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Calcium in PDB 3qxg: Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron Complexed with Calcium, A Closed Cap Conformation

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

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

Protein crystallography data

The structure of Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron Complexed with Calcium, A Closed Cap Conformation, PDB code: 3qxg 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 / 1.24
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 114.065, 70.586, 76.323, 90.00, 119.77, 90.00
R / Rfree (%) 15.2 / 18.2

Other elements in 3qxg:

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

Magnesium (Mg) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron Complexed with Calcium, A Closed Cap Conformation (pdb code 3qxg). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron Complexed with Calcium, A Closed Cap Conformation, PDB code: 3qxg:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 3qxg

Go back to Calcium Binding Sites List in 3qxg
Calcium binding site 1 out of 7 in the Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron Complexed with Calcium, A Closed Cap Conformation


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 Complexed with Calcium, A Closed Cap Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca226

b:26.4
occ:0.50
 O A:HOH387 2.2 46.6 1.0
O A:PRO194 2.3 16.2 1.0
O A:HOH375 2.3 50.7 1.0
O A:HOH386 2.3 29.4 1.0
O A:HOH414 2.4 38.6 1.0
O A:HOH388 2.5 43.2 1.0
C A:PRO194 3.4 13.4 1.0
CA A:PRO194 4.1 14.4 1.0
O A:HOH426 4.4 20.9 1.0
OD1 A:ASP196 4.4 22.3 1.0
CB A:PRO194 4.5 15.4 1.0
O A:HOH433 4.5 41.9 1.0
N A:LEU195 4.5 13.0 1.0
O A:HOH479 4.6 31.9 1.0
C A:LEU195 4.7 13.6 1.0
CA A:LEU195 4.7 13.6 1.0
O A:LEU195 4.9 15.3 1.0

Calcium binding site 2 out of 7 in 3qxg

Go back to Calcium Binding Sites List in 3qxg
Calcium binding site 2 out of 7 in the Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron Complexed with Calcium, A Closed Cap Conformation


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 Complexed with Calcium, A Closed Cap Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca227

b:12.6
occ:1.00
 OD2 A:ASP11 2.2 17.0 1.0
O4 A:PO4228 2.2 24.5 0.3
O A:ASP13 2.3 12.9 1.0
OE2 A:GLU47 2.3 12.9 1.0
O A:HOH372 2.4 14.8 0.7
OD1 A:ASN172 2.4 12.8 1.0
O A:HOH239 2.4 13.7 1.0
CG A:ASP11 3.3 15.7 1.0
CG A:ASN172 3.4 10.3 1.0
CD A:GLU47 3.4 12.2 1.0
C A:ASP13 3.5 11.3 1.0
P A:PO4228 3.5 21.3 0.3
ND2 A:ASN172 3.7 11.5 1.0
CG A:GLU47 3.8 13.5 1.0
OD1 A:ASP11 3.9 17.6 1.0
O2 A:PO4228 4.1 22.6 0.3
CB A:ASP13 4.1 13.8 1.0
OE1 A:GLU171 4.1 13.7 1.0
O1 A:PO4228 4.2 26.9 0.3
CA A:ASP13 4.2 11.6 1.0
OXT A:ACT230 4.2 22.2 0.7
N A:ASP13 4.3 12.1 1.0
O A:HOH371 4.3 16.8 0.7
CB A:ALA173 4.4 14.6 1.0
CB A:ASP11 4.5 13.9 1.0
OE1 A:GLU47 4.5 13.2 1.0
N A:GLY14 4.5 10.1 1.0
O3 A:PO4228 4.6 20.0 0.3
CB A:ASN172 4.7 12.3 1.0
O A:HOH285 4.8 22.6 1.0
CA A:GLY14 4.8 12.7 1.0
N A:ASN172 4.9 10.8 1.0
N A:ALA173 4.9 11.5 1.0

Calcium binding site 3 out of 7 in 3qxg

Go back to Calcium Binding Sites List in 3qxg
Calcium binding site 3 out of 7 in the Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron Complexed with Calcium, A Closed Cap Conformation


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 Complexed with Calcium, A Closed Cap Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca226

b:18.4
occ:1.00
 O B:HOH463 2.3 34.9 1.0
O B:HOH312 2.3 19.4 1.0
O B:ALA205 4.3 15.4 1.0
O B:LEU201 4.5 13.5 1.0
O B:HOH276 4.5 39.4 1.0
O B:HOH414 4.6 41.9 1.0
O B:HOH430 4.7 28.6 1.0
O B:HOH465 4.9 31.6 1.0

Calcium binding site 4 out of 7 in 3qxg

Go back to Calcium Binding Sites List in 3qxg
Calcium binding site 4 out of 7 in the Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron Complexed with Calcium, A Closed Cap Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron Complexed with Calcium, A Closed Cap Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca227

b:18.4
occ:1.00
 O B:HOH418 2.2 70.9 1.0
O B:HOH309 2.4 18.7 1.0
O B:HOH319 2.4 21.8 1.0
O B:HOH252 2.5 28.1 1.0
O B:HOH497 4.4 33.1 1.0
OD1 B:ASP196 4.5 21.9 1.0
OXT B:ACT228 4.5 17.7 1.0
O B:HOH251 4.7 43.8 1.0
OE1 B:GLN198 4.7 14.6 1.0
CG B:ASP196 4.9 19.1 1.0
NE2 B:GLN198 4.9 16.0 1.0

