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Magnesium in PDB 3qu4: Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, ASP13ALA Mutant

Enzymatic activity of Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, ASP13ALA Mutant

All present enzymatic activity of Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, ASP13ALA Mutant:
3.6.1.1;

Protein crystallography data

The structure of Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, ASP13ALA Mutant, PDB code: 3qu4 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 / 2.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 69.945, 76.217, 95.588, 89.97, 89.97, 90.00
R / Rfree (%) 21.6 / 28.6

Other elements in 3qu4:

The structure of Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, ASP13ALA Mutant also contains other interesting chemical elements:

Chlorine (Cl) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, ASP13ALA Mutant (pdb code 3qu4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, ASP13ALA Mutant, PDB code: 3qu4:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3qu4

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Magnesium binding site 1 out of 8 in the Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, ASP13ALA Mutant


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, ASP13ALA Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg225

b:10.3
occ:1.00
 O A:HOH950 2.1 31.7 1.0
O A:ALA13 2.2 40.9 1.0
OD1 A:ASN172 2.2 24.4 1.0
OD2 A:ASP11 2.2 12.7 1.0
OE2 A:GLU47 2.3 27.1 1.0
O A:HOH943 2.5 33.2 1.0
CG A:ASN172 3.2 24.7 1.0
CD A:GLU47 3.3 33.7 1.0
C A:ALA13 3.4 32.3 1.0
CG A:ASP11 3.5 39.3 1.0
ND2 A:ASN172 3.5 18.1 1.0
CG A:GLU47 3.8 22.3 1.0
OD1 A:ASP11 4.1 39.7 1.0
CB A:ALA13 4.1 26.9 1.0
O A:HOH842 4.2 26.7 1.0
OE1 A:GLU171 4.2 42.9 1.0
CA A:ALA13 4.2 28.1 1.0
CB A:ALA173 4.2 18.6 1.0
OE1 A:GLU47 4.4 34.3 1.0
N A:GLY14 4.4 35.1 1.0
N A:ALA13 4.5 26.5 1.0
CB A:ASN172 4.6 30.1 1.0
CA A:GLY14 4.6 29.1 1.0
CB A:ASP11 4.6 27.2 1.0
O A:ACT226 4.7 45.0 1.0
O A:HOH228 4.8 16.2 1.0
N A:ASN172 4.9 29.5 1.0
CG2 A:VAL15 5.0 26.6 1.0

Magnesium binding site 2 out of 8 in 3qu4

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Magnesium binding site 2 out of 8 in the Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, ASP13ALA Mutant


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, ASP13ALA Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg225

b:14.0
occ:1.00
 O B:ALA13 2.1 27.5 1.0
O B:HOH974 2.2 29.9 1.0
O B:HOH246 2.2 33.0 1.0
OE2 B:GLU47 2.3 26.6 1.0
OD2 B:ASP11 2.4 16.4 1.0
OD1 B:ASN172 2.4 19.5 1.0
C B:ALA13 3.4 30.3 1.0
CD B:GLU47 3.4 35.7 1.0
CG B:ASN172 3.4 33.7 1.0
CG B:ASP11 3.7 38.6 1.0
O B:HOH917 3.7 43.7 1.0
ND2 B:ASN172 3.8 16.0 1.0
CG B:GLU47 3.9 30.8 1.0
CA B:ALA13 4.1 27.8 1.0
CB B:ALA13 4.1 27.2 1.0
N B:ALA13 4.4 23.5 1.0
OE1 B:GLU171 4.4 19.2 1.0
N B:GLY14 4.4 32.0 1.0
OD1 B:ASP11 4.5 31.0 1.0
CB B:ALA173 4.5 31.4 1.0
OE1 B:GLU47 4.5 32.5 1.0
CB B:ASP11 4.6 22.9 1.0
CA B:GLY14 4.6 30.6 1.0
CB B:ASN172 4.8 29.4 1.0
O B:HOH232 4.8 20.7 1.0
O B:HOH487 5.0 41.7 1.0

Magnesium binding site 3 out of 8 in 3qu4

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Magnesium binding site 3 out of 8 in the Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, ASP13ALA Mutant


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, ASP13ALA Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg225

