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Calcium in PDB 6g4g: Full Length Ectodomain of Ectonucleotide Phosphodiesterase/Pyrophosphatase-3 (NPP3) Including the Smb Domains But with A Partially Disordered Active Site Structure

Enzymatic activity of Full Length Ectodomain of Ectonucleotide Phosphodiesterase/Pyrophosphatase-3 (NPP3) Including the Smb Domains But with A Partially Disordered Active Site Structure

All present enzymatic activity of Full Length Ectodomain of Ectonucleotide Phosphodiesterase/Pyrophosphatase-3 (NPP3) Including the Smb Domains But with A Partially Disordered Active Site Structure:
3.1.4.1; 3.6.1.9;

Protein crystallography data

The structure of Full Length Ectodomain of Ectonucleotide Phosphodiesterase/Pyrophosphatase-3 (NPP3) Including the Smb Domains But with A Partially Disordered Active Site Structure, PDB code: 6g4g was solved by C.Dohler, M.Zebisch, N.Strater, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.22 / 2.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 76.360, 116.300, 124.160, 86.77, 87.76, 88.20
R / Rfree (%) 19.6 / 23.7

Calcium Binding Sites:

The binding sites of Calcium atom in the Full Length Ectodomain of Ectonucleotide Phosphodiesterase/Pyrophosphatase-3 (NPP3) Including the Smb Domains But with A Partially Disordered Active Site Structure (pdb code 6g4g). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Full Length Ectodomain of Ectonucleotide Phosphodiesterase/Pyrophosphatase-3 (NPP3) Including the Smb Domains But with A Partially Disordered Active Site Structure, PDB code: 6g4g:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6g4g

Go back to Calcium Binding Sites List in 6g4g
Calcium binding site 1 out of 4 in the Full Length Ectodomain of Ectonucleotide Phosphodiesterase/Pyrophosphatase-3 (NPP3) Including the Smb Domains But with A Partially Disordered Active Site Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Full Length Ectodomain of Ectonucleotide Phosphodiesterase/Pyrophosphatase-3 (NPP3) Including the Smb Domains But with A Partially Disordered Active Site Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca901

b:72.6
occ:1.00
 OD1 A:ASP756 2.4 61.9 1.0
OD1 A:ASP760 2.5 42.8 1.0
OD1 A:ASN754 2.6 65.8 1.0
O A:HIS758 2.7 56.8 1.0
OD1 A:ASP752 2.7 47.2 1.0
O A:PHE759 3.3 53.9 1.0
C A:PHE759 3.5 53.5 1.0
CG A:ASP756 3.5 60.2 1.0
C A:HIS758 3.6 55.8 1.0
N A:ASP760 3.6 47.7 1.0
CA A:ASP760 3.7 46.5 1.0
CG A:ASP760 3.7 45.5 1.0
CG A:ASP752 3.7 47.0 1.0
CG A:ASN754 3.8 69.7 1.0
OD2 A:ASP756 4.0 66.1 1.0
OE2 A:GLU764 4.0 79.5 1.0
CB A:HIS758 4.2 54.2 1.0
CB A:ASP760 4.2 46.4 1.0
CA A:ASP752 4.2 45.0 1.0
ND2 A:ASN754 4.3 63.2 1.0
CA A:HIS758 4.3 51.9 1.0
N A:HIS758 4.3 50.0 1.0
N A:PHE759 4.3 50.7 1.0
CA A:PHE759 4.4 50.3 1.0
CB A:ASP752 4.4 44.1 1.0
O A:PHE751 4.5 54.5 1.0
CD A:GLU764 4.6 75.9 1.0
OE1 A:GLU764 4.6 85.4 1.0
N A:ASP756 4.6 43.5 1.0
OD2 A:ASP752 4.6 48.1 1.0
OD2 A:ASP760 4.6 55.8 1.0
CB A:ASP756 4.7 45.1 1.0
C A:ASP752 4.8 49.7 1.0
N A:ASN754 4.9 47.0 1.0
CB A:ASN754 5.0 46.6 1.0
C A:ASP760 5.0 52.4 1.0