Calcium binding site 5 out of 7 in 3qxg

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Calcium binding site 5 out of 7 in the Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron Complexed with Calcium, A Closed Cap Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron Complexed with Calcium, A Closed Cap Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca229

b:24.6
occ:0.50
 O B:HOH274 2.1 47.9 1.0
O B:PRO194 2.3 16.5 1.0
O B:HOH287 2.3 51.6 1.0
O B:HOH261 2.3 42.8 1.0
O B:HOH460 2.4 26.2 1.0
O B:HOH288 2.6 41.3 1.0
C B:PRO194 3.4 15.2 1.0
CA B:PRO194 4.1 13.9 1.0
OD1 B:ASP196 4.4 21.9 1.0
CB B:PRO194 4.4 16.1 1.0
O B:HOH323 4.4 19.7 1.0
N B:LEU195 4.5 14.9 1.0
O B:HOH403 4.6 39.7 1.0
O B:HOH497 4.7 33.1 1.0
CA B:LEU195 4.7 14.5 1.0
C B:LEU195 4.7 12.7 1.0
O B:LEU195 4.9 14.4 1.0

Calcium binding site 6 out of 7 in 3qxg

Go back to Calcium Binding Sites List in 3qxg
Calcium binding site 6 out of 7 in the Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron Complexed with Calcium, A Closed Cap Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron Complexed with Calcium, A Closed Cap Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca230

b:12.5
occ:1.00
 OD2 B:ASP11 2.2 18.1 1.0
OE2 B:GLU47 2.3 13.4 1.0
OD1 B:ASN172 2.3 12.8 1.0
O B:HOH247 2.3 13.9 1.0
O B:ASP13 2.3 13.2 1.0
O B:HOH246 2.4 14.6 1.0
CG B:ASN172 3.3 10.6 1.0
CG B:ASP11 3.3 15.7 1.0
CD B:GLU47 3.4 11.0 1.0
C B:ASP13 3.5 10.8 1.0
ND2 B:ASN172 3.7 12.0 1.0
CG B:GLU47 3.8 12.1 1.0
OD1 B:ASP11 4.0 17.2 1.0
CB B:ASP13 4.0 13.9 1.0
OE1 B:GLU171 4.1 12.9 1.0
CA B:ASP13 4.2 12.3 1.0
O B:ACT225 4.2 18.1 1.0
N B:ASP13 4.3 12.6 1.0
CB B:ALA173 4.4 14.7 1.0
O B:HOH256 4.4 16.3 1.0
OE1 B:GLU47 4.5 12.8 1.0
CB B:ASP11 4.5 14.8 1.0
N B:GLY14 4.6 11.3 1.0
CB B:ASN172 4.7 12.0 1.0
O B:HOH303 4.8 17.6 1.0
CA B:GLY14 4.8 13.2 1.0
N B:ASN172 4.9 11.3 1.0
N B:ALA173 4.9 12.2 1.0

Calcium binding site 7 out of 7 in 3qxg

Go back to Calcium Binding Sites List in 3qxg
Calcium binding site 7 out of 7 in the Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron Complexed with Calcium, A Closed Cap Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron Complexed with Calcium, A Closed Cap Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca231

b:16.2
occ:0.50
 O A:HOH405 2.2 26.3 1.0
O B:HOH395 2.4 28.0 1.0
OE2 B:GLU178 2.4 20.9 1.0
O3 A:TLA229 2.4 26.7 1.0
O B:HOH396 2.5 29.1 1.0
O B:HOH394 2.5 20.0 1.0
O4 A:TLA229 2.5 22.9 1.0
O2 A:TLA229 2.6 24.3 1.0
MG A:MG232 2.8 24.6 0.5
C4 A:TLA229 3.3 22.6 1.0
C3 A:TLA229 3.3 21.8 1.0
CD B:GLU178 3.4 15.9 1.0
OE1 B:GLU178 3.6 16.9 1.0
C2 A:TLA229 3.6 24.6 1.0
NZ B:LYS182 3.8 37.4 1.0
O11 A:TLA229 4.3 23.6 1.0
O B:HOH475 4.3 44.7 1.0
C1 A:TLA229 4.3 24.7 1.0
O41 A:TLA229 4.5 23.2 1.0
O B:HOH443 4.5 25.4 1.0
O A:HOH250 4.5 44.5 1.0
OE1 A:GLU178 4.6 18.5 1.0
CG B:GLU178 4.8 14.4 1.0
OE2 A:GLU178 4.8 20.9 1.0
NH2 A:ARG49 4.9 21.5 1.0
O B:HOH370 4.9 34.8 1.0
O A:HOH482 4.9 25.8 1.0
CD2 A:LEU175 4.9 14.5 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: Sat Jul 13 17:42:07 2024

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