Atomistry » Calcium » PDB 3qgv-3r3t » 3qxg
Atomistry »
  Calcium »
    PDB 3qgv-3r3t »
      3qxg »

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

Go back to Calcium Binding Sites List in 3qxg
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 Dec 12 04:27:22 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy