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Calcium in PDB 2q17: Formylglycine Generating Enzyme From Streptomyces Coelicolor

Protein crystallography data

The structure of Formylglycine Generating Enzyme From Streptomyces Coelicolor, PDB code: 2q17 was solved by B.L.Carlson, E.R.Ballister, E.Skordalakes, D.S.King, M.A.Breidenbach, S.A.Gilmore, J.M.Berger, C.R.Bertozzi, 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 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 142.444, 142.444, 217.067, 90.00, 90.00, 120.00
R / Rfree (%) 19.9 / 24.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Formylglycine Generating Enzyme From Streptomyces Coelicolor (pdb code 2q17). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Formylglycine Generating Enzyme From Streptomyces Coelicolor, PDB code: 2q17:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 2q17

Go back to Calcium Binding Sites List in 2q17
Calcium binding site 1 out of 5 in the Formylglycine Generating Enzyme From Streptomyces Coelicolor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Formylglycine Generating Enzyme From Streptomyces Coelicolor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca315

b:34.3
occ:1.00
 O A:HIS210 2.3 40.2 1.0
O A:ILE195 2.3 40.2 1.0
OD1 A:ASN194 2.3 36.9 1.0
OD1 A:ASP208 2.4 39.9 1.0
O A:HOH342 2.4 31.6 1.0
OD2 A:ASP208 2.4 41.0 1.0
O A:HOH378 2.4 30.6 1.0
CG A:ASP208 2.8 40.6 1.0
C A:HIS210 3.4 40.5 1.0
C A:ILE195 3.5 40.5 1.0
CG A:ASN194 3.6 38.8 1.0
N A:ILE195 3.8 40.4 1.0
CA A:HIS210 4.2 40.6 1.0
C A:ASN194 4.2 40.2 1.0
CA A:ILE195 4.2 40.4 1.0
N A:HIS210 4.2 40.4 1.0
CB A:HIS210 4.3 40.7 1.0
CB A:ASP208 4.3 40.7 1.0
OE1 A:GLN197 4.3 40.8 1.0
CA A:ASN194 4.3 40.2 1.0
ND2 A:ASN194 4.5 36.9 1.0
O A:TYR270 4.5 40.9 1.0
N A:LEU211 4.5 40.6 1.0
N A:TRP196 4.5 40.7 1.0
CB A:ASN194 4.5 39.7 1.0
ND2 A:ASN204 4.6 40.4 1.0
O A:LEU211 4.6 41.0 1.0
NE2 A:GLN197 4.6 39.8 1.0
OD1 A:ASN204 4.7 38.7 1.0
CA A:TRP196 4.7 40.8 1.0
CA A:LEU211 4.7 40.8 1.0
CB A:TYR270 4.8 41.0 1.0
C A:LEU211 4.8 40.9 1.0
CD A:GLN197 4.8 40.3 1.0
O A:ASN194 4.9 39.9 1.0

Calcium binding site 2 out of 5 in 2q17

Go back to Calcium Binding Sites List in 2q17
Calcium binding site 2 out of 5 in the Formylglycine Generating Enzyme From Streptomyces Coelicolor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Formylglycine Generating Enzyme From Streptomyces Coelicolor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca315

