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Zinc in PDB 2w5w: Structure of TAB5 Alkaline Phosphatase Mutant His 135 Asp with Zn Bound in the M3 Site.

Enzymatic activity of Structure of TAB5 Alkaline Phosphatase Mutant His 135 Asp with Zn Bound in the M3 Site.

All present enzymatic activity of Structure of TAB5 Alkaline Phosphatase Mutant His 135 Asp with Zn Bound in the M3 Site.:
3.1.3.1;

Protein crystallography data

The structure of Structure of TAB5 Alkaline Phosphatase Mutant His 135 Asp with Zn Bound in the M3 Site., PDB code: 2w5w was solved by D.Koutsioulis, A.Lyskowski, S.Maki, E.Guthrie, G.Feller, V.Bouriotis, P.Heikinheimo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.33 / 1.79
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 70.110, 173.320, 55.190, 90.00, 90.00, 90.00
R / Rfree (%) 14 / 17

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of TAB5 Alkaline Phosphatase Mutant His 135 Asp with Zn Bound in the M3 Site. (pdb code 2w5w). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Structure of TAB5 Alkaline Phosphatase Mutant His 135 Asp with Zn Bound in the M3 Site., PDB code: 2w5w:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 2w5w

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Zinc binding site 1 out of 6 in the Structure of TAB5 Alkaline Phosphatase Mutant His 135 Asp with Zn Bound in the M3 Site.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of TAB5 Alkaline Phosphatase Mutant His 135 Asp with Zn Bound in the M3 Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1376

b:14.2
occ:0.81
 O3P A:SEP84 1.9 15.7 0.1
NE2 A:HIS263 2.1 17.7 1.0
NE2 A:HIS337 2.1 17.3 1.0
O A:HOH2513 2.1 28.8 1.0
OD2 A:ASP259 2.2 20.2 1.0
OD1 A:ASP259 2.6 13.1 1.0
CG A:ASP259 2.7 15.4 1.0
CD2 A:HIS263 3.0 15.4 1.0
CD2 A:HIS337 3.1 13.1 1.0
CE1 A:HIS263 3.1 21.8 1.0
CE1 A:HIS337 3.1 18.0 1.0
P A:SEP84 3.2 42.8 1.0
O2P A:SEP84 3.7 25.6 1.0
O1P A:SEP84 3.9 30.3 1.0
O B:HOH2395 4.0 36.6 1.0
O A:HOH2060 4.0 61.6 1.0
ND1 A:HIS263 4.2 17.3 1.0
CG A:HIS263 4.2 14.4 1.0
CE1 A:HIS302 4.2 10.1 1.0
ND1 A:HIS337 4.2 13.3 1.0
O A:HOH2124 4.2 56.9 1.0
CG A:HIS337 4.2 13.4 1.0
CB A:ASP259 4.2 12.8 1.0
OG A:SEP84 4.3 8.3 0.7
O A:HOH2125 4.4 28.5 1.0
NE2 A:HIS302 4.5 11.7 1.0
CG2 A:THR304 4.5 9.0 1.0
ZN A:ZN1377 4.5 8.8 0.8
O A:HOH2126 4.5 47.5 1.0
OD1 A:ASP43 4.8 11.5 1.0
O A:ASP259 4.9 13.7 1.0

Zinc binding site 2 out of 6 in 2w5w

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Zinc binding site 2 out of 6 in the Structure of TAB5 Alkaline Phosphatase Mutant His 135 Asp with Zn Bound in the M3 Site.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of TAB5 Alkaline Phosphatase Mutant His 135 Asp with Zn Bound in the M3 Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1377

b:8.8
occ:0.79
 OD1 A:ASP43 2.0 11.5 1.0
OD2 A:ASP301 2.0 15.2 1.0
OG A:SEP84 2.1 8.3 0.7
NE2 A:HIS302 2.1 11.7 1.0
CG A:ASP43 2.7 13.8 1.0
OD2 A:ASP43 2.8 13.4 1.0
CG A:ASP301 2.9 14.4 1.0
O3P A:SEP84 2.9 15.7 0.1
CD2 A:HIS302 3.0 9.3 1.0
CE1 A:HIS302 3.1 10.1 1.0
CB A:SEP84 3.1 15.5 1.0
OD1 A:ASP301 3.1 10.7 1.0
P A:SEP84 3.2 42.8 1.0
CA A:SEP84 3.5 13.2 1.0
N A:SEP84 4.0 11.5 1.0
CB A:ASP43 4.1 8.8 1.0
CG A:HIS302 4.1 10.3 1.0
ND1 A:HIS302 4.1 10.0 1.0
O A:HOH2228 4.1 13.4 1.0
O1P A:SEP84 4.2 30.3 1.0
OD1 A:ASP259 4.2 13.1 1.0
CB A:ASP301 4.3 11.4 1.0
CE1 A:HIS337 4.3 18.0 1.0
CG A:ASP259 4.3 15.4 1.0
N A:GLY44 4.4 9.2 1.0
O2P A:SEP84 4.4 25.6 1.0
NE2 A:HIS337 4.4 17.3 1.0
CA A:ASP43 4.5 8.5 1.0
O A:HOH2516 4.5 14.6 1.0
ZN A:ZN1376 4.5 14.2 0.8
OD2 A:ASP259 4.6 20.2 1.0
ZN A:ZN1378 4.6 5.9 0.6
C A:ASP43 4.6 12.5 1.0
CB A:ASP259 4.7 12.8 1.0
C A:ASP83 4.8 14.8 1.0
O A:HOH2125 4.9 28.5 1.0
C A:SEP84 4.9 10.6 0.9
CA A:GLY44 5.0 11.5 1.0

