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Calcium in PDB 2v15: Terbium Binding in Streptococcus Suis Dpr Protein

Protein crystallography data

The structure of Terbium Binding in Streptococcus Suis Dpr Protein, PDB code: 2v15 was solved by H.Havukainen, A.C.Papageorgiou, A.Kauko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.98 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 104.485, 137.715, 142.438, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 24.4

Other elements in 2v15:

The structure of Terbium Binding in Streptococcus Suis Dpr Protein also contains other interesting chemical elements:

Terbium (Tb) 12 atoms
Chlorine (Cl) 10 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Terbium Binding in Streptococcus Suis Dpr Protein (pdb code 2v15). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Terbium Binding in Streptococcus Suis Dpr Protein, PDB code: 2v15:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 2v15

Go back to Calcium Binding Sites List in 2v15
Calcium binding site 1 out of 4 in the Terbium Binding in Streptococcus Suis Dpr Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Terbium Binding in Streptococcus Suis Dpr Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1173

b:58.7
occ:1.00
OE2 B:GLU113 2.6 41.5 1.0
OE1 B:GLU113 2.6 37.5 1.0
CD B:GLU113 3.0 38.4 1.0
CG B:GLU113 4.5 31.5 1.0
CG2 B:THR110 4.7 27.9 1.0
O B:ASN108 4.7 37.1 1.0

Calcium binding site 2 out of 4 in 2v15

Go back to Calcium Binding Sites List in 2v15
Calcium binding site 2 out of 4 in the Terbium Binding in Streptococcus Suis Dpr Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Terbium Binding in Streptococcus Suis Dpr Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca173

b:74.7
occ:1.00
O G:HOH2039 3.2 47.6 1.0
O G:ASN108 4.0 40.5 1.0
OE1 G:GLU113 4.6 39.8 1.0

Calcium binding site 3 out of 4 in 2v15

Go back to Calcium Binding Sites List in 2v15
Calcium binding site 3 out of 4 in the Terbium Binding in Streptococcus Suis Dpr Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Terbium Binding in Streptococcus Suis Dpr Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca1174

b:28.8
occ:0.50
O H:ASN108 3.0 42.1 1.0
C H:ASN108 4.0 40.6 1.0
CA H:ASN108 4.3 40.6 1.0
O H:VAL109 4.7 39.5 1.0
O H:TYR107 4.8 38.8 1.0
ND2 H:ASN108 4.8 45.9 1.0
C H:VAL109 4.9 39.5 1.0
O K:GLY167 4.9 32.6 1.0
CG2 H:THR110 4.9 37.3 1.0
CB H:ASN108 4.9 40.7 1.0
CA H:THR110 5.0 37.6 1.0

Calcium binding site 4 out of 4 in 2v15

Go back to Calcium Binding Sites List in 2v15
Calcium binding site 4 out of 4 in the Terbium Binding in Streptococcus Suis Dpr Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Terbium Binding in Streptococcus Suis Dpr Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Ca1175

b:36.5
occ:1.00
OD2 K:ASP24 2.4 35.4 1.0
OE2 K:GLU139 2.4 36.3 1.0
CD K:GLU139 3.3 36.2 1.0
CG K:ASP24 3.4 35.0 1.0
CG K:GLU139 3.5 36.6 1.0
CB K:ASP24 3.8 33.2 1.0
N K:ASP24 4.4 33.6 1.0
OE1 K:GLU139 4.5 32.5 1.0
OD1 K:ASP24 4.5 34.6 1.0
O K:HOH2047 4.7 45.9 1.0
CA K:ASP24 4.8 32.8 1.0

Reference:

H.Havukainen, S.Haataja, A.Kauko, A.T.Pulliainen, A.Salminen, T.Haikarainen, J.Finne, A.C.Papageorgiou. Structural Basis of the Zinc- and Terbium-Mediated Inhibition of Ferroxidase Activity in Dps Ferritin-Like Proteins. Protein Sci. V. 17 1513 2008.
ISSN: ESSN 1469-896X
PubMed: 18552126
DOI: 10.1110/PS.036236.108
Page generated: Sat Dec 12 03:53:06 2020

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