Zinc in PDB 3mk1: Refinement of Placental Alkaline Phosphatase Complexed with Nitrophenyl

All present enzymatic activity of Refinement of Placental Alkaline Phosphatase Complexed with Nitrophenyl:
3.1.3.1;

The structure of Refinement of Placental Alkaline Phosphatase Complexed with Nitrophenyl, PDB code: 3mk1 was solved by B.Stec, A.Cheltsov, J.L.Millan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	70.01 / 1.57
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	88.346, 114.573, 106.568, 90.00, 90.00, 90.00
R / Rfree (%)	13.9 / 17.8

The structure of Refinement of Placental Alkaline Phosphatase Complexed with Nitrophenyl also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Calcium	(Ca)	1 atom
Sodium	(Na)	1 atom

The binding sites of Zinc atom in the Refinement of Placental Alkaline Phosphatase Complexed with Nitrophenyl (pdb code 3mk1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Refinement of Placental Alkaline Phosphatase Complexed with Nitrophenyl, PDB code: 3mk1:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Refinement of Placental Alkaline Phosphatase Complexed with Nitrophenyl


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Refinement of Placental Alkaline Phosphatase Complexed with Nitrophenyl within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:13.1 occ:1.00 O A:HOH1002 2.0 18.7 1.0 NE2 A:HIS432 2.1 12.4 1.0 NE2 A:HIS320 2.1 11.0 1.0 OD1 A:ASP316 2.1 12.2 1.0 O3P A:SEP92 2.2 12.8 1.0 OD2 A:ASP316 2.5 11.4 1.0 CG A:ASP316 2.6 11.2 1.0 CD2 A:HIS320 3.0 11.0 1.0 CE1 A:HIS432 3.0 11.7 1.0 CD2 A:HIS432 3.1 11.6 1.0 CE1 A:HIS320 3.1 10.3 1.0 P A:SEP92 3.2 14.6 1.0 O1P A:SEP92 3.6 15.1 1.0 O A:HOH1485 3.8 53.0 1.0 O A:HOH1032 3.9 14.1 1.0 O2P A:SEP92 3.9 14.5 1.0 O A:HOH1323 4.0 43.7 1.0 CB A:ASP316 4.1 11.1 1.0 ZN A:ZN902 4.1 12.4 1.0 ND1 A:HIS432 4.1 10.6 1.0 ND1 A:HIS320 4.2 12.0 1.0 CG A:HIS320 4.2 11.5 1.0 CE1 A:HIS358 4.2 12.1 1.0 CG A:HIS432 4.2 12.0 1.0 NE2 A:HIS358 4.3 11.9 1.0 CE1 A:HIS360 4.5 10.6 1.0 OG A:SEP92 4.5 10.5 1.0 NE2 A:HIS360 4.6 10.9 1.0 OD1 A:ASP42 4.6 10.9 1.0 O3 A:NPO911 4.6 53.7 1.0 CA A:ASP316 5.0 11.3 1.0 O A:ASP316 5.0 12.0 1.0

Zinc binding site 2 out of 3 in the Refinement of Placental Alkaline Phosphatase Complexed with Nitrophenyl


