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Magnesium in PDB 3nxl: Crystal Structure of Glucarate Dehydratase From Burkholderia Cepacia Complexed with Magnesium

Enzymatic activity of Crystal Structure of Glucarate Dehydratase From Burkholderia Cepacia Complexed with Magnesium

All present enzymatic activity of Crystal Structure of Glucarate Dehydratase From Burkholderia Cepacia Complexed with Magnesium:
4.2.1.40;

Protein crystallography data

The structure of Crystal Structure of Glucarate Dehydratase From Burkholderia Cepacia Complexed with Magnesium, PDB code: 3nxl 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) 34.23 / 1.89
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 165.289, 121.452, 108.652, 90.00, 92.60, 90.00
R / Rfree (%) 19 / 22.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Glucarate Dehydratase From Burkholderia Cepacia Complexed with Magnesium (pdb code 3nxl). 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 Glucarate Dehydratase From Burkholderia Cepacia Complexed with Magnesium, PDB code: 3nxl:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3nxl

Go back to Magnesium Binding Sites List in 3nxl
Magnesium binding site 1 out of 4 in the Crystal Structure of Glucarate Dehydratase From Burkholderia Cepacia Complexed with Magnesium


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 Glucarate Dehydratase From Burkholderia Cepacia Complexed with Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg476

b:43.5
occ:1.00
 O A:HOH491 2.3 26.9 1.0
OD2 A:ASP255 2.3 24.6 1.0
OD1 A:ASN309 2.4 43.6 1.0
OE2 A:GLU280 2.4 31.3 1.0
O A:HOH902 2.5 43.4 1.0
O A:HOH901 2.5 37.2 1.0
ND2 A:ASN309 3.0 33.2 1.0
CG A:ASN309 3.1 31.5 1.0
CG A:ASP255 3.2 23.3 1.0
CD A:GLU280 3.4 29.8 1.0
OD1 A:ASP255 3.6 23.4 1.0
CD2 A:HIS359 3.8 44.5 1.0
NZ A:LYS227 3.8 28.0 1.0
ND2 A:ASN257 3.9 32.5 1.0
CG A:GLU280 4.0 25.0 1.0
NE2 A:HIS359 4.0 41.8 1.0
NZ A:LYS225 4.2 36.3 1.0
OD2 A:ASP281 4.2 26.4 1.0
OE1 A:GLU280 4.4 33.2 1.0
CB A:ASP255 4.4 21.5 1.0
CB A:ASN309 4.5 26.2 1.0
OH A:TYR170 4.7 33.1 1.0
CG A:ASN257 4.8 33.3 1.0
N A:ASN309 4.8 23.1 1.0
CG A:HIS359 4.8 37.4 1.0
CE1 A:HIS359 5.0 39.5 1.0

Magnesium binding site 2 out of 4 in 3nxl

Go back to Magnesium Binding Sites List in 3nxl
Magnesium binding site 2 out of 4 in the Crystal Structure of Glucarate Dehydratase From Burkholderia Cepacia Complexed with Magnesium


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 Glucarate Dehydratase From Burkholderia Cepacia Complexed with Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg476

b:42.5
occ:1.00
 OD2 B:ASP255 2.3 25.8 1.0
OE2 B:GLU280 2.3 27.9 1.0
O B:HOH723 2.4 35.6 1.0
O B:HOH489 2.4 27.8 1.0
OD1 B:ASN309 2.5 42.8 1.0
O B:HOH684 2.6 44.7 1.0
CG B:ASP255 3.3 25.6 1.0
CG B:ASN309 3.4 36.8 1.0
CD B:GLU280 3.4 30.6 1.0
OD1 B:ASP255 3.7 19.8 1.0
NZ B:LYS227 3.7 28.1 1.0
NZ B:LYS225 3.9 34.9 1.0
ND2 B:ASN309 3.9 41.8 1.0
CG B:GLU280 4.1 23.8 1.0
ND2 B:ASN257 4.2 36.5 1.0
OE1 B:GLU280 4.3 37.1 1.0
OD2 B:ASP281 4.4 23.5 1.0
CB B:ASP255 4.4 24.4 1.0
CB B:ASN309 4.4 27.4 1.0
OH B:TYR170 4.5 36.2 1.0
N B:ASN309 4.9 25.0 1.0
CE B:LYS227 5.0 26.5 1.0
CG B:ASN257 5.0 33.5 1.0

