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Zinc in PDB 1b8j: Alkaline Phosphatase Complexed with Vanadate

Enzymatic activity of Alkaline Phosphatase Complexed with Vanadate

All present enzymatic activity of Alkaline Phosphatase Complexed with Vanadate:
3.1.3.1;

Protein crystallography data

The structure of Alkaline Phosphatase Complexed with Vanadate, PDB code: 1b8j was solved by K.M.Holtz, B.Stec, E.R.Kantrowitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 1.90
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 195.410, 167.810, 76.520, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 19.6

Other elements in 1b8j:

The structure of Alkaline Phosphatase Complexed with Vanadate also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Vanadium (V) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Alkaline Phosphatase Complexed with Vanadate (pdb code 1b8j). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Alkaline Phosphatase Complexed with Vanadate, PDB code: 1b8j:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1b8j

Go back to Zinc Binding Sites List in 1b8j
Zinc binding site 1 out of 4 in the Alkaline Phosphatase Complexed with Vanadate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Alkaline Phosphatase Complexed with Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn450

b:25.1
occ:1.00
NE2 A:HIS412 2.1 16.9 1.0
O2 A:SVA102 2.1 47.5 1.0
NE2 A:HIS331 2.1 17.4 1.0
OD2 A:ASP327 2.2 17.9 1.0
O4 A:SVA102 2.4 41.6 1.0
OD1 A:ASP327 2.5 15.3 1.0
CG A:ASP327 2.7 19.6 1.0
CE1 A:HIS412 2.9 21.2 1.0
V A:SVA102 3.0 42.4 1.0
CE1 A:HIS331 3.1 16.4 1.0
CD2 A:HIS331 3.1 23.3 1.0
CD2 A:HIS412 3.2 24.0 1.0
O3 A:SVA102 3.7 41.5 1.0
NE2 A:HIS372 3.8 20.8 1.0
OG A:SVA102 4.1 34.5 1.0
CE1 A:HIS370 4.1 13.8 1.0
NE2 A:HIS370 4.1 16.8 1.0
ZN A:ZN451 4.1 20.1 1.0
ND1 A:HIS412 4.1 24.1 1.0
CB A:ASP327 4.2 20.3 1.0
O1 A:SVA102 4.2 44.8 1.0
ND1 A:HIS331 4.2 17.1 1.0
O A:HOH1028 4.3 56.2 1.0
CG A:HIS412 4.3 23.1 1.0
CG A:HIS331 4.3 22.0 1.0
O A:HOH1471 4.5 19.2 1.0
CD2 A:HIS372 4.5 16.7 1.0
OD1 A:ASP51 4.6 23.4 1.0
CE1 A:HIS372 4.7 16.6 1.0
O A:ASP327 4.8 22.2 1.0
O A:HOH1026 4.8 58.9 1.0
C A:ASP327 4.9 14.8 1.0

Zinc binding site 2 out of 4 in 1b8j

Go back to Zinc Binding Sites List in 1b8j
Zinc binding site 2 out of 4 in the Alkaline Phosphatase Complexed with Vanadate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Alkaline Phosphatase Complexed with Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn451

b:20.1
occ:1.00
OD2 A:ASP369 1.9 16.1 1.0
OG A:SVA102 1.9 34.5 1.0
OD1 A:ASP51 2.1 23.4 1.0
NE2 A:HIS370 2.1 16.8 1.0
O2 A:SVA102 2.2 47.5 1.0
CG A:ASP51 2.9 20.2 1.0
CB A:SVA102 2.9 8.6 1.0
OD2 A:ASP51 3.0 22.7 1.0
CD2 A:HIS370 3.0 10.0 1.0
CG A:ASP369 3.0 17.1 1.0
V A:SVA102 3.1 42.4 1.0
CE1 A:HIS370 3.2 13.8 1.0
OD1 A:ASP369 3.4 11.6 1.0
CA A:SVA102 3.5 8.1 1.0
OD2 A:ASP327 3.7 17.9 1.0
O1 A:SVA102 3.9 44.8 1.0
N A:SVA102 4.0 6.7 1.0
CG A:ASP327 4.1 19.6 1.0
O A:HOH1472 4.1 16.0 1.0
ZN A:ZN450 4.1 25.1 1.0
CG A:HIS370 4.2 8.3 1.0
CE1 A:HIS412 4.2 21.2 1.0
O3 A:SVA102 4.2 41.5 1.0
ND1 A:HIS370 4.2 16.7 1.0
O A:HOH1473 4.2 11.5 1.0
CB A:ASP369 4.3 8.2 1.0
CB A:ASP51 4.3 18.7 1.0
NE2 A:HIS412 4.5 16.9 1.0
MG A:MG452 4.6 14.8 1.0
N A:GLY52 4.6 4.8 1.0
CB A:ASP327 4.6 20.3 1.0
OD1 A:ASP327 4.6 15.3 1.0
O4 A:SVA102 4.7 41.6 1.0
CA A:ASP51 4.8 13.4 1.0
C A:ASP101 4.8 6.5 1.0
C A:ASP51 4.8 12.0 1.0
C A:SVA102 4.9 8.9 1.0