Calcium binding site 2 out of 4 in 6g4g

Go back to Calcium Binding Sites List in 6g4g
Calcium binding site 2 out of 4 in the Full Length Ectodomain of Ectonucleotide Phosphodiesterase/Pyrophosphatase-3 (NPP3) Including the Smb Domains But with A Partially Disordered Active Site Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Full Length Ectodomain of Ectonucleotide Phosphodiesterase/Pyrophosphatase-3 (NPP3) Including the Smb Domains But with A Partially Disordered Active Site Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca901

b:95.3
occ:1.00
 OD1 B:ASP760 2.3 75.5 1.0
OD1 B:ASP756 2.3 84.0 1.0
OD1 B:ASN754 2.4 74.6 1.0
OD1 B:ASP752 2.6 74.2 1.0
O B:HIS758 2.9 66.7 1.0
CG B:ASP756 3.4 84.6 1.0
CG B:ASP760 3.4 74.3 1.0
CG B:ASN754 3.6 83.0 1.0
CG B:ASP752 3.7 72.2 1.0
C B:HIS758 3.8 68.8 1.0
O B:PHE759 3.8 71.7 1.0
CA B:ASP752 3.8 63.5 1.0
CA B:ASP760 3.8 67.7 1.0
N B:ASP760 3.9 67.7 1.0
C B:PHE759 3.9 71.5 1.0
OE2 B:GLU764 4.1 96.6 1.0
OD2 B:ASP756 4.1 95.3 1.0
CB B:ASP760 4.2 67.9 1.0
ND2 B:ASN754 4.3 67.5 1.0
CB B:ASP752 4.3 63.9 1.0
OD2 B:ASP760 4.3 79.6 1.0
C B:ASP752 4.4 67.6 1.0
O B:PHE751 4.4 67.2 1.0
CB B:ASP756 4.4 69.1 1.0
N B:HIS758 4.4 63.2 1.0
OE1 B:GLU764 4.4 1.0 1.0
CA B:HIS758 4.5 66.0 1.0
N B:ASP756 4.5 64.0 1.0
CD B:GLU764 4.5 0.1 1.0
CB B:HIS758 4.6 69.8 1.0
N B:ASN754 4.6 69.9 1.0
N B:TYR753 4.6 64.4 1.0
N B:PHE759 4.6 65.8 1.0
OD2 B:ASP752 4.8 76.3 1.0
CA B:PHE759 4.8 65.9 1.0
CB B:ASN754 4.8 73.3 1.0
N B:ASP752 4.9 63.8 1.0
N B:TYR755 4.9 66.5 1.0
CA B:ASP756 4.9 64.7 1.0

Calcium binding site 3 out of 4 in 6g4g

Go back to Calcium Binding Sites List in 6g4g
Calcium binding site 3 out of 4 in the Full Length Ectodomain of Ectonucleotide Phosphodiesterase/Pyrophosphatase-3 (NPP3) Including the Smb Domains But with A Partially Disordered Active Site Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Full Length Ectodomain of Ectonucleotide Phosphodiesterase/Pyrophosphatase-3 (NPP3) Including the Smb Domains But with A Partially Disordered Active Site Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca901

b:87.0
occ:1.00
 OD1 C:ASN754 2.2 76.0 1.0
OD1 C:ASP756 2.3 81.7 1.0
OD1 C:ASP760 2.4 90.0 1.0
O C:HIS758 2.5 70.0 1.0
OD1 C:ASP752 2.6 61.7 1.0
CG C:ASP756 3.3 79.3 1.0
CG C:ASN754 3.4 79.2 1.0
CG C:ASP760 3.6 91.0 1.0
C C:HIS758 3.6 69.1 1.0
OD2 C:ASP756 3.7 88.7 1.0
CG C:ASP752 3.8 64.2 1.0
N C:ASP760 3.8 74.9 1.0
CA C:ASP760 3.9 76.6 1.0
O C:PHE759 3.9 75.0 1.0
C C:PHE759 3.9 75.8 1.0
ND2 C:ASN754 4.1 67.8 1.0
CA C:ASP752 4.1 65.5 1.0
CB C:ASP760 4.3 80.2 1.0
OE2 C:GLU764 4.3 0.8 1.0
N C:ASP756 4.3 61.8 1.0
CA C:HIS758 4.4 62.5 1.0
CB C:ASP752 4.4 65.3 1.0
CB C:ASP756 4.4 62.2 1.0
N C:HIS758 4.4 63.3 1.0
CB C:ASN754 4.5 63.9 1.0
N C:ASN754 4.5 66.7 1.0
CB C:HIS758 4.5 61.9 1.0
N C:PHE759 4.5 67.3 1.0
OD2 C:ASP760 4.5 97.0 1.0
O C:PHE751 4.6 76.0 1.0
C C:ASP752 4.6 70.7 1.0
OE1 C:GLU764 4.6 0.3 1.0
CA C:PHE759 4.7 69.3 1.0
CD C:GLU764 4.7 0.7 1.0
OD2 C:ASP752 4.7 67.6 1.0
N C:TYR755 4.7 62.5 1.0
CA C:ASN754 4.8 65.1 1.0
N C:TYR753 4.8 68.4 1.0
CA C:ASP756 4.8 60.3 1.0
C C:ASN754 4.8 66.4 1.0

