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Magnesium in PDB 2w5v: Structure of TAB5 Alkaline Phosphatase Mutant His 135 Asp with Mg Bound in the M3 Site.

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

All present enzymatic activity of Structure of TAB5 Alkaline Phosphatase Mutant His 135 Asp with Mg 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 Mg Bound in the M3 Site., PDB code: 2w5v 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) 46.40 / 1.78
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 70.320, 173.020, 54.970, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 19.9

Other elements in 2w5v:

The structure of Structure of TAB5 Alkaline Phosphatase Mutant His 135 Asp with Mg Bound in the M3 Site. also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of TAB5 Alkaline Phosphatase Mutant His 135 Asp with Mg Bound in the M3 Site. (pdb code 2w5v). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of TAB5 Alkaline Phosphatase Mutant His 135 Asp with Mg Bound in the M3 Site., PDB code: 2w5v:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2w5v

Go back to Magnesium Binding Sites List in 2w5v
Magnesium binding site 1 out of 4 in the Structure of TAB5 Alkaline Phosphatase Mutant His 135 Asp with Mg Bound in the M3 Site.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of TAB5 Alkaline Phosphatase Mutant His 135 Asp with Mg Bound in the M3 Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1378

b:16.0
occ:1.00
OE2 A:GLU254 2.1 14.9 1.0
OG1 A:THR137 2.2 13.1 1.0
OD2 A:ASP43 2.2 15.4 1.0
O A:HOH2231 2.2 15.1 1.0
O A:HOH2064 2.2 15.2 1.0
O A:HOH2122 2.3 14.3 1.0
CD A:GLU254 3.1 18.5 1.0
CG A:ASP43 3.1 17.8 1.0
CB A:THR137 3.1 13.4 1.0
OE1 A:GLU254 3.5 15.8 1.0
CB A:ASP43 3.6 16.7 1.0
OD2 A:ASP135 3.8 21.4 1.0
O A:HOH2065 4.1 26.6 1.0
N A:THR137 4.1 17.6 1.0
CG2 A:THR137 4.1 15.4 1.0
OD1 A:ASP43 4.1 19.4 1.0
O A:HOH2125 4.2 14.7 1.0
CA A:THR137 4.2 15.3 1.0
OG A:SEP84 4.3 11.5 0.8
CG A:GLU254 4.4 14.5 1.0
CB A:SEP84 4.5 19.1 1.0
O A:SER256 4.6 16.5 1.0
ZN A:ZN1377 4.6 18.3 1.0
O1P A:SEP84 4.7 35.9 1.0
CA A:SER256 4.7 16.6 1.0
CB A:SER256 4.7 17.2 1.0
CG A:ASP135 4.8 24.6 1.0
OD2 A:ASP301 4.9 18.1 1.0
CA A:ASP43 5.0 12.7 1.0
CD A:PRO138 5.0 11.7 1.0

Magnesium binding site 2 out of 4 in 2w5v

Go back to Magnesium Binding Sites List in 2w5v
Magnesium binding site 2 out of 4 in the Structure of TAB5 Alkaline Phosphatase Mutant His 135 Asp with Mg Bound in the M3 Site.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of TAB5 Alkaline Phosphatase Mutant His 135 Asp with Mg Bound in the M3 Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1379

b:30.6
occ:1.00
OG A:SER268 2.4 20.7 1.0
O A:HOH2244 2.5 38.0 1.0
O A:HOH2239 2.5 34.0 1.0
OD1 A:ASN266 2.5 21.6 1.0
O A:HOH2242 2.5 24.3 1.0
O A:HOH2214 2.7 31.9 1.0
CG A:ASN266 3.3 23.1 1.0
CB A:SER268 3.4 18.3 1.0
ND2 A:ASN266 3.5 21.0 1.0
N A:SER268 3.9 16.2 1.0
CA A:SER268 4.1 21.0 1.0
N A:TYR269 4.3 19.8 1.0
O A:HOH2241 4.5 28.0 1.0
OE2 A:GLU224 4.5 29.0 1.0
O A:HOH2238 4.5 46.3 1.0
CB A:ASN266 4.6 16.6 1.0
C A:SER268 4.7 19.9 1.0
N A:ALA267 4.8 17.5 1.0
C A:ASN266 4.8 22.5 1.0
OE1 A:GLU224 4.9 40.8 1.0
CA A:ASN266 4.9 17.3 1.0