Magnesium binding site 3 out of 4 in 3nxl

Go back to Magnesium Binding Sites List in 3nxl
Magnesium binding site 3 out of 4 in the Crystal Structure of Glucarate Dehydratase From Burkholderia Cepacia Complexed with Magnesium


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 Glucarate Dehydratase From Burkholderia Cepacia Complexed with Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg476

b:39.9
occ:1.00
 OD2 C:ASP255 2.2 23.0 1.0
O C:HOH600 2.3 32.1 1.0
OE2 C:GLU280 2.4 28.9 1.0
OD1 C:ASN309 2.4 37.8 1.0
O C:HOH505 2.5 31.7 1.0
O C:HOH578 2.6 35.7 1.0
CG C:ASN309 3.1 32.3 1.0
ND2 C:ASN309 3.1 33.9 1.0
CG C:ASP255 3.2 26.1 1.0
CD C:GLU280 3.5 24.3 1.0
NZ C:LYS227 3.6 29.6 1.0
OD1 C:ASP255 3.7 21.2 1.0
NZ C:LYS225 3.8 30.7 1.0
ND2 C:ASN257 3.9 32.0 1.0
CG C:GLU280 4.2 24.7 1.0
OE1 C:GLU280 4.4 29.6 1.0
CB C:ASP255 4.5 20.9 1.0
OH C:TYR170 4.5 35.0 1.0
OD2 C:ASP281 4.5 25.2 1.0
CB C:ASN309 4.6 26.4 1.0
CG C:ASN257 4.7 32.0 1.0
CE C:LYS225 4.9 38.1 1.0
OD1 C:ASN257 4.9 30.6 1.0
CE C:LYS227 5.0 25.6 1.0

Magnesium binding site 4 out of 4 in 3nxl

Go back to Magnesium Binding Sites List in 3nxl
Magnesium binding site 4 out of 4 in the Crystal Structure of Glucarate Dehydratase From Burkholderia Cepacia Complexed with Magnesium


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 Glucarate Dehydratase From Burkholderia Cepacia Complexed with Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg476

b:36.2
occ:1.00
 OE2 D:GLU280 2.3 28.9 1.0
OD2 D:ASP255 2.3 22.8 1.0
O D:HOH496 2.4 25.0 1.0
OD1 D:ASN309 2.4 38.0 1.0
O D:HOH903 2.5 40.0 1.0
O D:HOH733 2.6 38.8 1.0
CG D:ASN309 3.2 30.2 1.0
CG D:ASP255 3.2 23.3 1.0
ND2 D:ASN309 3.3 30.5 1.0
CD D:GLU280 3.3 28.7 1.0
NZ D:LYS225 3.6 37.0 1.0
OD1 D:ASP255 3.6 20.3 1.0
NZ D:LYS227 3.8 23.4 1.0
CG D:GLU280 4.0 24.5 1.0
ND2 D:ASN257 4.2 27.2 1.0
OE1 D:GLU280 4.3 34.1 1.0
OD2 D:ASP281 4.3 23.7 1.0
ND1 D:HIS359 4.3 38.8 1.0
CE D:LYS225 4.4 34.8 1.0
CB D:ASP255 4.4 20.1 1.0
OH D:TYR170 4.5 36.4 1.0
CB D:ASN309 4.6 29.1 1.0
CG D:ASN257 4.9 28.5 1.0
CE1 D:HIS359 4.9 34.9 1.0

Reference:

A.A.Fedorov, E.V.Fedorov, J.A.Gerlt, S.K.Burley, S.C.Almo. Crystal Structure of Glucarate Dehydratase From Burkholderia Cepacia Complexed with Magnesium To Be Published.
Page generated: Mon Dec 14 08:30:20 2020

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