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Magnesium in PDB 1w23: Crystal Structure of Phosphoserine Aminotransferase From Bacillus Alcalophilus

Enzymatic activity of Crystal Structure of Phosphoserine Aminotransferase From Bacillus Alcalophilus

All present enzymatic activity of Crystal Structure of Phosphoserine Aminotransferase From Bacillus Alcalophilus:
2.6.1.52;

Protein crystallography data

The structure of Crystal Structure of Phosphoserine Aminotransferase From Bacillus Alcalophilus, PDB code: 1w23 was solved by A.Dubnovitsky, E.G.Kapetaniou, A.C.Papageorgiou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.08
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 144.467, 84.840, 67.469, 90.00, 90.00, 90.00
R / Rfree (%) 11.7 / 13.9

Other elements in 1w23:

The structure of Crystal Structure of Phosphoserine Aminotransferase From Bacillus Alcalophilus also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Phosphoserine Aminotransferase From Bacillus Alcalophilus (pdb code 1w23). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of Phosphoserine Aminotransferase From Bacillus Alcalophilus, PDB code: 1w23:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 1w23

Go back to Magnesium Binding Sites List in 1w23
Magnesium binding site 1 out of 5 in the Crystal Structure of Phosphoserine Aminotransferase From Bacillus Alcalophilus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Phosphoserine Aminotransferase From Bacillus Alcalophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:16.8
occ:0.50
 O B:HOH2197 2.0 20.6 0.5
O B:HOH2408 2.0 17.0 0.5
O B:HOH2196 2.1 22.7 0.5
O B:HOH2400 2.3 20.3 1.0
O B:HOH2399 2.3 21.1 0.5
O B:HOH2397 4.0 23.4 1.0
O B:HOH2199 4.0 34.2 1.0
OD2 B:ASP276 4.1 11.2 1.0
OE2 B:GLU280 4.1 22.7 1.0
CG B:ASP276 4.3 10.3 1.0
OD1 B:ASP276 4.4 12.2 1.0
NZ B:LYS272 4.4 15.5 1.0
O B:HOH2412 4.4 16.1 1.0

Magnesium binding site 2 out of 5 in 1w23

Go back to Magnesium Binding Sites List in 1w23
Magnesium binding site 2 out of 5 in the Crystal Structure of Phosphoserine Aminotransferase From Bacillus Alcalophilus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Phosphoserine Aminotransferase From Bacillus Alcalophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1361

b:15.8
occ:1.00
 OD1 A:ASP256 2.0 12.8 1.0
O A:HOH2316 2.0 22.4 1.0
O A:HOH2141 2.1 21.8 1.0
O A:HOH2315 2.1 19.1 1.0
O A:HOH2318 2.1 14.6 1.0
CG A:ASP256 3.0 11.8 1.0
OD2 A:ASP256 3.4 14.1 1.0
O A:ASP252 4.2 10.6 1.0
O A:HOH2309 4.3 28.1 1.0
OD1 A:ASP252 4.3 11.5 1.0
CB A:ASP256 4.3 12.1 1.0
O A:HOH2144 4.4 49.0 1.0
O A:HOH2147 4.4 51.3 1.0
CA A:ASP256 4.7 12.2 1.0
N A:ASP256 4.8 10.6 1.0
CG A:ASP252 4.9 10.3 1.0

Magnesium binding site 3 out of 5 in 1w23

Go back to Magnesium Binding Sites List in 1w23
Magnesium binding site 3 out of 5 in the Crystal Structure of Phosphoserine Aminotransferase From Bacillus Alcalophilus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Phosphoserine Aminotransferase From Bacillus Alcalophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1362

b:14.4
occ:1.00
 O A:HOH2425 2.0 20.7 1.0
OD2 A:ASP344 2.1 15.4 1.0
O A:HOH2424 2.1 14.0 1.0
CG A:ASP344 3.1 13.4 1.0
OD1 A:ASP344 3.5 13.1 1.0
O A:HOH2002 4.1 27.1 1.0
O A:HOH2421 4.2 23.6 1.0
O A:HOH2420 4.2 33.8 1.0
CB A:ASP344 4.4 12.5 1.0
O A:HOH2423 4.9 28.1 1.0

