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Calcium in PDB 2yhg: Ab Initio Phasing of A Nucleoside Hydrolase-Related Hypothetical Protein From Saccharophagus Degradans That Is Associated with Carbohydrate Metabolism

Protein crystallography data

The structure of Ab Initio Phasing of A Nucleoside Hydrolase-Related Hypothetical Protein From Saccharophagus Degradans That Is Associated with Carbohydrate Metabolism, PDB code: 2yhg was solved by J.H.Hehemann, C.Marsters, A.B.Boraston, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 62.73 / 1.08
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.580, 61.580, 125.460, 90.00, 90.00, 90.00
R / Rfree (%) 13.3 / 15.1

Other elements in 2yhg:

The structure of Ab Initio Phasing of A Nucleoside Hydrolase-Related Hypothetical Protein From Saccharophagus Degradans That Is Associated with Carbohydrate Metabolism also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Zinc (Zn) 1 atom
Magnesium (Mg) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Ab Initio Phasing of A Nucleoside Hydrolase-Related Hypothetical Protein From Saccharophagus Degradans That Is Associated with Carbohydrate Metabolism (pdb code 2yhg). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Ab Initio Phasing of A Nucleoside Hydrolase-Related Hypothetical Protein From Saccharophagus Degradans That Is Associated with Carbohydrate Metabolism, PDB code: 2yhg:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 2yhg

Go back to Calcium Binding Sites List in 2yhg
Calcium binding site 1 out of 2 in the Ab Initio Phasing of A Nucleoside Hydrolase-Related Hypothetical Protein From Saccharophagus Degradans That Is Associated with Carbohydrate Metabolism


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Ab Initio Phasing of A Nucleoside Hydrolase-Related Hypothetical Protein From Saccharophagus Degradans That Is Associated with Carbohydrate Metabolism within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1934

b:7.6
occ:0.50
O A:TRP647 2.4 7.2 1.0
OD1 A:ASP539 2.4 10.1 1.0
O A:HOH2013 2.5 13.3 1.0
OD2 A:ASP740 2.5 8.9 1.0
O A:HOH2026 2.6 85.4 1.0
OD2 A:ASP539 2.6 9.2 1.0
OD1 A:ASP532 2.6 10.4 1.0
CG A:ASP539 2.9 9.7 1.0
O A:HOH2130 3.0 15.4 1.0
C A:TRP647 3.3 6.0 1.0
CG A:ASP740 3.4 7.8 1.0
CG A:ASP532 3.6 7.8 1.0
OD1 A:ASP740 3.6 10.0 1.0
OD2 A:ASP532 3.9 10.8 1.0
CB A:TRP647 4.0 6.0 1.0
N A:GLY648 4.1 6.3 1.0
CA A:TRP647 4.2 5.7 1.0
OD1 A:ASP538 4.2 4.0 0.5
O A:HOH2012 4.3 11.3 1.0
CB A:ASP539 4.4 7.8 1.0
OE1 A:GLN684 4.4 7.5 1.0
CA A:GLY648 4.5 6.7 1.0
NE2 A:GLN684 4.6 7.3 1.0
CB A:ASP740 4.8 7.3 1.0
N A:ASP532 4.8 6.8 1.0
CD A:GLN684 5.0 6.1 1.0
O A:HOH2025 5.0 7.2 1.0
CA A:ASP539 5.0 7.1 1.0
CB A:ASP532 5.0 8.3 1.0

Calcium binding site 2 out of 2 in 2yhg

Go back to Calcium Binding Sites List in 2yhg
Calcium binding site 2 out of 2 in the Ab Initio Phasing of A Nucleoside Hydrolase-Related Hypothetical Protein From Saccharophagus Degradans That Is Associated with Carbohydrate Metabolism


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Ab Initio Phasing of A Nucleoside Hydrolase-Related Hypothetical Protein From Saccharophagus Degradans That Is Associated with Carbohydrate Metabolism within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1936

b:12.5
occ:1.00
OD2 A:ASP866 2.3 16.0 1.0
OD2 A:ASP916 2.3 12.9 1.0
O A:HIS828 2.4 12.3 1.0
OD2 A:ASP864 2.4 13.4 1.0
OD1 A:ASP862 2.4 14.8 1.0
OD1 A:ASN827 2.4 12.7 1.0
OD2 A:ASP862 2.7 15.1 1.0
CG A:ASP862 2.9 13.8 1.0
CG A:ASP916 3.3 12.1 1.0
CG A:ASP866 3.4 16.1 1.0
CG A:ASN827 3.5 11.9 1.0
CG A:ASP864 3.5 13.2 1.0
C A:HIS828 3.5 11.7 1.0
N A:HIS828 3.8 11.7 1.0
CB A:ASP916 3.9 12.3 1.0
CB A:ASP864 3.9 15.0 1.0
ND2 A:ASN827 3.9 12.1 1.0
O A:HOH2346 4.1 18.2 1.0
CB A:ASP866 4.1 14.4 1.0
OD1 A:ASP916 4.2 12.2 1.0
OD1 A:ASP866 4.2 17.6 1.0
CA A:HIS828 4.3 11.9 1.0
CB A:ASP862 4.4 13.9 1.0
N A:ASP864 4.5 14.7 1.0
OD1 A:ASP864 4.6 14.9 1.0
C A:HIS829 4.6 11.1 1.0
N A:HIS829 4.6 11.3 1.0
CD A:PRO863 4.7 14.4 1.0
N A:PRO830 4.7 11.7 1.0
CB A:ASN827 4.8 11.3 1.0
C A:ASN827 4.8 11.7 1.0
CA A:HIS829 4.8 10.7 1.0
CD A:PRO830 4.8 11.3 1.0
CA A:ASP864 4.8 15.9 1.0
CA A:ASN827 4.9 12.4 1.0
O A:HIS829 5.0 12.1 1.0
CB A:HIS828 5.0 11.8 1.0
N A:PRO863 5.0 14.5 1.0

Reference:

J.H.Hehemann, C.Marsters, A.B.Boraston. Ab Initio Phasing of A Nucleoside Hydrolase-Related Hypothetical Protein From Saccharophagus Degradans That Is Associated with Carbohydrate Metabolism. Proteins V. 79 2992 2011.
ISSN: ESSN 1097-0134
PubMed: 21905122
DOI: 10.1002/PROT.23126
Page generated: Sat Dec 12 04:00:28 2020

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