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Zinc in PDB 1ew9: Alkaline Phosphatase (E.C. 3.1.3.1) Complex with Mercaptomethyl Phosphonate

Enzymatic activity of Alkaline Phosphatase (E.C. 3.1.3.1) Complex with Mercaptomethyl Phosphonate

All present enzymatic activity of Alkaline Phosphatase (E.C. 3.1.3.1) Complex with Mercaptomethyl Phosphonate:
3.1.3.1;

Protein crystallography data

The structure of Alkaline Phosphatase (E.C. 3.1.3.1) Complex with Mercaptomethyl Phosphonate, PDB code: 1ew9 was solved by K.M.Holtz, B.Stec, J.K.Meyers, S.M.Antonelli, T.S.Widlanski, E.R.Kantrowitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 12.00 / 2.00
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 194.830, 167.100, 76.670, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 22.9

Other elements in 1ew9:

The structure of Alkaline Phosphatase (E.C. 3.1.3.1) Complex with Mercaptomethyl Phosphonate also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Alkaline Phosphatase (E.C. 3.1.3.1) Complex with Mercaptomethyl Phosphonate (pdb code 1ew9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Alkaline Phosphatase (E.C. 3.1.3.1) Complex with Mercaptomethyl Phosphonate, PDB code: 1ew9:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 1ew9

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Zinc binding site 1 out of 6 in the Alkaline Phosphatase (E.C. 3.1.3.1) Complex with Mercaptomethyl Phosphonate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Alkaline Phosphatase (E.C. 3.1.3.1) Complex with Mercaptomethyl Phosphonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn450

b:13.2
occ:1.00
 NE2 A:HIS412 1.9 12.9 1.0
NE2 A:HIS331 2.0 16.8 1.0
OD1 A:ASP327 2.1 13.5 1.0
S1 A:MMQ559 2.3 23.1 0.7
OD2 A:ASP327 2.4 14.9 1.0
CG A:ASP327 2.6 9.1 1.0
CE1 A:HIS412 2.8 14.2 1.0
CD2 A:HIS412 3.0 12.3 1.0
CE1 A:HIS331 3.0 13.7 1.0
CD2 A:HIS331 3.1 13.8 1.0
O3P A:MMQ559 3.1 86.1 0.7
C1P A:MMQ559 3.5 55.4 0.7
P A:MMQ559 3.7 82.7 0.7
ND1 A:HIS412 4.0 11.2 1.0
CE1 A:HIS370 4.0 15.4 1.0
CG A:HIS412 4.1 8.3 1.0
CB A:ASP327 4.1 9.5 1.0
OG A:SER102 4.1 14.2 1.0
NE2 A:HIS370 4.1 14.1 1.0
ND1 A:HIS331 4.1 9.3 1.0
NE2 A:HIS372 4.2 16.2 1.0
ZN A:ZN451 4.2 13.5 1.0
CG A:HIS331 4.2 13.0 1.0
O2P A:MMQ559 4.2 77.6 0.7
O A:HOH583 4.3 14.2 1.0
OD1 A:ASP51 4.5 8.1 1.0
CD2 A:HIS372 4.6 13.5 1.0
O A:ASP327 4.9 14.5 1.0
C A:ASP327 5.0 8.3 1.0

Zinc binding site 2 out of 6 in 1ew9

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Zinc binding site 2 out of 6 in the Alkaline Phosphatase (E.C. 3.1.3.1) Complex with Mercaptomethyl Phosphonate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Alkaline Phosphatase (E.C. 3.1.3.1) Complex with Mercaptomethyl Phosphonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn451

b:13.5
occ:1.00
 OG A:SER102 1.8 14.2 1.0
OD1 A:ASP369 1.9 19.7 1.0
OD1 A:ASP51 2.0 8.1 1.0
NE2 A:HIS370 2.2 14.1 1.0
CG A:ASP51 2.7 11.8 1.0
OD2 A:ASP51 2.9 16.6 1.0
CG A:ASP369 2.9 7.4 1.0
CD2 A:HIS370 3.0 10.9 1.0
CB A:SER102 3.0 18.4 1.0
CE1 A:HIS370 3.2 15.4 1.0
OD2 A:ASP369 3.3 9.8 1.0
CA A:SER102 3.5 15.7 1.0
S1 A:MMQ559 3.7 23.1 0.7
OD1 A:ASP327 3.8 13.5 1.0
CE1 A:HIS412 4.1 14.2 1.0
CG A:ASP327 4.1 9.1 1.0
CG A:HIS370 4.1 11.7 1.0
N A:SER102 4.1 12.8 1.0
CB A:ASP51 4.2 12.4 1.0
ZN A:ZN450 4.2 13.2 1.0
ND1 A:HIS370 4.2 12.1 1.0
O A:HOH881 4.2 14.9 0.7
O A:HOH884 4.2 14.9 0.3
CB A:ASP369 4.2 8.5 1.0
O A:HOH683 4.2 10.5 1.0
NE2 A:HIS412 4.3 12.9 1.0
N A:GLY52 4.4 10.0 1.0
C1P A:MMQ559 4.5 55.4 0.7
OD2 A:ASP327 4.5 14.9 1.0
CB A:ASP327 4.6 9.5 1.0
CA A:ASP51 4.6 16.8 1.0
MG A:MG452 4.6 17.4 0.7
ZN A:ZN453 4.6 17.4 0.3
C A:ASP51 4.7 12.9 1.0
C A:SER102 4.8 15.0 1.0
C A:ASP101 4.9 12.9 1.0
ND1 A:HIS412 4.9 11.2 1.0
OG1 A:THR155 5.0 12.6 1.0

