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Magnesium in PDB 3p0w: Crystal Structure of D-Glucarate Dehydratase From Ralstonia Solanacearum Complexed with Mg and D-Glucarate

Protein crystallography data

The structure of Crystal Structure of D-Glucarate Dehydratase From Ralstonia Solanacearum Complexed with Mg and D-Glucarate, PDB code: 3p0w was solved by A.A.Fedorov, E.V.Fedorov, J.A.Gerlt, S.K.Burley, S.C.Almo, New York Sgxresearch Center For Structural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.01 / 1.71
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 79.958, 128.822, 178.100, 90.00, 90.00, 90.00
R / Rfree (%) 22.7 / 26.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of D-Glucarate Dehydratase From Ralstonia Solanacearum Complexed with Mg and D-Glucarate (pdb code 3p0w). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of D-Glucarate Dehydratase From Ralstonia Solanacearum Complexed with Mg and D-Glucarate, PDB code: 3p0w:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3p0w

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Magnesium binding site 1 out of 4 in the Crystal Structure of D-Glucarate Dehydratase From Ralstonia Solanacearum Complexed with Mg and D-Glucarate


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 D-Glucarate Dehydratase From Ralstonia Solanacearum Complexed with Mg and D-Glucarate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg471

b:40.2
occ:1.00
O A:HOH512 2.1 33.7 1.0
OE2 A:GLU276 2.2 37.4 1.0
OD1 A:ASN305 2.2 43.4 1.0
OD2 A:ASP251 2.3 34.6 1.0
O6B A:GKR472 2.4 42.6 1.0
O6A A:GKR472 2.4 46.2 1.0
C6 A:GKR472 2.7 48.4 1.0
CG A:ASN305 2.9 39.6 1.0
ND2 A:ASN305 2.9 39.8 1.0
CG A:ASP251 3.1 35.5 1.0
CD A:GLU276 3.2 35.4 1.0
OD1 A:ASP251 3.3 33.2 1.0
CG A:GLU276 3.6 36.1 1.0
OD2 A:ASP277 3.9 32.7 1.0
NZ A:LYS221 4.2 42.2 1.0
C5 A:GKR472 4.2 50.6 1.0
OE1 A:GLU276 4.2 39.7 1.0
CB A:ASN305 4.4 33.9 1.0
ND2 A:ASN253 4.4 43.6 1.0
CB A:ASP251 4.5 35.4 1.0
N A:ASN305 4.7 33.2 1.0
NZ A:LYS223 4.7 42.6 1.0
CG A:ASN253 4.9 44.1 1.0
O5 A:GKR472 4.9 47.0 1.0
CG A:ASP277 4.9 33.4 1.0
OD1 A:ASN253 4.9 46.5 1.0
OH A:TYR166 4.9 47.6 1.0

Magnesium binding site 2 out of 4 in 3p0w

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Magnesium binding site 2 out of 4 in the Crystal Structure of D-Glucarate Dehydratase From Ralstonia Solanacearum Complexed with Mg and D-Glucarate


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 D-Glucarate Dehydratase From Ralstonia Solanacearum Complexed with Mg and D-Glucarate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg471

b:38.8
occ:1.00
O B:HOH563 2.1 27.5 1.0
OE2 B:GLU276 2.1 30.5 1.0
OD1 B:ASN305 2.2 34.8 1.0
O6B B:GKR472 2.3 36.3 1.0
OD2 B:ASP251 2.4 31.6 1.0
O6A B:GKR472 2.4 35.4 1.0
C6 B:GKR472 2.6 38.5 1.0
CD B:GLU276 3.0 30.4 1.0
CG B:ASP251 3.0 33.0 1.0
CG B:ASN305 3.2 34.2 1.0
OD1 B:ASP251 3.3 33.6 1.0
CG B:GLU276 3.4 32.8 1.0
ND2 B:ASN305 3.5 32.4 1.0
NZ B:LYS221 3.7 38.3 1.0
OE1 B:GLU276 4.1 37.1 1.0
ND2 B:ASN253 4.1 40.7 1.0
C5 B:GKR472 4.1 41.6 1.0
OD2 B:ASP277 4.1 31.2 1.0
CB B:ASP251 4.2 34.8 1.0
NZ B:LYS223 4.2 41.0 1.0
CE B:LYS221 4.5 36.5 1.0
CB B:ASN305 4.5 32.8 1.0
CD1 B:LEU327 4.7 35.2 1.0
N B:ASN305 4.8 26.6 1.0
CB B:GLU276 4.8 32.5 1.0
O5 B:GKR472 4.8 41.3 1.0
CD2 B:HIS355 4.9 36.2 1.0
CG B:ASN253 4.9 42.2 1.0
OH B:TYR166 5.0 40.8 1.0