Zinc binding site 3 out of 6 in 2w5w

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Zinc binding site 3 out of 6 in the Structure of TAB5 Alkaline Phosphatase Mutant His 135 Asp with Zn Bound in the M3 Site.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of TAB5 Alkaline Phosphatase Mutant His 135 Asp with Zn Bound in the M3 Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1378

b:5.9
occ:0.64
 OE2 A:GLU254 2.0 13.2 1.0
OD2 A:ASP43 2.0 13.4 1.0
O A:HOH2516 2.1 14.6 1.0
OG1 A:THR137 2.2 13.0 1.0
O A:HOH2514 2.2 17.1 1.0
O A:HOH2515 2.2 15.1 1.0
CG A:ASP43 3.0 13.8 1.0
CD A:GLU254 3.0 14.5 1.0
CB A:THR137 3.1 9.1 1.0
OE1 A:GLU254 3.4 14.8 1.0
CB A:ASP43 3.5 8.8 1.0
OD2 A:ASP135 3.9 21.5 1.0
O A:HOH2125 3.9 28.5 1.0
OD1 A:ASP43 4.1 11.5 1.0
CG2 A:THR137 4.1 8.3 1.0
N A:THR137 4.1 11.3 1.0
O A:HOH2228 4.2 13.4 1.0
CA A:THR137 4.2 7.5 1.0
CG A:GLU254 4.3 13.7 1.0
CB A:SEP84 4.5 15.5 1.0
OG A:SEP84 4.5 8.3 0.7
O1P A:SEP84 4.5 30.3 1.0
O A:SER256 4.6 11.5 1.0
ZN A:ZN1377 4.6 8.8 0.8
CA A:SER256 4.6 9.7 1.0
CB A:SER256 4.7 13.5 1.0
CG A:ASP135 4.9 26.6 1.0
OD2 A:ASP301 4.9 15.2 1.0
CA A:ASP43 4.9 8.5 1.0
CD A:PRO138 4.9 11.6 1.0
OG A:SER256 5.0 12.3 1.0

Zinc binding site 4 out of 6 in 2w5w

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Zinc binding site 4 out of 6 in the Structure of TAB5 Alkaline Phosphatase Mutant His 135 Asp with Zn Bound in the M3 Site.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of TAB5 Alkaline Phosphatase Mutant His 135 Asp with Zn Bound in the M3 Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1376

b:13.1
occ:0.82
 O3P B:SEP84 2.0 26.8 0.5
NE2 B:HIS263 2.0 14.6 1.0
O B:HOH2452 2.1 26.0 1.0
NE2 B:HIS337 2.1 14.6 1.0
OD2 B:ASP259 2.2 22.4 1.0
OD1 B:ASP259 2.5 16.5 1.0
CG B:ASP259 2.7 15.6 1.0
CD2 B:HIS263 2.9 17.9 1.0
CE1 B:HIS337 3.0 18.9 1.0
CE1 B:HIS263 3.1 18.4 1.0
CD2 B:HIS337 3.1 14.2 1.0
P B:SEP84 3.3 20.4 0.5
O2P B:SEP84 3.7 31.6 1.0
O1P B:SEP84 3.9 24.2 1.0
O B:HOH2121 4.0 53.8 1.0
CG B:HIS263 4.1 13.6 1.0
CE1 B:HIS302 4.1 12.4 1.0
ND1 B:HIS263 4.1 16.1 1.0
O A:HOH2448 4.2 34.9 1.0
ND1 B:HIS337 4.2 9.4 1.0
O B:HOH2120 4.2 24.3 1.0
CB B:ASP259 4.2 15.9 1.0
CG B:HIS337 4.2 11.2 1.0
O B:HOH2119 4.4 46.1 1.0
NE2 B:HIS302 4.4 10.8 1.0
OG B:SEP84 4.5 13.7 1.0
ZN B:ZN1377 4.5 11.7 0.9
CG2 B:THR304 4.6 7.2 1.0
OD1 B:ASP43 4.8 10.4 1.0

