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Zinc in PDB 4yr1: Crystal Structure of E. Coli Alkaline Phosphatase D101A/D153A in Complex with Inorganic Phosphate

Enzymatic activity of Crystal Structure of E. Coli Alkaline Phosphatase D101A/D153A in Complex with Inorganic Phosphate

All present enzymatic activity of Crystal Structure of E. Coli Alkaline Phosphatase D101A/D153A in Complex with Inorganic Phosphate:
3.1.3.1;

Protein crystallography data

The structure of Crystal Structure of E. Coli Alkaline Phosphatase D101A/D153A in Complex with Inorganic Phosphate, PDB code: 4yr1 was solved by A.Peck, D.Herschlag, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 52.89 / 2.24
Space group P 63 2 2
Cell size a, b, c (Å), α, β, γ (°) 161.420, 161.420, 140.051, 90.00, 90.00, 120.00
R / Rfree (%) 21.7 / 25.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of E. Coli Alkaline Phosphatase D101A/D153A in Complex with Inorganic Phosphate (pdb code 4yr1). 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 E. Coli Alkaline Phosphatase D101A/D153A in Complex with Inorganic Phosphate, PDB code: 4yr1:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4yr1

Go back to Zinc Binding Sites List in 4yr1
Zinc binding site 1 out of 4 in the Crystal Structure of E. Coli Alkaline Phosphatase D101A/D153A in Complex with Inorganic Phosphate


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 E. Coli Alkaline Phosphatase D101A/D153A in Complex with Inorganic Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:31.0
occ:1.00
 OD2 A:ASP369 2.0 29.9 1.0
OD1 A:ASP51 2.0 34.1 1.0
O2 A:PO4503 2.0 28.6 0.2
O2 A:PO4503 2.1 34.1 0.8
NE2 A:HIS370 2.1 29.6 1.0
CG A:ASP369 2.9 29.6 1.0
P A:PO4503 2.9 35.9 0.8
CD2 A:HIS370 2.9 29.0 1.0
CG A:ASP51 3.0 34.9 1.0
OD1 A:ASP369 3.1 31.2 1.0
CE1 A:HIS370 3.1 29.3 1.0
O1 A:PO4503 3.2 34.5 0.8
O3 A:PO4503 3.2 34.4 0.8
OD2 A:ASP51 3.3 36.2 1.0
P A:PO4503 3.5 28.1 0.2
OD1 A:ASP327 3.6 33.9 1.0
CB A:SER102 3.6 36.3 1.0
N A:SER102 4.0 32.5 1.0
CG A:ASP327 4.0 33.0 1.0
CA A:SER102 4.1 33.8 1.0
ZN A:ZN502 4.1 32.1 1.0
CG A:HIS370 4.1 28.3 1.0
CE1 A:HIS412 4.1 35.3 1.0
O1 A:PO4503 4.1 27.9 0.2
ND1 A:HIS370 4.1 29.5 1.0
CB A:ASP369 4.2 28.6 1.0
O4 A:PO4503 4.3 33.9 0.8
N A:GLY52 4.3 32.0 1.0
CB A:ASP51 4.3 33.4 1.0
O4 A:PO4503 4.4 27.7 0.2
O3 A:PO4503 4.4 27.7 0.2
OG A:SER102 4.4 38.3 1.0
CB A:ASP327 4.4 32.2 1.0
OD2 A:ASP327 4.5 34.8 1.0
NE2 A:HIS412 4.5 34.4 1.0
C A:ALA101 4.6 31.9 1.0
CA A:ASP51 4.6 32.5 1.0
C A:ASP51 4.6 32.0 1.0
ND1 A:HIS412 4.8 35.0 1.0
CA A:GLY52 4.9 31.4 1.0
CA A:ALA101 5.0 31.5 1.0

Zinc binding site 2 out of 4 in 4yr1

Go back to Zinc Binding Sites List in 4yr1
Zinc binding site 2 out of 4 in the Crystal Structure of E. Coli Alkaline Phosphatase D101A/D153A in Complex with Inorganic Phosphate


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 E. Coli Alkaline Phosphatase D101A/D153A in Complex with Inorganic Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:32.1
occ:1.00
 O4 A:PO4503 2.0 33.9 0.8
OD1 A:ASP327 2.1 33.9 1.0
O2 A:PO4503 2.1 34.1 0.8
OD2 A:ASP327 2.1 34.8 1.0
NE2 A:HIS331 2.1 32.6 1.0
NE2 A:HIS412 2.1 34.4 1.0
CG A:ASP327 2.4 33.0 1.0
P A:PO4503 2.6 35.9 0.8
O4 A:PO4503 3.0 27.7 0.2
CE1 A:HIS412 3.0 35.3 1.0
CD2 A:HIS331 3.1 33.2 1.0
O1 A:PO4503 3.2 27.9 0.2
CE1 A:HIS331 3.2 33.6 1.0
CD2 A:HIS412 3.2 34.4 1.0
P A:PO4503 3.3 28.1 0.2
O2 A:PO4503 3.3 28.6 0.2
O1 A:PO4503 3.6 34.5 0.8
O3 A:PO4503 3.8 34.4 0.8
NE2 A:HIS372 3.9 26.1 1.0
CB A:ASP327 4.0 32.2 1.0
ZN A:ZN501 4.1 31.0 1.0
ND1 A:HIS412 4.1 35.0 1.0
CE1 A:HIS370 4.2 29.3 1.0
CG A:HIS331 4.2 33.5 1.0
ND1 A:HIS331 4.2 34.1 1.0
CG A:HIS412 4.3 34.0 1.0
NE2 A:HIS370 4.3 29.6 1.0
CD2 A:HIS372 4.6 25.9 1.0
OD1 A:ASP51 4.7 34.1 1.0
O3 A:PO4503 4.8 27.7 0.2
CE1 A:HIS372 4.8 25.7 1.0
CA A:ASP327 4.9 31.5 1.0
O A:ASP327 4.9 30.9 1.0
C A:ASP327 5.0 31.7 1.0