Magnesium binding site 3 out of 4 in 2w5v

Go back to Magnesium Binding Sites List in 2w5v
Magnesium binding site 3 out of 4 in the Structure of TAB5 Alkaline Phosphatase Mutant His 135 Asp with Mg Bound in the M3 Site.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of TAB5 Alkaline Phosphatase Mutant His 135 Asp with Mg Bound in the M3 Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1378

b:18.2
occ:1.00
OD2 B:ASP43 2.1 15.9 1.0
OE2 B:GLU254 2.1 14.4 1.0
OG1 B:THR137 2.2 14.5 1.0
O B:HOH2170 2.2 17.1 1.0
O B:HOH2093 2.3 17.0 1.0
O B:HOH2054 2.3 20.7 1.0
CG B:ASP43 3.1 17.9 1.0
CD B:GLU254 3.2 21.2 1.0
CB B:THR137 3.3 19.1 1.0
CB B:ASP43 3.6 13.2 1.0
OE1 B:GLU254 3.6 18.7 1.0
OD2 B:ASP135 3.7 26.0 1.0
O B:HOH2053 3.9 30.1 1.0
OD1 B:ASP43 4.1 16.6 1.0
N B:THR137 4.1 13.9 1.0
CG2 B:THR137 4.2 12.8 1.0
O B:HOH2205 4.3 17.1 1.0
CA B:THR137 4.3 15.9 1.0
OG B:SEP84 4.3 17.6 1.0
CG B:GLU254 4.5 17.4 1.0
CB B:SEP84 4.5 19.0 1.0
O B:SER256 4.5 21.8 1.0
O1P B:SEP84 4.6 29.6 1.0
ZN B:ZN1377 4.6 19.0 1.0
CA B:SER256 4.6 17.8 1.0
CB B:SER256 4.7 20.5 1.0
CG B:ASP135 4.8 28.4 1.0
OD2 B:ASP301 4.9 15.4 1.0
OG B:SER256 5.0 20.0 1.0
CA B:ASP43 5.0 14.4 1.0

Magnesium binding site 4 out of 4 in 2w5v

Go back to Magnesium Binding Sites List in 2w5v
Magnesium binding site 4 out of 4 in the Structure of TAB5 Alkaline Phosphatase Mutant His 135 Asp with Mg Bound in the M3 Site.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of TAB5 Alkaline Phosphatase Mutant His 135 Asp with Mg Bound in the M3 Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1379

b:30.4
occ:0.91
O B:HOH2176 2.4 34.1 1.0
OD1 B:ASN266 2.5 27.0 1.0
OG B:SER268 2.5 25.5 1.0
O B:HOH2180 2.5 27.9 1.0
O B:HOH2178 2.5 47.7 1.0
O B:HOH2182 2.6 35.9 1.0
CG B:ASN266 3.3 30.8 1.0
ND2 B:ASN266 3.5 26.8 1.0
CB B:SER268 3.6 22.9 1.0
N B:SER268 4.0 22.4 1.0
CA B:SER268 4.3 26.8 1.0
N B:TYR269 4.4 22.7 1.0
CB B:ASN266 4.6 24.9 1.0
OE2 B:GLU224 4.8 36.4 1.0
O B:HOH2179 4.8 30.7 1.0
C B:SER268 4.8 17.4 1.0
C B:ASN266 4.9 23.7 1.0
N B:ALA267 4.9 21.8 1.0
CA B:ASN266 4.9 24.2 1.0
OE1 B:GLU224 5.0 53.3 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: Mon Dec 14 07:43:33 2020

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