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Magnesium in PDB 3qu2: Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, A Closed Cap Conformation

Enzymatic activity of Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, A Closed Cap Conformation

All present enzymatic activity of Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, A Closed Cap Conformation:
3.6.1.1;

Protein crystallography data

The structure of Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, A Closed Cap Conformation, PDB code: 3qu2 was solved by Y.Patskovsky, H.Huang, R.Toro, J.A.Gerlt, S.K.Burley, D.Dunaway-Mariano, S.C.Almo, New York Sgx Research Center For Structural Genomics(Nysgxrc), Enzyme Function Initiative (Efi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.95
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 137.602, 71.761, 114.525, 90.00, 105.80, 90.00
R / Rfree (%) 23.2 / 27.5

Other elements in 3qu2:

The structure of Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, A Closed Cap Conformation also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, A Closed Cap Conformation (pdb code 3qu2). 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 Pyrophosphatase From Bacteroides Thetaiotaomicron, A Closed Cap Conformation, PDB code: 3qu2:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3qu2

Go back to Magnesium Binding Sites List in 3qu2
Magnesium binding site 1 out of 4 in the Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, A Closed Cap Conformation


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 Pyrophosphatase From Bacteroides Thetaiotaomicron, A Closed Cap Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg225

b:12.5
occ:1.00
 OD2 A:ASP11 2.0 30.7 1.0
OE2 A:GLU47 2.1 33.9 1.0
OD1 A:ASN172 2.3 16.4 1.0
O A:ASP13 2.4 16.7 1.0
O A:HOH549 2.7 26.6 1.0
CD A:GLU47 3.2 21.0 1.0
CG A:ASP11 3.2 19.0 1.0
CG A:ASN172 3.3 12.1 1.0
C A:ASP13 3.5 24.5 1.0
ND2 A:ASN172 3.6 13.2 1.0
CG A:GLU47 3.7 22.2 1.0
OE1 A:GLU171 3.9 23.7 1.0
CB A:ASP11 4.0 21.5 1.0
OD1 A:ASP11 4.1 24.6 1.0
OE1 A:GLU47 4.1 28.7 1.0
CB A:ALA173 4.2 11.9 1.0
CB A:ASP13 4.3 16.2 1.0
CA A:ASP13 4.3 14.6 1.0
N A:ASP13 4.4 17.4 1.0
O A:HOH228 4.4 11.9 1.0
N A:GLY14 4.5 17.2 1.0
O4 A:CIT227 4.5 30.9 1.0
CB A:ASN172 4.6 13.6 1.0
CA A:GLY14 4.6 18.7 1.0
CG2 A:VAL15 4.7 20.4 1.0
N A:ALA173 4.7 13.4 1.0
N A:ASN172 4.7 21.7 1.0
O A:HOH298 4.8 14.2 1.0
CD A:GLU171 4.9 24.8 1.0

Magnesium binding site 2 out of 4 in 3qu2

Go back to Magnesium Binding Sites List in 3qu2
Magnesium binding site 2 out of 4 in the Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, A Closed Cap Conformation


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 Pyrophosphatase From Bacteroides Thetaiotaomicron, A Closed Cap Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg225

b:13.3
occ:1.00
 OE2 B:GLU47 2.1 25.2 1.0
O B:ASP13 2.3 14.6 1.0
OD1 B:ASN172 2.3 17.8 1.0
O B:HOH263 2.5 10.3 1.0
OD2 B:ASP11 2.5 19.8 1.0
O B:HOH276 2.9 32.8 1.0
CD B:GLU47 3.1 21.1 1.0
CG B:ASN172 3.3 8.3 1.0
CG B:ASP11 3.3 28.5 1.0
C B:ASP13 3.4 24.9 1.0
ND2 B:ASN172 3.6 14.0 1.0
CG B:GLU47 3.6 19.1 1.0
OD1 B:ASP11 3.9 28.9 1.0
OE1 B:GLU171 4.0 26.9 1.0
OE1 B:GLU47 4.1 32.9 1.0
CB B:ASP13 4.2 27.5 1.0
CB B:ALA173 4.2 11.6 1.0
CA B:ASP13 4.3 18.9 1.0
CB B:ASP11 4.3 16.3 1.0
N B:GLY14 4.3 18.4 1.0
CA B:GLY14 4.5 14.3 1.0
N B:ASP13 4.6 16.0 1.0
CB B:ASN172 4.7 15.2 1.0
O1 B:GOL226 4.8 22.1 1.0
N B:ALA173 4.8 17.4 1.0
N B:ASN172 4.9 18.0 1.0
C B:GLY14 4.9 19.2 1.0
CD B:GLU171 5.0 21.7 1.0

