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Magnesium in PDB 2bi3: Radiation Damage of the Schiff Base in Phosphoserine Aminotransferase (Structure D)

Enzymatic activity of Radiation Damage of the Schiff Base in Phosphoserine Aminotransferase (Structure D)

All present enzymatic activity of Radiation Damage of the Schiff Base in Phosphoserine Aminotransferase (Structure D):
2.6.1.52;

Protein crystallography data

The structure of Radiation Damage of the Schiff Base in Phosphoserine Aminotransferase (Structure D), PDB code: 2bi3 was solved by A.P.Dubnovitsky, R.B.G.Ravelli, A.N.Popov, A.C.Papageorgiou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 1.69
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 143.061, 83.772, 66.719, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 22.9

Other elements in 2bi3:

The structure of Radiation Damage of the Schiff Base in Phosphoserine Aminotransferase (Structure D) also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Radiation Damage of the Schiff Base in Phosphoserine Aminotransferase (Structure D) (pdb code 2bi3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Radiation Damage of the Schiff Base in Phosphoserine Aminotransferase (Structure D), PDB code: 2bi3:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2bi3

Go back to Magnesium Binding Sites List in 2bi3
Magnesium binding site 1 out of 4 in the Radiation Damage of the Schiff Base in Phosphoserine Aminotransferase (Structure D)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Radiation Damage of the Schiff Base in Phosphoserine Aminotransferase (Structure D) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1362

b:21.4
occ:1.00
 OD1 A:ASP256 2.0 16.5 1.0
O A:HOH2188 2.1 19.6 1.0
O A:HOH2187 2.1 24.8 1.0
O A:HOH2183 2.2 16.2 1.0
CG A:ASP256 3.0 16.8 1.0
OD2 A:ASP256 3.3 18.4 1.0
O A:ASP252 4.1 13.4 1.0
OD1 A:ASP252 4.2 15.6 1.0
O A:HOH2184 4.3 25.1 1.0
CB A:ASP256 4.4 14.5 1.0
CA A:ASP256 4.6 13.8 1.0
N A:ASP256 4.7 11.6 1.0
CG A:ASP252 4.8 16.9 1.0
C A:ASP252 4.9 17.0 1.0
CG A:LYS255 4.9 16.6 1.0
CD A:LYS255 4.9 15.0 1.0
CB A:ASP252 4.9 9.5 1.0

Magnesium binding site 2 out of 4 in 2bi3

Go back to Magnesium Binding Sites List in 2bi3
Magnesium binding site 2 out of 4 in the Radiation Damage of the Schiff Base in Phosphoserine Aminotransferase (Structure D)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Radiation Damage of the Schiff Base in Phosphoserine Aminotransferase (Structure D) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1363

b:17.4
occ:1.00
 OD2 A:ASP344 2.0 17.2 1.0
O A:HOH2268 2.2 12.6 1.0
CG A:ASP344 3.1 20.1 1.0
OD1 A:ASP344 3.4 16.5 1.0
O A:HOH2266 3.9 32.4 1.0
O A:HOH2269 4.2 23.8 1.0
CB A:ASP344 4.3 12.4 1.0
O A:HOH2267 4.6 23.8 1.0

Magnesium binding site 3 out of 4 in 2bi3

Go back to Magnesium Binding Sites List in 2bi3
Magnesium binding site 3 out of 4 in the Radiation Damage of the Schiff Base in Phosphoserine Aminotransferase (Structure D)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Radiation Damage of the Schiff Base in Phosphoserine Aminotransferase (Structure D) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1362

b:24.1
occ:1.00
 O B:HOH2252 2.1 21.1 1.0
O B:HOH2110 2.1 29.9 1.0
O B:HOH2242 2.3 30.2 1.0
O B:HOH2249 2.3 25.3 1.0
OD2 B:ASP276 4.0 15.6 1.0
OE2 B:GLU280 4.1 22.8 1.0
O B:HOH2111 4.1 29.3 1.0
O B:HOH2109 4.2 36.2 1.0
OD1 B:ASP276 4.2 13.5 1.0
CG B:ASP276 4.3 16.1 1.0
NZ B:LYS272 4.3 13.1 1.0
O B:HOH2250 4.4 40.2 1.0
O B:HOH2251 4.4 20.5 1.0

Magnesium binding site 4 out of 4 in 2bi3

Go back to Magnesium Binding Sites List in 2bi3
Magnesium binding site 4 out of 4 in the Radiation Damage of the Schiff Base in Phosphoserine Aminotransferase (Structure D)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Radiation Damage of the Schiff Base in Phosphoserine Aminotransferase (Structure D) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1363

b:47.8
occ:0.50
 O B:HOH2221 2.5 40.4 1.0
OD1 B:ASP256 2.6 18.4 1.0
O B:HOH2215 2.6 24.1 1.0
O B:HOH2223 2.8 36.2 1.0
CG B:ASP256 3.4 20.7 1.0
OD2 B:ASP256 3.6 23.5 1.0
OD1 B:ASP252 4.2 16.1 1.0
O B:HOH2216 4.4 29.1 1.0
O B:ASP252 4.6 13.2 1.0
CG B:ASP252 4.8 17.4 1.0
CB B:ASP256 4.8 14.6 1.0

Reference:

A.P.Dubnovitsky, R.B.G.Ravelli, A.N.Popov, A.C.Papageorgiou. Strain Relief at the Active Site of Phosphoserine Aminotransferase Induced By Radiation Damage. Protein Sci. V. 14 1498 2005.
ISSN: ISSN 0961-8368
PubMed: 15883191
DOI: 10.1110/PS.051397905
Page generated: Tue Aug 13 21:52:43 2024

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