Magnesium binding site 4 out of 5 in 1w23

Go back to Magnesium Binding Sites List in 1w23
Magnesium binding site 4 out of 5 in the Crystal Structure of Phosphoserine Aminotransferase From Bacillus Alcalophilus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Phosphoserine Aminotransferase From Bacillus Alcalophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1361

b:20.6
occ:0.60
 ND1 B:HIS288 1.7 16.7 0.6
CE1 B:HIS288 2.2 15.7 0.6
O B:TYR127 2.7 17.1 1.0
O B:TYR154 2.9 12.9 1.0
CG B:HIS288 2.9 13.5 0.6
NE2 B:HIS288 3.4 18.0 0.6
CA B:GLN128 3.4 13.1 1.0
C B:TYR127 3.6 14.4 1.0
CG2 B:THR156 3.6 11.5 1.0
O B:HIS288 3.7 13.3 1.0
C B:HIS288 3.7 11.5 1.0
CD2 B:HIS288 3.8 14.6 0.6
CA B:ALA289 3.8 11.4 1.0
N B:ALA289 3.8 11.1 1.0
CB B:TYR154 3.8 11.0 1.0
CB B:HIS288 3.8 11.5 0.6
CB B:HIS288 3.8 12.0 0.4
C B:TYR154 3.8 10.5 1.0
N B:GLN128 3.9 13.1 1.0
CD2 B:TYR154 4.1 14.1 1.0
C B:GLN128 4.1 12.4 1.0
CA B:TYR154 4.2 10.7 1.0
O B:SER126 4.2 14.0 1.0
CB B:ALA289 4.3 11.7 1.0
O B:GLN128 4.3 13.0 1.0
CG B:GLN128 4.3 16.5 1.0
CB B:GLN128 4.4 14.7 1.0
CA B:HIS288 4.4 11.2 1.0
CG B:TYR154 4.5 11.2 1.0
O B:HOH2282 4.7 29.3 1.0
CA B:TYR127 4.9 13.2 1.0
OG1 B:THR300 4.9 11.2 1.0
O B:HOH2421 5.0 29.6 1.0
N B:GLY155 5.0 10.2 1.0
CB B:THR156 5.0 10.2 1.0

Magnesium binding site 5 out of 5 in 1w23

Go back to Magnesium Binding Sites List in 1w23
Magnesium binding site 5 out of 5 in the Crystal Structure of Phosphoserine Aminotransferase From Bacillus Alcalophilus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Phosphoserine Aminotransferase From Bacillus Alcalophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1361

b:20.0
occ:0.40
 ND1 B:HIS288 1.8 14.5 0.4
ND2 B:ASN302 2.2 14.2 0.5
CE1 B:HIS288 2.6 14.4 0.4
O B:HOH2436 2.9 48.2 1.0
ND2 B:ASN302 2.9 15.8 0.6
O B:VAL286 3.0 12.2 1.0
CG B:HIS288 3.1 11.9 0.4
CG B:ASN302 3.3 13.3 0.5
N B:HIS288 3.4 11.5 1.0
C B:GLY287 3.5 11.1 1.0
CA B:HIS288 3.6 11.2 1.0
O B:GLY287 3.7 13.1 1.0
N B:ASN302 3.7 11.6 1.0
CB B:ASN302 3.8 13.6 0.6
CG B:ASN302 3.8 12.3 0.6
NE2 B:HIS288 3.8 16.7 0.4
C B:VAL286 3.9 10.8 1.0
CB B:HIS288 3.9 12.0 0.4
CB B:HIS288 3.9 11.5 0.6
CD2 B:HIS288 4.0 12.1 0.4
OD1 B:ASN302 4.1 16.7 0.5
C B:PHE301 4.2 10.5 1.0
CA B:PHE301 4.2 10.0 1.0
CB B:ASN302 4.3 14.7 0.5
CA B:GLY287 4.3 11.1 1.0
CG1 B:VAL286 4.3 20.6 1.0
O B:HOH2437 4.4 45.2 1.0
CA B:ASN302 4.5 12.5 1.0
N B:GLY287 4.5 11.0 1.0
CB B:VAL286 4.5 14.8 1.0
CD2 B:HIS288 4.7 14.6 0.6
CG B:HIS288 4.8 13.5 0.6
CA B:VAL286 4.8 11.4 1.0
N B:PHE301 5.0 9.9 1.0
OD1 B:ASN302 5.0 14.4 0.6
O B:PHE301 5.0 11.9 1.0

Reference:

A.Dubnovitsky, E.G.Kapetaniou, A.C.Papageorgiou. Enzyme Adaptation to Alkaline pH: Atomic Resolution (1.08 A) Structure of Phosphoserine Aminotransferase From Bacillus Alcalophilus Protein Sci. V. 14 97 2005.
ISSN: ISSN 0961-8368
PubMed: 15608117
DOI: 10.1110/PS.041029805
Page generated: Tue Aug 13 16:40:12 2024

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