b:10.3
occ:1.00
 OD2 C:ASP11 2.1 35.7 1.0
OE2 C:GLU47 2.1 33.3 1.0
O C:ALA13 2.2 27.4 1.0
O C:HOH922 2.3 12.9 1.0
O C:HOH583 2.3 28.2 1.0
OD1 C:ASN172 2.4 18.4 1.0
CG C:ASP11 3.2 26.9 1.0
CD C:GLU47 3.3 40.5 1.0
CG C:ASN172 3.3 30.1 1.0
C C:ALA13 3.4 23.4 1.0
ND2 C:ASN172 3.5 19.3 1.0
OD1 C:ASP11 3.8 19.9 1.0
CG C:GLU47 3.8 34.7 1.0
O C:HOH351 4.1 29.5 1.0
CA C:ALA13 4.1 16.9 1.0
CB C:ALA13 4.2 20.7 1.0
N C:ALA13 4.3 20.0 1.0
OE1 C:GLU47 4.3 33.8 1.0
OE1 C:GLU171 4.3 21.4 1.0
N C:GLY14 4.4 20.5 1.0
CB C:ASP11 4.5 20.0 1.0
CB C:ALA173 4.5 26.9 1.0
O C:HOH227 4.5 14.8 1.0
CA C:GLY14 4.7 26.1 1.0
CB C:ASN172 4.7 28.9 1.0
O C:HOH356 4.9 15.9 1.0

Magnesium binding site 4 out of 8 in 3qu4

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Magnesium binding site 4 out of 8 in the Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, ASP13ALA Mutant


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, ASP13ALA Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg225

b:4.3
occ:1.00
 OE2 D:GLU47 2.1 26.6 1.0
O D:HOH457 2.1 24.9 1.0
OD2 D:ASP11 2.1 30.0 1.0
O D:ALA13 2.2 24.7 1.0
OD1 D:ASN172 2.3 7.1 1.0
O D:HOH925 2.3 7.7 1.0
CG D:ASN172 3.1 29.2 1.0
CD D:GLU47 3.3 30.0 1.0
ND2 D:ASN172 3.3 18.2 1.0
CG D:ASP11 3.4 30.6 1.0
C D:ALA13 3.4 23.3 1.0
CG D:GLU47 3.9 26.1 1.0
O D:HOH257 4.0 18.7 1.0
OD1 D:ASP11 4.0 29.7 1.0
OE1 D:GLU171 4.2 30.5 1.0
CA D:ALA13 4.2 24.7 1.0
OE1 D:GLU47 4.3 29.0 1.0
CB D:ALA13 4.3 18.6 1.0
N D:GLY14 4.4 26.9 1.0
N D:ALA13 4.4 20.5 1.0
CB D:ALA173 4.4 18.8 1.0
CB D:ASP11 4.4 31.1 1.0
CB D:ASN172 4.6 18.5 1.0
CA D:GLY14 4.6 27.3 1.0
O D:HOH240 4.8 24.7 1.0
N D:ASN172 4.8 15.7 1.0
OXT D:ACT226 4.8 31.6 1.0
CG2 D:VAL15 4.9 21.7 1.0
CD D:GLU171 5.0 22.2 1.0
N D:ALA173 5.0 22.4 1.0
C D:GLY14 5.0 29.2 1.0

Magnesium binding site 5 out of 8 in 3qu4

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Magnesium binding site 5 out of 8 in the Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, ASP13ALA Mutant


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 Pyrophosphatase From Bacteroides Thetaiotaomicron, ASP13ALA Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg225

b:9.3
occ:1.00
 O E:HOH355 2.1 30.7 1.0
OD2 E:ASP11 2.1 34.7 1.0
OE2 E:GLU47 2.2 32.6 1.0
O E:ALA13 2.2 30.7 1.0
OD1 E:ASN172 2.3 10.0 1.0
O E:HOH734 2.4 19.2 1.0
CG E:ASN172 3.2 22.5 1.0
CD E:GLU47 3.3 25.3 1.0
C E:ALA13 3.4 25.8 1.0
CG E:ASP11 3.4 30.2 1.0
ND2 E:ASN172 3.5 18.0 1.0
CG E:GLU47 3.8 23.6 1.0
OD1 E:ASP11 4.0 22.4 1.0
CA E:ALA13 4.1 26.1 1.0
CB E:ALA13 4.1 20.4 1.0
O E:HOH1038 4.3 25.5 1.0
N E:ALA13 4.3 21.4 1.0
OE1 E:GLU47 4.3 29.0 1.0
OE1 E:GLU171 4.3 15.3 1.0
N E:GLY14 4.4 28.9 1.0
CB E:ALA173 4.4 23.2 1.0
CB E:ASP11 4.5 20.2 1.0
CB E:ASN172 4.6 19.8 1.0
O E:HOH233 4.7 21.1 1.0
CA E:GLY14 4.7 30.9 1.0
O E:HOH1039 4.9 30.3 1.0
N E:ASN172 4.9 19.9 1.0
N E:ALA173 4.9 24.2 1.0
CG2 E:VAL15 5.0 8.3 1.0

