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Zinc in PDB 5tpq: E. Coli Alkaline Phosphatase D101A, D153A, R166S, E322A, K328A Mutant

Enzymatic activity of E. Coli Alkaline Phosphatase D101A, D153A, R166S, E322A, K328A Mutant

All present enzymatic activity of E. Coli Alkaline Phosphatase D101A, D153A, R166S, E322A, K328A Mutant:
3.1.3.1;

Protein crystallography data

The structure of E. Coli Alkaline Phosphatase D101A, D153A, R166S, E322A, K328A Mutant, PDB code: 5tpq was solved by F.Sunden, I.Alsadhan, A.Y.Lyubimov, T.Doukov, J.Swan, D.Herschlag, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.60 / 2.45
Space group P 63 2 2
Cell size a, b, c (Å), α, β, γ (°) 160.720, 160.720, 138.360, 90.00, 90.00, 120.00
R / Rfree (%) 16.5 / 21.9

Zinc Binding Sites:

The binding sites of Zinc atom in the E. Coli Alkaline Phosphatase D101A, D153A, R166S, E322A, K328A Mutant (pdb code 5tpq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the E. Coli Alkaline Phosphatase D101A, D153A, R166S, E322A, K328A Mutant, PDB code: 5tpq:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 5tpq

Go back to Zinc Binding Sites List in 5tpq
Zinc binding site 1 out of 7 in the E. Coli Alkaline Phosphatase D101A, D153A, R166S, E322A, K328A Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of E. Coli Alkaline Phosphatase D101A, D153A, R166S, E322A, K328A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:45.7
occ:1.00
OD1 A:ASP51 1.9 43.9 1.0
OD2 A:ASP369 2.0 58.0 1.0
NE2 A:HIS370 2.0 42.8 1.0
OG A:SER102 2.4 86.2 1.0
CB A:SER102 2.8 60.5 1.0
CG A:ASP369 2.8 49.0 1.0
O2 A:PO4504 2.8 92.5 1.0
CG A:ASP51 2.9 48.0 1.0
CD2 A:HIS370 2.9 42.5 1.0
CE1 A:HIS370 3.0 42.3 1.0
OD1 A:ASP369 3.0 48.5 1.0
OD2 A:ASP51 3.3 60.1 1.0
CA A:SER102 3.4 52.5 1.0
OD1 A:ASP327 3.8 45.6 1.0
N A:SER102 4.0 50.8 1.0
CG A:HIS370 4.0 41.3 1.0
CG A:ASP327 4.1 48.3 1.0
ND1 A:HIS370 4.1 42.6 1.0
P A:PO4504 4.1 97.9 1.0
O1 A:PO4504 4.1 91.3 1.0
ZN A:ZN502 4.1 43.7 1.0
CE1 A:HIS412 4.1 42.5 1.0
CB A:ASP51 4.2 39.5 1.0
CB A:ASP369 4.2 40.1 1.0
N A:GLY52 4.3 35.4 1.0
O A:HOH645 4.3 38.8 1.0
NE2 A:HIS412 4.4 42.5 1.0
OD2 A:ASP327 4.4 59.3 1.0
CA A:ASP51 4.5 37.4 1.0
CB A:ASP327 4.6 39.1 1.0
C A:ASP51 4.6 39.4 1.0
C A:SER102 4.7 54.8 1.0
C A:ALA101 4.8 49.6 1.0
ND1 A:HIS412 4.8 43.5 1.0
O4 A:PO4504 4.9 99.9 1.0

Zinc binding site 2 out of 7 in 5tpq

Go back to Zinc Binding Sites List in 5tpq
Zinc binding site 2 out of 7 in the E. Coli Alkaline Phosphatase D101A, D153A, R166S, E322A, K328A Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of E. Coli Alkaline Phosphatase D101A, D153A, R166S, E322A, K328A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:43.7
occ:1.00
NE2 A:HIS412 1.9 42.5 1.0
NE2 A:HIS331 2.0 37.4 1.0
O4 A:PO4504 2.0 99.9 1.0
OD1 A:ASP327 2.1 45.6 1.0
OD2 A:ASP327 2.5 59.3 1.0
CG A:ASP327 2.6 48.3 1.0
O2 A:PO4504 2.7 92.5 1.0
P A:PO4504 2.8 97.9 1.0
CE1 A:HIS412 2.8 42.5 1.0
CE1 A:HIS331 2.9 37.7 1.0
CD2 A:HIS412 3.0 43.0 1.0
CD2 A:HIS331 3.0 38.2 1.0
O1 A:PO4504 3.6 91.3 1.0
OG A:SER102 3.7 86.2 1.0
NE2 A:HIS372 4.0 39.8 1.0
ND1 A:HIS412 4.0 43.5 1.0
CG A:HIS412 4.1 41.7 1.0
O3 A:PO4504 4.1 99.3 1.0
ND1 A:HIS331 4.1 39.7 1.0
CG A:HIS331 4.1 37.8 1.0
CB A:ASP327 4.1 39.1 1.0
ZN A:ZN501 4.1 45.7 1.0
CE1 A:HIS370 4.1 42.3 1.0
NE2 A:HIS370 4.2 42.8 1.0
OD1 A:ASP51 4.6 43.9 1.0
CD2 A:HIS372 4.6 39.7 1.0
CE1 A:HIS372 5.0 39.8 1.0