b:31.3
occ:1.00
 OD1 B:ASN194 2.3 39.7 1.0
O B:HOH410 2.3 29.7 1.0
O B:ILE195 2.3 41.0 1.0
O B:HIS210 2.4 40.3 1.0
OD1 B:ASP208 2.6 37.8 1.0
O B:HOH359 2.6 28.9 1.0
OD2 B:ASP208 2.6 39.9 1.0
CG B:ASP208 2.9 39.6 1.0
CG B:ASN194 3.5 39.9 1.0
C B:ILE195 3.5 40.7 1.0
C B:HIS210 3.5 40.9 1.0
N B:ILE195 3.8 40.3 1.0
C B:ASN194 4.1 40.3 1.0
CA B:ILE195 4.2 40.4 1.0
CA B:ASN194 4.3 40.4 1.0
OE1 B:GLN197 4.3 40.0 1.0
CA B:HIS210 4.3 40.7 1.0
ND2 B:ASN194 4.4 39.1 1.0
N B:HIS210 4.4 40.5 1.0
O B:TYR270 4.4 41.1 1.0
O B:LEU211 4.4 40.2 1.0
CB B:ASP208 4.5 40.2 1.0
CB B:ASN194 4.5 40.0 1.0
ND2 B:ASN204 4.5 39.7 1.0
CB B:HIS210 4.5 40.8 1.0
N B:LEU211 4.5 40.9 1.0
N B:TRP196 4.6 40.5 1.0
OD1 B:ASN204 4.6 39.0 1.0
NE2 B:GLN197 4.6 37.6 1.0
CB B:TYR270 4.6 40.9 1.0
CA B:LEU211 4.7 40.8 1.0
CA B:TRP196 4.7 40.3 1.0
C B:LEU211 4.8 40.6 1.0
CD B:GLN197 4.9 39.6 1.0
O B:ASN194 4.9 40.1 1.0
CA B:TYR270 4.9 40.9 1.0
CG B:ASN204 5.0 39.9 1.0

Calcium binding site 3 out of 5 in 2q17

Go back to Calcium Binding Sites List in 2q17
Calcium binding site 3 out of 5 in the Formylglycine Generating Enzyme From Streptomyces Coelicolor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Formylglycine Generating Enzyme From Streptomyces Coelicolor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca315

b:32.3
occ:1.00
 O C:HOH428 2.2 33.1 1.0
OD1 C:ASN194 2.3 40.3 1.0
O C:ILE195 2.3 40.6 1.0
OD1 C:ASP208 2.3 39.4 1.0
O C:HIS210 2.3 40.5 1.0
O C:HOH324 2.5 31.4 1.0
OD2 C:ASP208 2.5 38.1 1.0
CG C:ASP208 2.8 39.6 1.0
C C:HIS210 3.5 40.6 1.0
C C:ILE195 3.5 40.7 1.0
CG C:ASN194 3.5 40.9 1.0
N C:ILE195 3.8 40.2 1.0
C C:ASN194 4.1 40.6 1.0
CA C:HIS210 4.2 40.5 1.0
CA C:ILE195 4.2 40.6 1.0
CA C:ASN194 4.2 40.6 1.0
OE1 C:GLN197 4.3 39.9 1.0
CB C:ASP208 4.3 40.5 1.0
N C:HIS210 4.3 40.4 1.0
CB C:HIS210 4.3 40.4 1.0
ND2 C:ASN194 4.4 40.9 1.0
CB C:ASN194 4.4 40.5 1.0
O C:TYR270 4.5 41.0 1.0
O C:LEU211 4.5 41.1 1.0
N C:TRP196 4.5 41.0 1.0
N C:LEU211 4.5 40.6 1.0
ND2 C:ASN204 4.6 39.1 1.0
NE2 C:GLN197 4.6 39.3 1.0
OD1 C:ASN204 4.7 40.5 1.0
CA C:TRP196 4.7 40.9 1.0
CA C:LEU211 4.8 40.8 1.0
CB C:TYR270 4.8 41.1 1.0
C C:LEU211 4.8 40.9 1.0
CD C:GLN197 4.8 40.0 1.0
O C:ASN194 4.9 40.5 1.0
CA C:TYR270 5.0 40.8 1.0

Calcium binding site 4 out of 5 in 2q17

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Calcium binding site 4 out of 5 in the Formylglycine Generating Enzyme From Streptomyces Coelicolor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Formylglycine Generating Enzyme From Streptomyces Coelicolor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca315