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Refinement of Placental Alkaline Phosphatase Complexed with Nitrophenyl within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:12.4 occ:1.00 OD1 A:ASP42 1.9 10.9 1.0 OD2 A:ASP357 2.0 9.4 1.0 NE2 A:HIS358 2.1 11.9 1.0 OG A:SEP92 2.1 10.5 1.0 O3P A:SEP92 2.2 12.8 1.0 CG A:ASP42 2.7 11.6 1.0 OD2 A:ASP42 2.9 11.4 1.0 CG A:ASP357 2.9 10.7 1.0 P A:SEP92 2.9 14.6 1.0 CD2 A:HIS358 3.0 10.0 1.0 CE1 A:HIS358 3.0 12.1 1.0 OD1 A:ASP357 3.1 11.0 1.0 CB A:SEP92 3.3 11.7 1.0 OD2 A:ASP316 3.7 11.4 1.0 O1P A:SEP92 3.9 15.1 1.0 CA A:SEP92 3.9 12.0 1.0 CG A:ASP316 4.0 11.2 1.0 O2P A:SEP92 4.0 14.5 1.0 CB A:ASP42 4.1 11.6 1.0 ND1 A:HIS358 4.1 10.9 1.0 ZN A:ZN901 4.1 13.1 1.0 CG A:HIS358 4.1 9.1 1.0 CE1 A:HIS432 4.1 11.7 1.0 N A:SEP92 4.2 12.0 1.0 NE2 A:HIS432 4.2 12.4 1.0 N A:GLY43 4.2 10.6 1.0 CB A:ASP357 4.3 10.7 1.0 OD1 A:ASP316 4.3 12.2 1.0 O A:HOH1016 4.4 12.2 1.0 CA A:ASP42 4.5 11.3 1.0 C A:ASP42 4.5 11.2 1.0 CB A:ASP316 4.6 11.1 1.0 O A:HOH1005 4.6 12.6 1.0 ZN A:ZN903 4.7 14.7 0.8 MG A:MG904 4.7 14.7 0.2 O A:HOH1032 4.7 14.1 1.0 ND1 A:HIS432 4.9 10.6 1.0 CA A:GLY43 4.9 10.1 1.0 C A:ASP91 4.9 12.6 1.0 OG A:SER155 5.0 11.9 1.0

Zinc binding site 3 out of 3 in the Refinement of Placental Alkaline Phosphatase Complexed with Nitrophenyl


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Refinement of Placental Alkaline Phosphatase Complexed with Nitrophenyl within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn903 b:14.7 occ:0.80 MG A:MG904 0.0 14.7 0.2 OD2 A:ASP42 2.0 11.4 1.0 OE2 A:GLU311 2.0 12.2 1.0 O A:HOH1003 2.1 12.7 1.0 O A:HOH1005 2.2 12.6 1.0 O A:HOH1004 2.2 12.1 1.0 OG A:SER155 2.2 11.9 1.0 CG A:ASP42 3.0 11.6 1.0 CD A:GLU311 3.0 10.9 1.0 CB A:SER155 3.2 12.3 1.0 OE1 A:GLU311 3.4 12.0 1.0 CB A:ASP42 3.5 11.6 1.0 ND1 A:HIS153 4.1 15.4 1.0 N A:SER155 4.1 12.7 1.0 OD1 A:ASP42 4.1 10.9 1.0 O A:HOH1032 4.1 14.1 1.0 CA A:SER155 4.2 12.3 1.0 OG A:SEP92 4.3 10.5 1.0 CG A:GLU311 4.3 11.8 1.0 O A:GLY313 4.4 12.8 1.0 O2P A:SEP92 4.4 14.5 1.0 CB A:SEP92 4.4 11.7 1.0 O A:HOH1016 4.5 12.2 1.0 CA A:GLY313 4.5 12.0 1.0 ZN A:ZN902 4.7 12.4 1.0 CG2 A:THR149 4.7 11.0 1.0 CE1 A:HIS153 4.7 15.5 1.0 OD2 A:ASP357 4.8 9.4 1.0 CD A:PRO156 4.8 12.3 1.0 OG1 A:THR149 4.9 12.7 1.0 CA A:ASP42 4.9 11.3 1.0 C A:GLY313 4.9 11.9 1.0

B.Stec, A.Cheltsov, J.L.Millan. Refined Structures of Placental Alkaline Phosphatase Show A Consistent Pattern of Interactions at the Peripheral Site. Acta Crystallogr.,Sect.F V. 66 866 2010.
ISSN: ESSN 1744-3091
PubMed: 20693656
DOI: 10.1107/S1744309110019767