Magnesium binding site 6 out of 8 in 3qu4

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Magnesium binding site 6 out of 8 in the Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, ASP13ALA Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, ASP13ALA Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg225

b:12.6
occ:1.00
 O F:HOH772 1.9 38.8 1.0
O F:HOH235 2.1 27.4 1.0
O F:ALA13 2.2 32.9 1.0
OD1 F:ASN172 2.3 22.1 1.0
OE2 F:GLU47 2.3 17.7 1.0
OD2 F:ASP11 2.4 23.9 1.0
CG F:ASN172 3.3 29.5 1.0
CD F:GLU47 3.4 31.5 1.0
C F:ALA13 3.4 25.8 1.0
CG F:ASP11 3.5 37.5 1.0
ND2 F:ASN172 3.6 16.6 1.0
CG F:GLU47 3.9 31.5 1.0
OE1 F:GLU171 4.2 25.8 1.0
CB F:ALA13 4.2 21.7 1.0
CA F:ALA13 4.2 24.1 1.0
CB F:ASP11 4.3 28.1 1.0
OD1 F:ASP11 4.3 35.3 1.0
N F:ALA13 4.4 18.4 1.0
OE1 F:GLU47 4.5 37.4 1.0
N F:GLY14 4.5 32.7 1.0
CB F:ALA173 4.5 18.2 1.0
O F:HOH359 4.6 56.9 1.0
O F:HOH240 4.6 23.4 1.0
CB F:ASN172 4.7 26.4 1.0
CA F:GLY14 4.7 31.7 1.0
O F:HOH473 4.7 31.8 1.0
N F:ASN172 4.9 23.1 1.0
CD F:GLU171 4.9 31.4 1.0
N F:ALA173 4.9 29.0 1.0
O F:HOH928 4.9 57.8 1.0
OE2 F:GLU171 5.0 30.0 1.0

Magnesium binding site 7 out of 8 in 3qu4

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Magnesium binding site 7 out of 8 in the Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, ASP13ALA Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, ASP13ALA Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg225

b:6.5
occ:1.00
 O G:ALA13 2.1 22.1 1.0
O G:HOH827 2.1 25.9 1.0
OE2 G:GLU47 2.1 26.8 1.0
OD2 G:ASP11 2.1 28.6 1.0
OD1 G:ASN172 2.3 12.6 1.0
O G:HOH856 2.4 22.6 1.0
CG G:ASN172 3.2 24.1 1.0
C G:ALA13 3.3 24.9 1.0
CD G:GLU47 3.3 40.3 1.0
CG G:ASP11 3.3 28.4 1.0
ND2 G:ASN172 3.4 15.4 1.0
CG G:GLU47 3.8 24.4 1.0
OD1 G:ASP11 3.9 21.9 1.0
O G:HOH245 3.9 23.9 1.0
CA G:ALA13 4.0 16.9 1.0
CB G:ALA13 4.0 24.4 1.0
N G:ALA13 4.2 19.0 1.0
OE1 G:GLU171 4.3 25.2 1.0
N G:GLY14 4.3 22.7 1.0
OE1 G:GLU47 4.3 26.9 1.0
CB G:ALA173 4.5 28.4 1.0
CB G:ASP11 4.5 22.5 1.0
CB G:ASN172 4.6 11.8 1.0
CA G:GLY14 4.6 27.3 1.0
O G:HOH229 4.6 27.0 1.0
N G:ASN172 4.9 9.5 1.0
CG2 G:VAL15 5.0 7.9 1.0

Magnesium binding site 8 out of 8 in 3qu4

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Magnesium binding site 8 out of 8 in the Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, ASP13ALA Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, ASP13ALA Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg225

b:18.6
occ:1.00
 O H:HOH815 1.9 42.0 1.0
OE2 H:GLU47 2.2 34.3 1.0
O H:HOH252 2.2 32.3 1.0
OD2 H:ASP11 2.2 15.5 1.0
O H:ALA13 2.3 34.6 1.0
OD1 H:ASN172 2.3 32.8 1.0
CG H:ASN172 3.3 16.1 1.0
CD H:GLU47 3.3 33.5 1.0
CG H:ASP11 3.5 35.8 1.0
C H:ALA13 3.5 22.5 1.0
ND2 H:ASN172 3.6 22.9 1.0
CG H:GLU47 3.8 27.4 1.0
OE1 H:GLU171 4.0 36.1 1.0
OD1 H:ASP11 4.2 28.1 1.0
CB H:ALA13 4.2 21.7 1.0
O H:HOH234 4.2 22.3 1.0
CA H:ALA13 4.2 26.2 1.0
CB H:ALA173 4.4 25.2 1.0
OE1 H:GLU47 4.4 24.4 1.0
N H:ALA13 4.5 18.6 1.0
N H:GLY14 4.5 27.9 1.0
CB H:ASP11 4.6 28.0 1.0
CB H:ASN172 4.7 24.6 1.0
CA H:GLY14 4.7 27.2 1.0
O H:HOH228 4.8 22.4 1.0
OXT H:ACT226 4.8 45.1 1.0
CD H:GLU171 4.9 25.2 1.0
OE2 H:GLU171 5.0 25.2 1.0
N H:ASN172 5.0 24.2 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 10:10:35 2024

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