b:28.9
occ:1.00
 O D:HIS210 2.2 40.9 1.0
O D:ILE195 2.3 40.1 1.0
OD1 D:ASN194 2.4 40.0 1.0
O D:HOH354 2.4 27.8 1.0
OD1 D:ASP208 2.5 39.7 1.0
OD2 D:ASP208 2.5 41.4 1.0
O D:HOH352 2.5 31.2 1.0
CG D:ASP208 2.8 40.5 1.0
C D:HIS210 3.4 40.7 1.0
C D:ILE195 3.5 40.3 1.0
CG D:ASN194 3.6 40.4 1.0
N D:ILE195 3.7 40.2 1.0
C D:ASN194 4.1 40.5 1.0
CA D:ILE195 4.2 40.3 1.0
CA D:HIS210 4.2 40.4 1.0
CA D:ASN194 4.2 40.4 1.0
OE1 D:GLN197 4.2 39.8 1.0
N D:HIS210 4.3 40.4 1.0
CB D:ASP208 4.4 40.0 1.0
O D:TYR270 4.4 40.3 1.0
CB D:HIS210 4.4 40.2 1.0
N D:LEU211 4.4 40.6 1.0
CB D:ASN194 4.5 40.1 1.0
OD1 D:ASN204 4.5 40.0 1.0
N D:TRP196 4.5 40.6 1.0
ND2 D:ASN194 4.5 39.8 1.0
O D:LEU211 4.5 40.5 1.0
NE2 D:GLN197 4.5 37.7 1.0
CA D:LEU211 4.6 40.7 1.0
ND2 D:ASN204 4.6 38.9 1.0
CB D:TYR270 4.7 40.7 1.0
CA D:TRP196 4.7 40.4 1.0
C D:LEU211 4.7 40.7 1.0
CD D:GLN197 4.8 39.4 1.0
O D:ASN194 4.9 40.4 1.0
CA D:TYR270 4.9 40.5 1.0
CA D:ALA206 5.0 40.5 1.0

Calcium binding site 5 out of 5 in 2q17

Go back to Calcium Binding Sites List in 2q17
Calcium binding site 5 out of 5 in the Formylglycine Generating Enzyme From Streptomyces Coelicolor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Formylglycine Generating Enzyme From Streptomyces Coelicolor within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca315

b:44.0
occ:1.00
 O E:HIS210 2.2 41.0 1.0
O E:ILE195 2.3 40.5 1.0
OD1 E:ASN194 2.4 38.6 1.0
O E:HOH456 2.4 33.2 1.0
OD1 E:ASP208 2.5 41.1 1.0
OD2 E:ASP208 2.7 42.6 1.0
CG E:ASP208 3.0 41.4 1.0
C E:ILE195 3.5 40.7 1.0
C E:HIS210 3.5 40.9 1.0
CG E:ASN194 3.6 39.6 1.0
N E:ILE195 3.8 40.6 1.0
C E:ASN194 4.2 40.7 1.0
CA E:ILE195 4.2 40.8 1.0
CA E:HIS210 4.3 40.9 1.0
O E:TYR270 4.3 40.9 1.0
CA E:ASN194 4.3 40.6 1.0
N E:HIS210 4.4 40.9 1.0
CB E:HIS210 4.4 40.9 1.0
O E:LEU211 4.4 40.7 1.0
NE2 E:GLN197 4.4 39.2 1.0
ND2 E:ASN204 4.4 40.3 1.0
N E:LEU211 4.5 40.6 1.0
ND2 E:ASN194 4.5 39.3 1.0
CB E:ASP208 4.5 41.1 1.0
N E:TRP196 4.5 40.5 1.0
CB E:ASN194 4.5 40.4 1.0
OE1 E:GLN197 4.6 41.2 1.0
CA E:LEU211 4.6 40.6 1.0
OD1 E:ASN204 4.6 40.7 1.0
CA E:TRP196 4.7 40.5 1.0
C E:LEU211 4.7 40.7 1.0
CB E:TYR270 4.8 41.1 1.0
CD E:GLN197 4.9 40.4 1.0
CA E:TYR270 4.9 40.9 1.0
O E:ASN194 4.9 41.0 1.0

Reference:

B.L.Carlson, E.R.Ballister, E.Skordalakes, D.S.King, M.A.Breidenbach, S.A.Gilmore, J.M.Berger, C.R.Bertozzi. Function and Structure of A Prokaryotic Formylglycine-Generating Enzyme. J.Biol.Chem. V. 283 20117 2008.
ISSN: ISSN 0021-9258
PubMed: 18390551
DOI: 10.1074/JBC.M800217200
Page generated: Sat Dec 12 03:50:44 2020

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