Magnesium binding site 3 out of 4 in 3p0w

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Magnesium binding site 3 out of 4 in the Crystal Structure of D-Glucarate Dehydratase From Ralstonia Solanacearum Complexed with Mg and D-Glucarate


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 D-Glucarate Dehydratase From Ralstonia Solanacearum Complexed with Mg and D-Glucarate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg471

b:43.7
occ:1.00
O C:HOH513 2.1 37.5 1.0
OD2 C:ASP251 2.2 37.1 1.0
OD1 C:ASN305 2.2 45.1 1.0
OE2 C:GLU276 2.3 40.1 1.0
O6A C:GKR472 2.4 49.1 1.0
O6B C:GKR472 2.4 43.5 1.0
C6 C:GKR472 2.7 49.5 1.0
CG C:ASN305 3.0 37.9 1.0
CG C:ASP251 3.0 36.8 1.0
ND2 C:ASN305 3.2 40.0 1.0
CD C:GLU276 3.3 38.7 1.0
OD1 C:ASP251 3.3 36.0 1.0
OD2 C:ASP277 3.6 31.9 1.0
CG C:GLU276 3.7 35.6 1.0
ND2 C:ASN253 3.9 44.5 1.0
NZ C:LYS221 4.1 42.9 1.0
NZ C:LYS223 4.2 45.1 1.0
C5 C:GKR472 4.2 49.7 1.0
CB C:ASP251 4.3 35.6 1.0
CB C:ASN305 4.4 35.5 1.0
OE1 C:GLU276 4.4 41.1 1.0
CG C:ASP277 4.6 34.7 1.0
N C:ASN305 4.6 35.4 1.0
CG C:ASN253 4.7 43.9 1.0
CB C:ASP277 4.8 38.1 1.0
CE C:LYS221 4.9 44.3 1.0
C4 C:GKR472 5.0 47.9 1.0
CG C:MET306 5.0 36.1 1.0
O5 C:GKR472 5.0 45.8 1.0

Magnesium binding site 4 out of 4 in 3p0w

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Magnesium binding site 4 out of 4 in the Crystal Structure of D-Glucarate Dehydratase From Ralstonia Solanacearum Complexed with Mg and D-Glucarate


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 D-Glucarate Dehydratase From Ralstonia Solanacearum Complexed with Mg and D-Glucarate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg471

b:45.3
occ:1.00
OD1 D:ASN305 2.2 39.2 1.0
O D:HOH509 2.2 41.9 1.0
OE2 D:GLU276 2.2 44.7 1.0
OD2 D:ASP251 2.3 40.6 1.0
O6B D:GKR472 2.4 43.8 1.0
O6A D:GKR472 2.5 48.4 1.0
C6 D:GKR472 2.8 50.3 1.0
CG D:ASP251 3.0 37.8 1.0
OD1 D:ASP251 3.1 35.2 1.0
CD D:GLU276 3.2 34.9 1.0
CG D:ASN305 3.2 41.8 1.0
CG D:GLU276 3.7 36.7 1.0
OD2 D:ASP277 3.8 35.3 1.0
ND2 D:ASN305 3.9 42.3 1.0
O D:HOH504 4.0 45.0 1.0
OE1 D:GLU276 4.2 42.3 1.0
NZ D:LYS223 4.2 46.7 1.0
C5 D:GKR472 4.3 51.7 1.0
CB D:ASP251 4.3 40.4 1.0
CB D:ASN305 4.4 40.3 1.0
OD1 D:ASN253 4.5 45.3 1.0
N D:ASN305 4.6 39.6 1.0
CG D:ASN253 4.8 46.2 1.0
CG D:MET306 4.9 42.4 1.0
CG D:ASP277 4.9 38.4 1.0
ND2 D:ASN253 4.9 44.6 1.0
CB D:GLU276 4.9 36.7 1.0
CA D:ASN305 5.0 39.3 1.0

Reference:

A.A.Fedorov, E.V.Fedorov, J.A.Gerlt, S.K.Burley, S.C.Almo. Crystal Structure of D-Glucarate Dehydratase From Ralstonia Solanacearum Complexed with Mg and D-Glucarate To Be Published.
Page generated: Mon Dec 14 08:38:28 2020

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