9 12.9 1.0 ND1 A:HIS353 4.1 9.6 1.0 N A:TPO79 4.1 8.1 1.0 CG A:HIS353 4.1 8.2 1.0 CB A:ASP38 4.1 4.1 1.0 NZ A:LYS162 4.1 13.8 1.0 CG A:ASP305 4.2 9.8 1.0 O2P A:TPO79 4.2 15.9 1.0 ZN A:ZN602 4.2 17.1 1.0 CB A:ASP352 4.2 9.8 1.0 N A:GLN39 4.3 9.4 1.0 CE1 A:HIS486 4.4 12.6 1.0 NE2 A:HIS486 4.4 9.9 1.0 CA A:ASP38 4.4 6.2 1.0 OD2 A:ASP305 4.6 12.9 1.0 CB A:ASP305 4.7 10.6 1.0 C A:ASP38 4.7 8.0 1.0 CE1 A:HIS83 4.8 6.2 1.0 C A:VAL78 4.8 10.3 1.0 C A:TPO79 5.0 7.4 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Wild Type Alkaline Phosphatase Pafa to 1.7A 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 Wild Type Alkaline Phosphatase Pafa to 1.7A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:17.1 occ:1.00 O3P A:TPO79 1.9 18.1 1.0 NE2 A:HIS309 2.0 9.2 1.0 NE2 A:HIS486 2.2 9.9 1.0 OD1 A:ASP305 2.2 9.9 1.0 O A:HOH896 2.4 21.2 1.0 OD2 A:ASP305 2.7 12.9 1.0 CG A:ASP305 2.8 9.8 1.0 CD2 A:HIS309 2.9 10.7 1.0 CD2 A:HIS486 3.1 12.5 1.0 CE1 A:HIS309 3.1 10.6 1.0 CE1 A:HIS486 3.2 12.6 1.0 P A:TPO79 3.3 16.7 1.0 O1P A:TPO79 3.7 12.9 1.0 CE1 A:HIS353 4.0 10.3 1.0 NE2 A:GLN39 4.0 12.0 1.0 O A:HOH1020 4.0 25.8 1.0 NE2 A:HIS353 4.1 11.5 1.0 CG A:HIS309 4.1 10.9 1.0 O2P A:TPO79 4.1 15.9 1.0 ND1 A:HIS309 4.2 10.8 1.0 ZN A:ZN601 4.2 12.7 1.0 CG A:HIS486 4.3 10.7 1.0 CB A:ASP305 4.3 10.6 1.0 ND1 A:HIS486 4.3 12.7 1.0 OG1 A:TPO79 4.4 8.2 1.0 O A:HOH805 4.5 51.6 1.0 NZ A:LYS162 4.5 13.8 1.0 OD1 A:ASP38 4.6 13.0 1.0 O A:ASP305 4.9 10.5 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Wild Type Alkaline Phosphatase Pafa to 1.7A 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 Wild Type Alkaline Phosphatase Pafa to 1.7A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn603 b:30.2 occ:1.00 O A:PRO247 2.3 11.7 1.0 OE2 A:GLU238 2.4 8.8 1.0 O A:ASP233 2.4 11.8 1.0 OD1 A:ASP233 2.4 16.3 1.0 OE2 A:GLU317 2.6 9.9 1.0 OE1 A:GLU317 2.6 5.7 1.0 O A:HOH717 2.6 8.8 1.0 CD A:GLU317 3.0 8.2 1.0 CD A:GLU238 3.3 12.8 1.0 C A:ASP233 3.3 13.7 1.0 OE1 A:GLU238 3.5 15.5 1.0 CG A:ASP233 3.5 15.8 1.0 C A:PRO247 3.5 11.8 1.0 CA A:ASP233 3.6 16.8 1.0 CB A:ASP233 4.2 15.3 1.0 CA A:THR248 4.3 12.1 1.0 N A:THR248 4.3 10.8 1.0 CB A:PRO247 4.4 13.0 1.0 OD2 A:ASP233 4.5 14.5 1.0 CG A:GLU317 4.5 8.2 1.0 N A:ASN234 4.5 12.4 1.0 CA A:PRO247 4.6 12.8 1.0 O A:GLU232 4.6 17.4 1.0 CD1 A:PHE311 4.7 12.3 1.0 CG A:GLU238 4.7 12.9 1.0 OH A:TYR251 4.7 13.5 1.0 N A:ILE316 4.8 7.0 1.0 CE1 A:PHE311 4.9 13.3 1.0 CG A:PRO247 4.9 12.1 1.0 N A:ASP233 4.9 17.5 1.0 CB A:ILE316 4.9 6.2 1.0 N A:GLU317 5.0 8.1 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Wild Type Alkaline Phosphatase Pafa to 1.7A 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 Wild Type Alkaline Phosphatase Pafa to 1.7A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn604 b:0.7 occ:1.00 OD1 A:ASP291 2.3 24.4 1.0 O A:ILE293 2.3 12.3 1.0 OD2 A:ASP295 2.4 14.4 1.0 O A:HOH847 2.4 13.1 1.0 O A:HOH810 2.7 24.9 1.0 O A:HOH907 2.7 15.5 1.0 OD1 A:ASP295 2.9 15.6 1.0 CG A:ASP295 2.9 13.2 1.0 CG A:ASP291 3.4 25.5 1.0 C A:ILE293 3.4 12.7 1.0 OD2 A:ASP291 3.8 28.4 1.0 CB A:ILE293 3.9 17.2 1.0 CA A:ILE293 4.0 17.4 1.0 N A:ILE293 4.0 22.8 1.0 O A:HOH1007 4.2 22.2 1.0 O A:ASP291 4.3 22.3 1.0 CB A:ASP295 4.3 9.5 1.0 N A:ASP291 4.4 23.8 1.0 N A:GLY289 4.4 14.3 1.0 N A:ASP295 4.4 7.1 1.0 C A:ASP291 4.5 21.5 1.0 O A:LYS30 4.5 8.1 1.0 N A:THR294 4.6 8.2 1.0 O A:GLN287 4.6 17.7 1.0 CB A:ASP291 4.6 23.7 1.0 C A:THR294 4.6 7.6 1.0 CG2 A:ILE293 4.6 18.8 1.0 CA A:ASP291 4.7 22.4 1.0 N A:VAL290 4.9 18.8 1.0 CA A:ASP295 4.9 8.9 1.0 O A:HOH1096 4.9 21.2 1.0 CA A:GLY289 4.9 13.4 1.0 CA A:THR294 4.9 5.7 1.0

F.Sunden, I.Alsadhan, A.Y.Lyubimov, S.Ressl, H.Wiersma-Koch, J.Borland, C.L.Brown, T.A.Johnson, Z.Singh, D.Herschlag. Mechanistic and Evolutionary Insights From Comparative Enzymology of Phosphomonoesterases and Phosphodiesterases Across the Alkaline Phosphatase Superfamily. J.Am.Chem.Soc. V. 138 14273 2016.
ISSN: ESSN 1520-5126
PubMed: 27670607
DOI: 10.1021/JACS.6B06186