Zinc binding site 3 out of 4 in 1b8j

Go back to Zinc Binding Sites List in 1b8j
Zinc binding site 3 out of 4 in the Alkaline Phosphatase Complexed with Vanadate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Alkaline Phosphatase Complexed with Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn450

b:27.4
occ:1.00
O2 B:SVA102 2.1 41.3 1.0
NE2 B:HIS412 2.1 23.2 1.0
NE2 B:HIS331 2.1 18.6 1.0
OD2 B:ASP327 2.3 26.8 1.0
O4 B:SVA102 2.4 33.4 1.0
OD1 B:ASP327 2.4 29.4 1.0
CG B:ASP327 2.6 25.6 1.0
CE1 B:HIS412 3.0 27.7 1.0
V B:SVA102 3.0 34.7 1.0
CD2 B:HIS331 3.1 20.5 1.0
CE1 B:HIS331 3.2 16.8 1.0
CD2 B:HIS412 3.2 27.4 1.0
NE2 B:HIS372 3.7 25.2 1.0
O3 B:SVA102 3.8 36.8 1.0
O B:HOH1320 3.9 45.3 1.0
CE1 B:HIS370 3.9 11.8 1.0
O B:HOH1330 4.0 53.6 1.0
NE2 B:HIS370 4.1 10.3 1.0
OG B:SVA102 4.1 42.2 1.0
O1 B:SVA102 4.1 36.2 1.0
ZN B:ZN451 4.1 23.3 1.0
CB B:ASP327 4.1 22.6 1.0
ND1 B:HIS412 4.2 23.4 1.0
O B:HOH1224 4.2 66.4 1.0
CG B:HIS331 4.3 17.1 1.0
CG B:HIS412 4.3 25.1 1.0
ND1 B:HIS331 4.3 19.0 1.0
CD2 B:HIS372 4.4 16.8 1.0
OD1 B:ASP51 4.5 28.8 1.0
CE1 B:HIS372 4.6 20.5 1.0
O B:ASP327 4.8 16.5 1.0
C B:ASP327 4.9 18.9 1.0

Zinc binding site 4 out of 4 in 1b8j

Go back to Zinc Binding Sites List in 1b8j
Zinc binding site 4 out of 4 in the Alkaline Phosphatase Complexed with Vanadate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Alkaline Phosphatase Complexed with Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn451

b:23.3
occ:1.00
OG B:SVA102 1.9 42.2 1.0
OD2 B:ASP369 2.0 12.8 1.0
OD1 B:ASP51 2.1 28.8 1.0
NE2 B:HIS370 2.1 10.3 1.0
O2 B:SVA102 2.1 41.3 1.0
CG B:ASP51 2.8 24.6 1.0
CB B:SVA102 2.9 8.1 1.0
OD2 B:ASP51 2.9 24.9 1.0
CD2 B:HIS370 3.0 7.3 1.0
CG B:ASP369 3.0 17.8 1.0
V B:SVA102 3.1 34.7 1.0
CE1 B:HIS370 3.1 11.8 1.0
OD1 B:ASP369 3.4 19.5 1.0
CA B:SVA102 3.5 11.2 1.0
OD2 B:ASP327 3.7 26.8 1.0
O1 B:SVA102 3.9 36.2 1.0
O B:HOH1407 4.0 19.2 1.0
N B:SVA102 4.0 8.0 1.0
ZN B:ZN450 4.1 27.4 1.0
CG B:ASP327 4.1 25.6 1.0
CG B:HIS370 4.2 8.7 1.0
O3 B:SVA102 4.2 36.8 1.0
CB B:ASP51 4.2 21.8 1.0
ND1 B:HIS370 4.2 10.2 1.0
CE1 B:HIS412 4.3 27.7 1.0
O B:HOH1409 4.3 20.8 1.0
CB B:ASP369 4.3 9.9 1.0
N B:GLY52 4.5 9.2 1.0
NE2 B:HIS412 4.5 23.2 1.0
CB B:ASP327 4.6 22.6 1.0
MG B:MG452 4.6 21.4 1.0
O4 B:SVA102 4.6 33.4 1.0
OD1 B:ASP327 4.6 29.4 1.0
CA B:ASP51 4.7 13.5 1.0
C B:ASP51 4.8 14.1 1.0
C B:ASP101 4.8 7.2 1.0
O B:HOH1320 4.9 45.3 1.0
C B:SVA102 4.9 10.8 1.0

Reference:

K.M.Holtz, B.Stec, E.R.Kantrowitz. A Model of the Transition State in the Alkaline Phosphatase Reaction. J.Biol.Chem. V. 274 8351 1999.
ISSN: ISSN 0021-9258
PubMed: 10085061
DOI: 10.1074/JBC.274.13.8351
Page generated: Wed Dec 16 02:45:24 2020

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