Zinc binding site 3 out of 7 in 5tpq

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Zinc binding site 3 out of 7 in the E. Coli Alkaline Phosphatase D101A, D153A, R166S, E322A, K328A Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of E. Coli Alkaline Phosphatase D101A, D153A, R166S, E322A, K328A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:70.0
occ:1.00
O A:HOH720 1.9 57.8 1.0
NE2 A:HIS162 1.9 56.4 1.0
OE2 A:GLU134 2.0 56.6 1.0
NE2 A:HIS452 2.2 78.1 1.0
CD A:GLU134 2.8 74.8 1.0
CD2 A:HIS162 2.8 56.6 1.0
OE1 A:GLU134 2.8 71.9 1.0
CE1 A:HIS162 3.1 55.4 1.0
CD2 A:HIS452 3.1 79.6 1.0
CE1 A:HIS452 3.2 77.8 1.0
O A:HOH623 3.8 51.5 1.0
CG A:HIS162 4.0 54.3 1.0
ND1 A:HIS162 4.1 55.5 1.0
CG A:GLU134 4.2 63.5 1.0
CG A:HIS452 4.2 79.5 1.0
ND1 A:HIS452 4.3 79.9 1.0
O A:HIS129 4.9 51.1 1.0
CA A:PRO130 5.0 50.9 1.0
CE A:LYS188 5.0 64.7 1.0

Zinc binding site 4 out of 7 in 5tpq

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Zinc binding site 4 out of 7 in the E. Coli Alkaline Phosphatase D101A, D153A, R166S, E322A, K328A Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of E. Coli Alkaline Phosphatase D101A, D153A, R166S, E322A, K328A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn505

b:97.2
occ:1.00
OD2 A:ASP304 2.1 85.5 1.0
OE2 A:GLU308 2.9 64.1 0.5
CG A:ASP304 3.3 77.6 1.0
CD A:GLU308 3.7 76.2 0.5
OE1 A:GLU308 3.8 56.1 0.5
OD1 A:ASP304 4.1 78.7 1.0
CB A:ASP304 4.2 57.3 1.0

Zinc binding site 5 out of 7 in 5tpq

Go back to Zinc Binding Sites List in 5tpq
Zinc binding site 5 out of 7 in the E. Coli Alkaline Phosphatase D101A, D153A, R166S, E322A, K328A Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of E. Coli Alkaline Phosphatase D101A, D153A, R166S, E322A, K328A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:51.1
occ:1.00
OD1 B:ASP51 1.9 45.0 1.0
NE2 B:HIS370 2.0 42.9 1.0
OD2 B:ASP369 2.1 53.1 1.0
OG B:SER102 2.3 86.5 1.0
CB B:SER102 2.8 62.5 1.0
O1 B:PO4504 2.9 91.4 1.0
CG B:ASP51 2.9 47.9 1.0
CG B:ASP369 2.9 43.2 1.0
CD2 B:HIS370 3.0 42.4 1.0
CE1 B:HIS370 3.0 42.2 1.0
OD1 B:ASP369 3.1 38.4 1.0
OD2 B:ASP51 3.3 55.5 1.0
CA B:SER102 3.4 54.8 1.0
OD1 B:ASP327 3.5 52.8 1.0
CG B:ASP327 3.9 53.1 1.0
N B:SER102 3.9 53.2 1.0
O2 B:PO4504 4.0 95.1 1.0
CG B:HIS370 4.0 40.0 1.0
ND1 B:HIS370 4.1 41.8 1.0
P B:PO4504 4.1 97.6 1.0
CE1 B:HIS412 4.1 44.8 1.0
ZN B:ZN502 4.2 46.5 1.0
CB B:ASP51 4.2 41.3 1.0
OD2 B:ASP327 4.2 59.2 1.0
CB B:ASP369 4.3 38.1 1.0
NE2 B:HIS412 4.3 45.4 1.0
N B:GLY52 4.3 41.9 1.0
O B:HOH663 4.4 37.8 1.0
CB B:ASP327 4.5 42.7 1.0
CA B:ASP51 4.6 39.3 1.0
C B:ASP51 4.6 44.8 1.0
C B:SER102 4.7 57.2 1.0
ND1 B:HIS412 4.8 44.9 1.0
C B:ALA101 4.9 54.0 1.0
O3 B:PO4504 4.9 97.4 1.0

