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Zinc in PDB 1alk: Reaction Mechanism of Alkaline Phosphatase Based on Crystal Structures. Two Metal Ion Catalysis

Enzymatic activity of Reaction Mechanism of Alkaline Phosphatase Based on Crystal Structures. Two Metal Ion Catalysis

All present enzymatic activity of Reaction Mechanism of Alkaline Phosphatase Based on Crystal Structures. Two Metal Ion Catalysis:
3.1.3.1;

Protein crystallography data

The structure of Reaction Mechanism of Alkaline Phosphatase Based on Crystal Structures. Two Metal Ion Catalysis, PDB code: 1alk was solved by E.E.Kim, W.Wyckoff, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) N/A / 2.00
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 195.300, 167.400, 76.700, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 1alk:

The structure of Reaction Mechanism of Alkaline Phosphatase Based on Crystal Structures. Two Metal Ion Catalysis also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Reaction Mechanism of Alkaline Phosphatase Based on Crystal Structures. Two Metal Ion Catalysis (pdb code 1alk). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Reaction Mechanism of Alkaline Phosphatase Based on Crystal Structures. Two Metal Ion Catalysis, PDB code: 1alk:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1alk

Go back to Zinc Binding Sites List in 1alk
Zinc binding site 1 out of 4 in the Reaction Mechanism of Alkaline Phosphatase Based on Crystal Structures. Two Metal Ion Catalysis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Reaction Mechanism of Alkaline Phosphatase Based on Crystal Structures. Two Metal Ion Catalysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn450

b:12.9
occ:1.00
 O1 A:PO4453 1.9 21.2 1.0
NE2 A:HIS412 2.1 9.2 1.0
OD1 A:ASP327 2.2 7.9 1.0
NE2 A:HIS331 2.2 9.9 1.0
OD2 A:ASP327 2.4 7.9 1.0
CG A:ASP327 2.6 6.7 1.0
P A:PO4453 2.9 21.7 1.0
O2 A:PO4453 2.9 19.4 1.0
CE1 A:HIS412 3.1 8.2 1.0
CD2 A:HIS331 3.1 11.5 1.0
CD2 A:HIS412 3.1 8.8 1.0
CE1 A:HIS331 3.2 13.2 1.0
O4 A:PO4453 3.8 21.2 1.0
NE2 A:HIS372 3.9 6.2 1.0
ZN A:ZN451 4.0 12.8 1.0
CE1 A:HIS370 4.1 9.6 1.0
CB A:ASP327 4.1 7.6 1.0
NE2 A:HIS370 4.1 7.7 1.0
O3 A:PO4453 4.1 22.1 1.0
ND1 A:HIS412 4.2 9.5 1.0
CG A:HIS412 4.3 9.4 1.0
CG A:HIS331 4.3 11.8 1.0
ND1 A:HIS331 4.3 11.9 1.0
OD1 A:ASP51 4.4 8.2 1.0
CD2 A:HIS372 4.5 7.2 1.0
CE1 A:HIS372 4.8 7.7 1.0
OG A:SER102 4.9 17.3 1.0
O A:ASP327 4.9 6.0 1.0
CA A:ASP327 5.0 6.5 1.0

Zinc binding site 2 out of 4 in 1alk

Go back to Zinc Binding Sites List in 1alk
Zinc binding site 2 out of 4 in the Reaction Mechanism of Alkaline Phosphatase Based on Crystal Structures. Two Metal Ion Catalysis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Reaction Mechanism of Alkaline Phosphatase Based on Crystal Structures. Two Metal Ion Catalysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn451

b:12.8
occ:1.00
 OD2 A:ASP369 1.8 8.8 1.0
O2 A:PO4453 1.9 19.4 1.0
OD1 A:ASP51 2.0 8.2 1.0
OG A:SER102 2.1 17.3 1.0
NE2 A:HIS370 2.2 7.7 1.0
CG A:ASP51 2.7 9.1 1.0
CG A:ASP369 2.8 11.3 1.0
OD2 A:ASP51 2.9 8.2 1.0
CD2 A:HIS370 3.0 9.6 1.0
OD1 A:ASP369 3.1 9.9 1.0
CE1 A:HIS370 3.2 9.6 1.0
P A:PO4453 3.4 21.7 1.0
OD1 A:ASP327 3.5 7.9 1.0
CB A:SER102 3.5 11.8 1.0
CG A:ASP327 3.9 6.7 1.0
ZN A:ZN450 4.0 12.9 1.0
CA A:SER102 4.1 9.7 1.0
CE1 A:HIS412 4.1 8.2 1.0
O3 A:PO4453 4.1 22.1 1.0
CB A:ASP51 4.1 7.7 1.0
O4 A:PO4453 4.1 21.2 1.0
CG A:HIS370 4.2 9.2 1.0
CB A:ASP369 4.2 8.6 1.0
ND1 A:HIS370 4.2 9.8 1.0
O1 A:PO4453 4.2 21.2 1.0
N A:GLY52 4.3 6.9 1.0
NE2 A:HIS412 4.3 9.2 1.0
N A:SER102 4.3 9.3 1.0
CB A:ASP327 4.4 7.6 1.0
OD2 A:ASP327 4.4 7.9 1.0
CA A:ASP51 4.6 7.6 1.0
MG A:MG452 4.6 5.2 1.0
C A:ASP51 4.7 7.7 1.0
ND1 A:HIS412 4.9 9.5 1.0
CA A:GLY52 4.9 5.6 1.0
C A:ASP101 5.0 9.8 1.0
O A:HOH455 5.0 8.0 1.0