Zinc binding site 3 out of 6 in 1ew9

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Zinc binding site 3 out of 6 in the Alkaline Phosphatase (E.C. 3.1.3.1) Complex with Mercaptomethyl Phosphonate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Alkaline Phosphatase (E.C. 3.1.3.1) Complex with Mercaptomethyl Phosphonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn453

b:17.4
occ:0.35
 MG A:MG452 0.0 17.4 0.7
OE2 A:GLU322 2.0 9.8 1.0
OD2 A:ASP51 2.0 16.6 1.0
O A:HOH882 2.2 12.8 0.7
O A:HOH885 2.2 12.8 0.3
OG1 A:THR155 2.2 12.6 1.0
O A:HOH883 2.3 8.7 0.7
O A:HOH886 2.3 8.7 0.3
O A:HOH881 2.3 14.9 0.7
O A:HOH884 2.3 14.9 0.3
CD A:GLU322 3.0 10.6 1.0
CG A:ASP51 3.0 11.8 1.0
CB A:THR155 3.2 11.4 1.0
OE1 A:GLU322 3.4 8.8 1.0
CB A:ASP51 3.6 12.4 1.0
OD2 A:ASP153 3.7 16.2 1.0
OD1 A:ASP51 4.0 8.1 1.0
O A:HOH583 4.1 14.2 1.0
CG2 A:THR155 4.1 8.4 1.0
N A:THR155 4.2 15.9 1.0
CG A:GLU322 4.3 9.2 1.0
CB A:ALA324 4.3 15.3 1.0
CA A:THR155 4.3 14.6 1.0
O A:HOH683 4.3 10.5 1.0
O A:HOH877 4.3 38.2 1.0
OG A:SER102 4.5 14.2 1.0
O A:ALA324 4.5 17.1 1.0
CA A:ALA324 4.6 17.1 1.0
ZN A:ZN451 4.6 13.5 1.0
CB A:SER102 4.7 18.4 1.0
CG A:ASP153 4.7 16.8 1.0
CA A:ASP51 4.9 16.8 1.0
OD1 A:ASP369 5.0 19.7 1.0

Zinc binding site 4 out of 6 in 1ew9

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Zinc binding site 4 out of 6 in the Alkaline Phosphatase (E.C. 3.1.3.1) Complex with Mercaptomethyl Phosphonate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Alkaline Phosphatase (E.C. 3.1.3.1) Complex with Mercaptomethyl Phosphonate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn450

b:18.7
occ:1.00
 NE2 B:HIS331 2.0 10.3 1.0
NE2 B:HIS412 2.1 17.3 1.0
OD1 B:ASP327 2.2 11.6 1.0
S1 B:MMQ559 2.3 33.5 0.8
OD2 B:ASP327 2.5 18.8 1.0
CG B:ASP327 2.7 17.2 1.0
CD2 B:HIS331 2.9 12.1 1.0
CE1 B:HIS331 3.0 12.0 1.0
CE1 B:HIS412 3.0 18.1 1.0
CD2 B:HIS412 3.1 18.7 1.0
O3P B:MMQ559 3.5 42.7 0.8
C1P B:MMQ559 3.5 34.3 0.8
NE2 B:HIS372 3.9 21.8 1.0
P B:MMQ559 4.0 51.4 0.8
ND1 B:HIS331 4.1 10.5 1.0
CE1 B:HIS370 4.1 13.7 1.0
CG B:HIS331 4.1 13.3 1.0
OG B:SER102 4.1 14.9 1.0
ND1 B:HIS412 4.1 16.2 1.0
CB B:ASP327 4.2 13.6 1.0
CG B:HIS412 4.2 18.7 1.0
NE2 B:HIS370 4.2 13.3 1.0
ZN B:ZN451 4.3 15.7 1.0
O B:HOH997 4.3 24.2 1.0
O2P B:MMQ559 4.6 47.0 0.8
OD1 B:ASP51 4.6 8.2 1.0
CD2 B:HIS372 4.6 17.0 1.0
O B:ASP327 4.6 10.9 1.0
CE1 B:HIS372 4.8 18.4 1.0
C B:ASP327 4.9 9.5 1.0