Zinc binding site 5 out of 6 in 2w5w

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Zinc binding site 5 out of 6 in the Structure of TAB5 Alkaline Phosphatase Mutant His 135 Asp with Zn Bound in the M3 Site.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of TAB5 Alkaline Phosphatase Mutant His 135 Asp with Zn Bound in the M3 Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1377

b:11.7
occ:0.93
 OD2 B:ASP301 2.0 13.2 1.0
OD1 B:ASP43 2.0 10.4 1.0
OG B:SEP84 2.0 13.7 1.0
NE2 B:HIS302 2.1 10.8 1.0
CG B:ASP43 2.7 14.6 1.0
O3P B:SEP84 2.7 26.8 0.5
OD2 B:ASP43 2.8 12.4 1.0
CG B:ASP301 2.9 11.9 1.0
CD2 B:HIS302 2.9 12.5 1.0
P B:SEP84 3.0 20.4 0.5
CE1 B:HIS302 3.1 12.4 1.0
OD1 B:ASP301 3.1 10.6 1.0
CB B:SEP84 3.1 15.5 1.0
CA B:SEP84 3.6 10.7 1.0
N B:SEP84 4.0 10.9 1.0
CG B:HIS302 4.1 10.4 1.0
ND1 B:HIS302 4.1 10.1 1.0
O1P B:SEP84 4.1 24.2 1.0
CB B:ASP43 4.1 9.3 1.0
O B:HOH2386 4.1 12.1 1.0
O2P B:SEP84 4.2 31.6 1.0
OD1 B:ASP259 4.2 16.5 1.0
CE1 B:HIS337 4.2 18.9 1.0
CB B:ASP301 4.3 13.9 1.0
CG B:ASP259 4.3 15.6 1.0
N B:GLY44 4.3 9.6 1.0
NE2 B:HIS337 4.4 14.6 1.0
CA B:ASP43 4.5 8.7 1.0
O B:HOH2455 4.5 17.3 1.0
ZN B:ZN1376 4.5 13.1 0.8
OD2 B:ASP259 4.6 22.4 1.0
C B:ASP43 4.7 10.4 1.0
ZN B:ZN1378 4.7 7.1 0.6
CB B:ASP259 4.7 15.9 1.0
O B:HOH2120 4.8 24.3 1.0
C B:ASP83 4.8 16.2 1.0
C B:SEP84 4.9 11.7 1.0
ND1 B:HIS337 5.0 9.4 1.0
CA B:GLY44 5.0 12.4 1.0

Zinc binding site 6 out of 6 in 2w5w

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Zinc binding site 6 out of 6 in the Structure of TAB5 Alkaline Phosphatase Mutant His 135 Asp with Zn Bound in the M3 Site.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of TAB5 Alkaline Phosphatase Mutant His 135 Asp with Zn Bound in the M3 Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1378

b:7.1
occ:0.63
 OE2 B:GLU254 2.0 14.3 1.0
OD2 B:ASP43 2.1 12.4 1.0
O B:HOH2453 2.1 16.4 1.0
OG1 B:THR137 2.1 12.9 1.0
O B:HOH2455 2.2 17.3 1.0
O B:HOH2454 2.2 17.9 1.0
CG B:ASP43 3.0 14.6 1.0
CD B:GLU254 3.1 15.7 1.0
CB B:THR137 3.2 15.2 1.0
OE1 B:GLU254 3.5 15.4 1.0
CB B:ASP43 3.5 9.3 1.0
OD2 B:ASP135 3.7 24.0 1.0
O B:HOH2120 4.0 24.3 1.0
OD1 B:ASP43 4.1 10.4 1.0
N B:THR137 4.1 11.3 1.0
CG2 B:THR137 4.2 10.1 1.0
CA B:THR137 4.2 11.9 1.0
O B:HOH2386 4.3 12.1 1.0
OG B:SEP84 4.4 13.7 1.0
CG B:GLU254 4.4 12.9 1.0
CB B:SEP84 4.5 15.5 1.0
O1P B:SEP84 4.6 24.2 1.0
O B:SER256 4.6 13.9 1.0
CA B:SER256 4.6 12.3 1.0
CB B:SER256 4.6 15.6 1.0
ZN B:ZN1377 4.7 11.7 0.9
CG B:ASP135 4.8 22.4 1.0
OD2 B:ASP301 4.9 13.2 1.0
CA B:ASP43 4.9 8.7 1.0
OG B:SER256 4.9 14.3 1.0
CD B:PRO138 4.9 11.0 1.0

Reference:

D.Koutsioulis, A.Lyskowski, S.Maki, E.Guthrie, G.Feller, V.Bouriotis, P.Heikinheimo. Coordination Sphere of the Third Metal Site Is Essential to the Activity and Metal Selectivity of Alkaline Phosphatases. Protein Sci. V. 19 75 2010.
ISSN: ISSN 0961-8368
PubMed: 19916164
DOI: 10.1002/PRO.284
Page generated: Thu Oct 17 04:45:01 2024

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