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Calcium in PDB 3qyp: Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, GLU47ASN Mutant Complexed with Calcium and Phosphate

Enzymatic activity of Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, GLU47ASN Mutant Complexed with Calcium and Phosphate

All present enzymatic activity of Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, GLU47ASN Mutant Complexed with Calcium and Phosphate:
3.6.1.1;

Protein crystallography data

The structure of Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, GLU47ASN Mutant Complexed with Calcium and Phosphate, PDB code: 3qyp 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) 50.00 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 42.936, 77.182, 70.803, 90.00, 90.21, 90.00
R / Rfree (%) 18.5 / 21.7

Other elements in 3qyp:

The structure of Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, GLU47ASN Mutant Complexed with Calcium and Phosphate also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, GLU47ASN Mutant Complexed with Calcium and Phosphate (pdb code 3qyp). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, GLU47ASN Mutant Complexed with Calcium and Phosphate, PDB code: 3qyp:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 3qyp

Go back to Calcium Binding Sites List in 3qyp
Calcium binding site 1 out of 3 in the Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, GLU47ASN Mutant Complexed with Calcium and Phosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, GLU47ASN Mutant Complexed with Calcium and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca226

b:20.1
occ:0.50
 OD2 A:ASP11 1.7 39.0 1.0
O A:HOH425 2.2 22.6 0.5
O1 A:PO4225 2.2 15.7 0.5
OD1 A:ASN172 2.3 32.7 1.0
O A:ASP13 2.5 25.9 1.0
OD1 A:ASN47 2.6 29.9 1.0
O A:HOH293 2.7 27.6 1.0
CG A:ASP11 2.9 23.4 1.0
CG A:ASN172 3.4 22.1 1.0
CG A:ASN47 3.4 22.9 1.0
P A:PO4225 3.5 20.6 0.5
OD1 A:ASP11 3.5 32.4 1.0
C A:ASP13 3.6 19.7 1.0
ND2 A:ASN47 3.7 19.6 1.0
ND2 A:ASN172 3.8 22.4 1.0
O3 A:PO4225 3.9 17.1 0.5
O4 A:PO4225 4.0 21.0 0.5
OE1 A:GLU171 4.0 25.8 1.0
CB A:ASP11 4.1 21.8 1.0
N A:ASP13 4.1 18.8 1.0
CA A:ASP13 4.2 15.7 1.0
O A:HOH423 4.2 21.0 0.5
CB A:ASP13 4.3 15.5 1.0
O A:HOH424 4.3 26.4 0.5
CB A:ALA173 4.4 31.0 1.0
O2 A:PO4225 4.6 20.2 0.5
CB A:ASN172 4.7 20.2 1.0
N A:GLY14 4.7 15.6 1.0
CB A:ASN47 4.7 19.5 1.0
N A:GLY48 4.8 21.3 1.0
N A:ASN172 4.8 23.9 1.0
N A:MET12 4.9 18.7 1.0
N A:ALA173 4.9 24.8 1.0
CD A:GLU171 4.9 20.5 1.0
C A:MET12 5.0 17.7 1.0
NZ A:LYS147 5.0 20.2 1.0
CA A:GLY48 5.0 26.3 1.0

Calcium binding site 2 out of 3 in 3qyp

Go back to Calcium Binding Sites List in 3qyp
Calcium binding site 2 out of 3 in the Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, GLU47ASN Mutant Complexed with Calcium and Phosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, GLU47ASN Mutant Complexed with Calcium and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca225

b:25.8
occ:0.50
 OE2 B:GLU166 2.3 30.6 1.0
O B:HOH475 2.3 30.9 1.0
O B:HOH429 2.4 34.3 1.0
O B:HOH471 2.5 33.5 1.0
O B:HOH255 2.7 38.8 1.0
CD B:GLU166 3.4 30.4 1.0
CG B:GLU166 3.8 24.5 1.0
NZ B:LYS6 4.2 35.6 1.0
CE B:LYS6 4.2 38.3 1.0
OE1 B:GLU166 4.5 27.2 1.0
O B:LYS4 4.7 26.6 1.0
O B:HOH249 4.8 58.3 1.0
O B:HOH467 4.9 44.1 1.0

Calcium binding site 3 out of 3 in 3qyp

Go back to Calcium Binding Sites List in 3qyp
Calcium binding site 3 out of 3 in the Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, GLU47ASN Mutant Complexed with Calcium and Phosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, GLU47ASN Mutant Complexed with Calcium and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca227

b:23.2
occ:0.50
 OD2 B:ASP11 1.7 40.7 1.0
O B:HOH422 2.1 21.0 0.5
O1 B:PO4226 2.1 18.7 0.5
OD1 B:ASN172 2.5 28.9 1.0
O B:ASP13 2.5 22.3 1.0
OD1 B:ASN47 2.8 34.9 1.0
CG B:ASP11 2.8 18.3 1.0
O B:HOH362 3.0 34.5 1.0
OD1 B:ASP11 3.3 26.3 1.0
P B:PO4226 3.4 27.2 0.5
CG B:ASN47 3.4 23.8 1.0
ND2 B:ASN47 3.4 18.6 1.0
CG B:ASN172 3.6 24.7 1.0
C B:ASP13 3.6 17.0 1.0
O B:HOH420 3.8 18.3 0.5
O4 B:PO4226 3.8 25.5 0.5
ND2 B:ASN172 4.0 25.5 1.0
O2 B:PO4226 4.0 21.0 0.5
CB B:ASP11 4.1 15.2 1.0
N B:ASP13 4.1 15.9 1.0
OE1 B:GLU171 4.2 20.3 1.0
CB B:ASP13 4.2 16.3 1.0
CA B:ASP13 4.2 15.5 1.0
O B:HOH421 4.4 12.5 0.5
O3 B:PO4226 4.5 15.9 0.5
CB B:ALA173 4.5 26.0 1.0
N B:GLY48 4.7 18.1 1.0
CB B:ASN47 4.8 17.6 1.0
N B:GLY14 4.8 16.1 1.0
N B:MET12 4.9 14.1 1.0
CB B:ASN172 4.9 17.6 1.0
N B:ASN172 4.9 16.2 1.0
C B:MET12 4.9 15.3 1.0
CA B:GLY48 4.9 25.8 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: Tue Jul 8 16:06:03 2025

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