Zinc binding site 5 out of 6 in 1ew9

Go back to Zinc Binding Sites List in 1ew9
Zinc binding site 5 out of 6 in the Alkaline Phosphatase (E.C. 3.1.3.1) Complex with Mercaptomethyl Phosphonate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Alkaline Phosphatase (E.C. 3.1.3.1) Complex with Mercaptomethyl Phosphonate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn451

b:15.7
occ:1.00
 OG B:SER102 1.8 14.9 1.0
OD1 B:ASP51 2.0 8.2 1.0
OD1 B:ASP369 2.1 21.3 1.0
NE2 B:HIS370 2.1 13.3 1.0
CG B:ASP51 2.7 14.2 1.0
OD2 B:ASP51 2.8 12.9 1.0
CG B:ASP369 2.9 16.6 1.0
CB B:SER102 2.9 19.5 1.0
CD2 B:HIS370 3.0 11.6 1.0
OD2 B:ASP369 3.0 14.4 1.0
CE1 B:HIS370 3.1 13.7 1.0
CA B:SER102 3.6 17.1 1.0
S1 B:MMQ559 3.9 33.5 0.8
OD1 B:ASP327 3.9 11.6 1.0
CG B:HIS370 4.1 11.4 1.0
O B:HOH1183 4.1 21.0 0.7
O B:HOH1186 4.1 21.0 0.3
ND1 B:HIS370 4.1 13.5 1.0
CB B:ASP51 4.1 15.0 1.0
CE1 B:HIS412 4.1 18.1 1.0
CG B:ASP327 4.1 17.2 1.0
O B:HOH995 4.1 13.1 1.0
N B:SER102 4.2 16.4 1.0
ZN B:ZN450 4.3 18.7 1.0
CB B:ASP369 4.3 15.2 1.0
NE2 B:HIS412 4.3 17.3 1.0
N B:GLY52 4.4 10.0 1.0
CB B:ASP327 4.5 13.6 1.0
CA B:ASP51 4.5 11.7 1.0
C1P B:MMQ559 4.6 34.3 0.8
MG B:MG452 4.7 22.5 0.7
ZN B:ZN453 4.7 22.5 0.3
C B:ASP51 4.7 13.1 1.0
OD2 B:ASP327 4.7 18.8 1.0
OG1 B:THR155 4.9 21.1 1.0
C B:SER102 4.9 18.1 1.0
C B:ASP101 4.9 14.0 1.0
O B:HOH1185 5.0 18.8 0.7
O B:HOH1188 5.0 18.8 0.3

Zinc binding site 6 out of 6 in 1ew9

Go back to Zinc Binding Sites List in 1ew9
Zinc binding site 6 out of 6 in the Alkaline Phosphatase (E.C. 3.1.3.1) Complex with Mercaptomethyl Phosphonate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Alkaline Phosphatase (E.C. 3.1.3.1) Complex with Mercaptomethyl Phosphonate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn453

b:22.5
occ:0.35
 MG B:MG452 0.0 22.5 0.7
O B:HOH1183 1.8 21.0 0.7
O B:HOH1186 1.8 21.0 0.3
OE1 B:GLU322 1.9 11.9 1.0
O B:HOH1184 2.1 10.8 0.7
O B:HOH1187 2.1 10.8 0.3
OD2 B:ASP51 2.1 12.9 1.0
O B:HOH1185 2.2 18.8 0.7
O B:HOH1188 2.2 18.8 0.3
OG1 B:THR155 2.2 21.1 1.0
CB B:THR155 3.0 11.1 1.0
CD B:GLU322 3.0 15.8 1.0
CG B:ASP51 3.1 14.2 1.0
OE2 B:GLU322 3.5 15.8 1.0
CB B:ASP51 3.6 15.0 1.0
OD2 B:ASP153 3.7 22.1 1.0
CG2 B:THR155 3.9 9.3 1.0
N B:THR155 4.1 16.9 1.0
CA B:THR155 4.1 16.3 1.0
O B:HOH997 4.1 24.2 1.0
O B:HOH1179 4.2 36.1 1.0
OD1 B:ASP51 4.2 8.2 1.0
O B:HOH995 4.2 13.1 1.0
CG B:GLU322 4.2 15.2 1.0
OG B:SER102 4.4 14.9 1.0
CB B:ALA324 4.5 22.2 1.0
CA B:ALA324 4.6 15.2 1.0
CB B:SER102 4.6 19.5 1.0
O B:ALA324 4.7 13.9 1.0
ZN B:ZN451 4.7 15.7 1.0
CG B:ASP153 4.7 23.2 1.0
OD1 B:ASP369 4.9 21.3 1.0
CA B:ASP51 5.0 11.7 1.0

Reference:

K.M.Holtz, B.Stec, J.K.Myers, S.M.Antonelli, T.S.Widlanski, E.R.Kantrowitz. Alternate Modes of Binding in Two Crystal Structures of Alkaline Phosphatase-Inhibitor Complexes. Protein Sci. V. 9 907 2000.
ISSN: ISSN 0961-8368
PubMed: 10850800
Page generated: Sun Oct 13 00:29:58 2024

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