Magnesium binding site 3 out of 4 in 3qu2

Go back to Magnesium Binding Sites List in 3qu2
Magnesium binding site 3 out of 4 in the Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, A Closed Cap Conformation


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 Pyrophosphatase From Bacteroides Thetaiotaomicron, A Closed Cap Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg225

b:16.9
occ:1.00
 OD2 C:ASP11 2.1 23.7 1.0
OD1 C:ASN172 2.1 16.3 1.0
OE2 C:GLU47 2.4 21.4 1.0
O C:ASP13 2.4 30.0 1.0
O C:HOH569 2.8 30.8 1.0
O C:HOH568 2.9 53.0 1.0
CG C:ASN172 3.2 11.1 1.0
CG C:ASP11 3.3 19.8 1.0
CD C:GLU47 3.4 22.6 1.0
ND2 C:ASN172 3.6 16.8 1.0
C C:ASP13 3.6 11.7 1.0
OE1 C:GLU171 3.7 22.8 1.0
CG C:GLU47 3.9 27.0 1.0
CB C:ASP11 4.0 22.1 1.0
CB C:ALA173 4.2 26.6 1.0
OD1 C:ASP11 4.3 16.5 1.0
CB C:ASP13 4.4 11.9 1.0
CA C:ASP13 4.4 19.0 1.0
OE1 C:GLU47 4.4 25.5 1.0
O C:HOH228 4.4 7.7 1.0
CB C:ASN172 4.5 16.8 1.0
N C:ASN172 4.5 20.8 1.0
N C:ASP13 4.6 13.9 1.0
N C:GLY14 4.6 17.2 1.0
N C:ALA173 4.6 15.0 1.0
O C:HOH271 4.6 17.2 1.0
CA C:GLY14 4.7 11.3 1.0
CG2 C:VAL15 4.8 17.2 1.0
CD C:GLU171 4.8 21.3 1.0
CA C:ASN172 4.9 18.6 1.0
C C:ASN172 5.0 16.0 1.0

Magnesium binding site 4 out of 4 in 3qu2

Go back to Magnesium Binding Sites List in 3qu2
Magnesium binding site 4 out of 4 in the Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, A Closed Cap Conformation


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 Pyrophosphatase From Bacteroides Thetaiotaomicron, A Closed Cap Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg225

b:13.0
occ:1.00
 OE2 D:GLU47 2.2 15.7 1.0
O D:ASP13 2.2 16.6 1.0
OD1 D:ASN172 2.3 13.6 1.0
OD2 D:ASP11 2.4 19.8 1.0
O D:HOH272 2.7 16.8 1.0
CG D:ASN172 3.2 20.8 1.0
CG D:ASP11 3.2 17.4 1.0
CD D:GLU47 3.3 16.2 1.0
C D:ASP13 3.4 19.1 1.0
ND2 D:ASN172 3.5 13.2 1.0
O D:HOH741 3.5 40.3 1.0
CG D:GLU47 3.7 14.4 1.0
OD1 D:ASP11 3.9 16.2 1.0
OE1 D:GLU171 4.0 21.9 1.0
CB D:ASP11 4.1 15.8 1.0
CB D:ASP13 4.2 21.0 1.0
CB D:ALA173 4.2 21.6 1.0
CA D:ASP13 4.2 15.9 1.0
N D:GLY14 4.3 14.8 1.0
OE1 D:GLU47 4.3 13.8 1.0
CA D:GLY14 4.4 9.8 1.0
N D:ASP13 4.6 14.1 1.0
CB D:ASN172 4.6 12.2 1.0
N D:ALA173 4.8 18.5 1.0
C D:GLY14 4.8 12.7 1.0
O3 D:GOL226 4.8 17.1 1.0
N D:ASN172 4.9 15.0 1.0
CG2 D:VAL15 4.9 8.3 1.0
N D:VAL15 5.0 12.9 1.0

Reference:

H.Huang, Y.Patskovsky, R.Toro, J.D.Farelli, C.Pandya, S.C.Almo, K.N.Allen, D.Dunaway-Mariano. Divergence of Structure and Function in the Haloacid Dehalogenase Enzyme Superfamily: Bacteroides Thetaiotaomicron BT2127 Is An Inorganic Pyrophosphatase. Biochemistry V. 50 8937 2011.
ISSN: ISSN 0006-2960
PubMed: 21894910
DOI: 10.1021/BI201181Q
Page generated: Thu Aug 15 10:10:21 2024

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