Zinc binding site 3 out of 4 in 1alk

Go back to Zinc Binding Sites List in 1alk
Zinc binding site 3 out of 4 in the Reaction Mechanism of Alkaline Phosphatase Based on Crystal Structures. Two Metal Ion Catalysis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Reaction Mechanism of Alkaline Phosphatase Based on Crystal Structures. Two Metal Ion Catalysis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn450

b:15.3
occ:1.00
 NE2 B:HIS412 2.0 14.8 1.0
NE2 B:HIS331 2.1 12.8 1.0
O4 B:PO4453 2.1 16.9 1.0
OD1 B:ASP327 2.3 18.9 1.0
OD2 B:ASP327 2.5 17.8 1.0
O2 B:PO4453 2.7 19.4 1.0
CG B:ASP327 2.7 15.7 1.0
CE1 B:HIS412 2.8 13.9 1.0
P B:PO4453 2.9 19.1 1.0
CD2 B:HIS331 3.0 14.5 1.0
CE1 B:HIS331 3.1 13.4 1.0
CD2 B:HIS412 3.2 12.6 1.0
O3 B:PO4453 3.9 19.3 1.0
NE2 B:HIS372 4.0 13.2 1.0
O1 B:PO4453 4.0 18.7 1.0
ND1 B:HIS412 4.0 11.2 1.0
ZN B:ZN451 4.1 15.0 1.0
ND1 B:HIS331 4.2 14.3 1.0
CG B:HIS331 4.2 14.4 1.0
CE1 B:HIS370 4.2 7.5 1.0
CB B:ASP327 4.2 13.7 1.0
CG B:HIS412 4.2 13.0 1.0
NE2 B:HIS370 4.3 5.8 1.0
CD2 B:HIS372 4.5 13.3 1.0
OG B:SER102 4.6 17.8 1.0
OD1 B:ASP51 4.6 12.7 1.0
O B:ASP327 4.9 10.7 1.0
CE1 B:HIS372 5.0 15.1 1.0
C B:ASP327 5.0 10.5 1.0

Zinc binding site 4 out of 4 in 1alk

Go back to Zinc Binding Sites List in 1alk
Zinc binding site 4 out of 4 in the Reaction Mechanism of Alkaline Phosphatase Based on Crystal Structures. Two Metal Ion Catalysis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Reaction Mechanism of Alkaline Phosphatase Based on Crystal Structures. Two Metal Ion Catalysis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn451

b:15.0
occ:1.00
 OD2 B:ASP369 1.8 10.3 1.0
NE2 B:HIS370 2.0 5.8 1.0
OD1 B:ASP51 2.0 12.7 1.0
O2 B:PO4453 2.1 19.4 1.0
OG B:SER102 2.2 17.8 1.0
CG B:ASP369 2.7 15.0 1.0
CG B:ASP51 2.8 14.3 1.0
OD2 B:ASP51 2.9 13.1 1.0
CD2 B:HIS370 2.9 7.2 1.0
OD1 B:ASP369 3.0 14.9 1.0
CE1 B:HIS370 3.0 7.5 1.0
CB B:SER102 3.4 16.8 1.0
P B:PO4453 3.5 19.1 1.0
OD1 B:ASP327 3.6 18.9 1.0
CG B:ASP327 3.9 15.7 1.0
O3 B:PO4453 4.0 19.3 1.0
CA B:SER102 4.0 13.7 1.0
CE1 B:HIS412 4.1 13.9 1.0
CG B:HIS370 4.1 8.4 1.0
ND1 B:HIS370 4.1 5.8 1.0
ZN B:ZN450 4.1 15.3 1.0
CB B:ASP369 4.2 10.9 1.0
O1 B:PO4453 4.2 18.7 1.0
CB B:ASP51 4.2 13.1 1.0
N B:SER102 4.3 13.4 1.0
N B:GLY52 4.3 9.8 1.0
CB B:ASP327 4.4 13.7 1.0
OD2 B:ASP327 4.4 17.8 1.0
CA B:ASP51 4.5 12.8 1.0
O B:HOH456 4.5 10.9 1.0
NE2 B:HIS412 4.5 14.8 1.0
O4 B:PO4453 4.5 16.9 1.0
C B:ASP51 4.6 11.6 1.0
MG B:MG452 4.7 7.2 1.0
ND1 B:HIS412 4.9 11.2 1.0
C B:ASP101 5.0 13.0 1.0

Reference:

E.E.Kim, H.W.Wyckoff. Reaction Mechanism of Alkaline Phosphatase Based on Crystal Structures. Two-Metal Ion Catalysis. J.Mol.Biol. V. 218 449 1991.
ISSN: ISSN 0022-2836
PubMed: 2010919
DOI: 10.1016/0022-2836(91)90724-K
Page generated: Sat Oct 12 22:09:20 2024

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