Zinc binding site 6 out of 7 in 5tpq

Go back to Zinc Binding Sites List in 5tpq
Zinc binding site 6 out of 7 in the E. Coli Alkaline Phosphatase D101A, D153A, R166S, E322A, K328A Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of E. Coli Alkaline Phosphatase D101A, D153A, R166S, E322A, K328A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:46.5
occ:1.00
NE2 B:HIS331 1.9 45.1 1.0
NE2 B:HIS412 2.0 45.4 1.0
O1 B:PO4504 2.1 91.4 1.0
OD1 B:ASP327 2.2 52.8 1.0
OD2 B:ASP327 2.4 59.2 1.0
CG B:ASP327 2.6 53.1 1.0
CE1 B:HIS331 2.9 44.8 1.0
CE1 B:HIS412 2.9 44.8 1.0
P B:PO4504 2.9 97.6 1.0
CD2 B:HIS331 3.0 46.0 1.0
O4 B:PO4504 3.0 0.0 1.0
CD2 B:HIS412 3.0 45.1 1.0
O3 B:PO4504 3.6 97.4 1.0
OG B:SER102 3.8 86.5 1.0
NE2 B:HIS372 4.0 51.4 1.0
O B:HOH644 4.0 55.4 1.0
ND1 B:HIS331 4.0 46.2 1.0
CG B:HIS331 4.1 44.8 1.0
ND1 B:HIS412 4.1 44.9 1.0
CG B:HIS412 4.1 42.7 1.0
CB B:ASP327 4.1 42.7 1.0
O2 B:PO4504 4.2 95.1 1.0
ZN B:ZN501 4.2 51.1 1.0
CE1 B:HIS370 4.2 42.2 1.0
NE2 B:HIS370 4.3 42.9 1.0
O B:HOH725 4.5 62.2 1.0
CD2 B:HIS372 4.6 50.4 1.0
OD1 B:ASP51 4.8 45.0 1.0
O B:HOH626 4.9 44.4 1.0
CE1 B:HIS372 4.9 50.7 1.0
O B:ASP327 4.9 42.3 1.0

Zinc binding site 7 out of 7 in 5tpq

Go back to Zinc Binding Sites List in 5tpq
Zinc binding site 7 out of 7 in the E. Coli Alkaline Phosphatase D101A, D153A, R166S, E322A, K328A Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of E. Coli Alkaline Phosphatase D101A, D153A, R166S, E322A, K328A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn503

b:70.0
occ:1.00
NE2 B:HIS452 2.0 83.1 1.0
OE2 B:GLU134 2.0 59.3 1.0
NE2 B:HIS162 2.1 56.9 1.0
CD B:GLU134 2.8 71.9 1.0
CD2 B:HIS162 2.8 57.2 1.0
OE1 B:GLU134 2.9 59.5 1.0
CE1 B:HIS452 3.0 82.8 1.0
CD2 B:HIS452 3.0 84.2 1.0
CE1 B:HIS162 3.2 55.1 1.0
O B:HOH779 3.7 52.3 1.0
CG B:HIS162 4.1 54.0 1.0
ND1 B:HIS452 4.1 84.4 1.0
CG B:HIS452 4.1 83.5 1.0
ND1 B:HIS162 4.2 55.0 1.0
CG B:GLU134 4.2 55.5 1.0
CE B:LYS188 4.9 88.1 1.0
O B:HIS129 5.0 57.1 1.0

Reference:

F.Sunden, I.Alsadhan, A.Lyubimov, T.Doukov, J.Swan, D.Herschlag. Differential Catalytic Promiscuity of the Alkaline Phosphatase Superfamily Bimetallo Core Reveals Mechanistic Features Underlying Enzyme Evolution. J. Biol. Chem. V. 292 20960 2017.
ISSN: ESSN 1083-351X
PubMed: 29070681
DOI: 10.1074/JBC.M117.788240
Page generated: Wed Dec 16 10:56:32 2020

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