Calcium binding site 4 out of 4 in 6g4g

Go back to Calcium Binding Sites List in 6g4g
Calcium binding site 4 out of 4 in the Full Length Ectodomain of Ectonucleotide Phosphodiesterase/Pyrophosphatase-3 (NPP3) Including the Smb Domains But with A Partially Disordered Active Site Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Full Length Ectodomain of Ectonucleotide Phosphodiesterase/Pyrophosphatase-3 (NPP3) Including the Smb Domains But with A Partially Disordered Active Site Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca901

b:0.1
occ:1.00
 OD1 D:ASN754 2.3 70.4 1.0
OD1 D:ASP752 2.4 42.5 1.0
O D:HIS758 2.4 46.0 1.0
OD1 D:ASP756 2.5 59.6 1.0
OD1 D:ASP760 2.9 64.8 1.0
CG D:ASP756 3.3 57.9 1.0
CG D:ASN754 3.4 78.5 1.0
CG D:ASP752 3.5 49.0 1.0
C D:HIS758 3.7 43.6 1.0
OD2 D:ASP756 3.9 61.5 1.0
O D:PHE759 3.9 50.1 1.0
C D:PHE759 3.9 48.0 1.0
ND2 D:ASN754 3.9 78.4 1.0
N D:ASP760 4.0 45.4 1.0
CG D:ASP760 4.0 63.5 1.0
N D:ASP756 4.1 44.3 1.0
CA D:ASP760 4.1 46.3 1.0
CB D:ASP756 4.2 46.0 1.0
CA D:ASP752 4.3 46.7 1.0
N D:HIS758 4.3 42.5 1.0
OD2 D:ASP752 4.3 59.3 1.0
CB D:ASP752 4.4 46.9 1.0
OE2 D:GLU764 4.4 58.7 1.0
CA D:ASP756 4.5 43.6 1.0
CA D:HIS758 4.5 42.0 1.0
N D:PHE759 4.5 38.2 1.0
OE1 D:GLU764 4.6 86.9 1.0
N D:ASN754 4.6 50.9 1.0
CA D:PHE759 4.6 38.6 1.0
CB D:ASP760 4.6 49.8 1.0
CB D:ASN754 4.7 52.3 1.0
C D:ASP752 4.7 52.1 1.0
N D:TYR755 4.7 45.8 1.0
C D:ASP756 4.8 46.9 1.0
N D:GLY757 4.8 44.0 1.0
CD D:GLU764 4.8 80.9 1.0
O D:PHE751 4.8 52.1 1.0
C D:ASN754 4.9 51.9 1.0
CA D:ASN754 4.9 50.9 1.0
N D:TYR753 5.0 49.9 1.0

Reference:

C.Dohler, M.Zebisch, D.Krinke, A.Robitzki, N.Strater. Crystallization of Ectonucleotide Phosphodiesterase/Pyrophosphatase-3 and Orientation of the Smb Domains in the Full-Length Ectodomain. Acta Crystallogr F Struct V. 74 696 2018BIOL Commun.
ISSN: ESSN 2053-230X
PubMed: 30387774
DOI: 10.1107/S2053230X18011111
Page generated: Tue Jul 16 08:00:27 2024

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