Zinc binding site 3 out of 4 in 4yr1

Go back to Zinc Binding Sites List in 4yr1
Zinc binding site 3 out of 4 in the Crystal Structure of E. Coli Alkaline Phosphatase D101A/D153A in Complex with Inorganic Phosphate


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 E. Coli Alkaline Phosphatase D101A/D153A in Complex with Inorganic Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:31.5
occ:1.00
 O1 B:PO4503 2.0 33.9 0.8
OD1 B:ASP327 2.1 34.2 1.0
O2 B:PO4503 2.1 34.6 0.8
OD2 B:ASP327 2.1 33.5 1.0
NE2 B:HIS331 2.1 27.7 1.0
NE2 B:HIS412 2.1 33.5 1.0
O1 B:PO4503 2.3 27.6 0.2
CG B:ASP327 2.4 33.0 1.0
P B:PO4503 2.6 35.4 0.8
CE1 B:HIS412 3.0 34.0 1.0
CD2 B:HIS331 3.0 27.8 1.0
P B:PO4503 3.1 27.7 0.2
CE1 B:HIS331 3.1 28.4 1.0
CD2 B:HIS412 3.2 33.5 1.0
O3 B:PO4503 3.3 27.8 0.2
O2 B:PO4503 3.3 28.2 0.2
O3 B:PO4503 3.7 34.6 0.8
O4 B:PO4503 3.8 33.8 0.8
CB B:ASP327 3.9 32.6 1.0
ZN B:ZN502 4.0 32.0 1.0
NE2 B:HIS372 4.0 28.3 1.0
ND1 B:HIS412 4.2 34.5 1.0
NE2 B:HIS370 4.2 29.7 1.0
CG B:HIS331 4.2 28.3 1.0
ND1 B:HIS331 4.2 29.1 1.0
CE1 B:HIS370 4.2 30.4 1.0
CG B:HIS412 4.3 33.7 1.0
OD1 B:ASP51 4.3 35.8 1.0
O4 B:PO4503 4.5 27.2 0.2
CD2 B:HIS372 4.6 28.7 1.0
NZ B:LYS328 4.7 50.0 1.0
OD2 B:ASP51 4.8 36.5 1.0
CG B:ASP51 4.9 33.9 1.0
O B:ASP327 4.9 32.5 1.0
CE1 B:HIS372 4.9 28.2 1.0
CA B:ASP327 4.9 32.2 1.0
C B:ASP327 4.9 32.7 1.0

Zinc binding site 4 out of 4 in 4yr1

Go back to Zinc Binding Sites List in 4yr1
Zinc binding site 4 out of 4 in the Crystal Structure of E. Coli Alkaline Phosphatase D101A/D153A in Complex with Inorganic Phosphate


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 E. Coli Alkaline Phosphatase D101A/D153A in Complex with Inorganic Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:32.0
occ:1.00
 OD1 B:ASP51 2.0 35.8 1.0
OD2 B:ASP369 2.0 28.6 1.0
O2 B:PO4503 2.0 28.2 0.2
O2 B:PO4503 2.0 34.6 0.8
OD2 B:ASP51 2.1 36.5 1.0
NE2 B:HIS370 2.1 29.7 1.0
CG B:ASP51 2.3 33.9 1.0
CD2 B:HIS370 2.9 29.4 1.0
CG B:ASP369 2.9 29.5 1.0
P B:PO4503 3.0 35.4 0.8
CE1 B:HIS370 3.2 30.4 1.0
OD1 B:ASP369 3.2 28.9 1.0
O3 B:PO4503 3.2 34.6 0.8
P B:PO4503 3.4 27.7 0.2
O4 B:PO4503 3.5 33.8 0.8
OD1 B:ASP327 3.7 34.2 1.0
O3 B:PO4503 3.7 27.8 0.2
N B:SER102 3.8 32.6 1.0
CB B:ASP51 3.9 31.4 1.0
CB B:SER102 3.9 34.8 1.0
ZN B:ZN501 4.0 31.5 1.0
CE1 B:HIS412 4.0 34.0 1.0
CG B:ASP327 4.0 33.0 1.0
CA B:SER102 4.0 33.4 1.0
CG B:HIS370 4.1 29.9 1.0
ND1 B:HIS370 4.2 30.4 1.0
O1 B:PO4503 4.2 27.6 0.2
NE2 B:HIS412 4.2 33.5 1.0
O1 B:PO4503 4.3 33.9 0.8
CB B:ASP369 4.3 29.6 1.0
N B:GLY52 4.3 28.5 1.0
OD2 B:ASP327 4.4 33.5 1.0
CB B:ASP327 4.4 32.6 1.0
O4 B:PO4503 4.5 27.2 0.2
C B:ALA101 4.5 31.5 1.0
CA B:ASP51 4.5 30.1 1.0
C B:ASP51 4.7 29.7 1.0
ND1 B:HIS412 4.7 34.5 1.0
OG B:SER102 4.8 38.2 1.0
CA B:ALA101 4.9 30.6 1.0

Reference:

F.Sunden, A.Peck, J.Salzman, S.Ressl, D.Herschlag. Extensive Site-Directed Mutagenesis Reveals Interconnected Functional Units in the Alkaline Phosphatase Active Site. Elife V. 4 2015.
ISSN: ESSN 2050-084X
PubMed: 25902402
DOI: 10.7554/ELIFE.06181
Page generated: Wed Dec 16 05:58:09 2020

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