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Calcium in PDB 3d0y: Crystal Structure of S100B in the Calcium and Zinc Loaded State at pH 6.5

Protein crystallography data

The structure of Crystal Structure of S100B in the Calcium and Zinc Loaded State at pH 6.5, PDB code: 3d0y was solved by T.Ostendorp, J.Diez, C.W.Heizmann, G.Fritz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 13.00 / 1.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 34.890, 58.150, 47.660, 90.00, 111.12, 90.00
R / Rfree (%) 20.6 / 26.1

Other elements in 3d0y:

The structure of Crystal Structure of S100B in the Calcium and Zinc Loaded State at pH 6.5 also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of S100B in the Calcium and Zinc Loaded State at pH 6.5 (pdb code 3d0y). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of S100B in the Calcium and Zinc Loaded State at pH 6.5, PDB code: 3d0y:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3d0y

Go back to Calcium Binding Sites List in 3d0y
Calcium binding site 1 out of 4 in the Crystal Structure of S100B in the Calcium and Zinc Loaded State at pH 6.5


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 S100B in the Calcium and Zinc Loaded State at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca92

b:29.1
occ:1.00
OD1 A:ASP61 2.2 17.5 1.0
OD2 A:ASP63 2.2 21.2 1.0
O A:GLU67 2.3 9.0 1.0
OD1 A:ASP65 2.3 16.9 1.0
O A:HOH96 2.4 39.1 1.0
OE1 A:GLU72 2.5 14.4 1.0
OE2 A:GLU72 2.6 14.1 1.0
CD A:GLU72 2.9 15.6 1.0
CG A:ASP63 3.2 20.0 1.0
CG A:ASP61 3.3 19.2 1.0
CG A:ASP65 3.3 19.4 1.0
C A:GLU67 3.5 11.4 1.0
OD1 A:ASP63 3.6 22.1 1.0
OD2 A:ASP65 3.7 18.9 1.0
N A:GLU67 4.1 14.0 1.0
CB A:ASP61 4.1 20.9 1.0
OD2 A:ASP61 4.1 20.2 1.0
CA A:ASP61 4.2 20.9 1.0
N A:ASP65 4.2 18.7 1.0
N A:ASP63 4.2 21.3 1.0
CA A:GLU67 4.3 12.6 1.0
N A:CYS68 4.4 10.8 1.0
CG A:GLU72 4.4 13.5 1.0
CB A:ASP63 4.4 20.1 1.0
N A:ASP69 4.5 12.5 1.0
N A:GLY64 4.5 20.6 1.0
CA A:CYS68 4.5 11.6 1.0
CB A:ASP65 4.5 17.7 1.0
C A:ASP61 4.5 21.5 1.0
N A:ASN62 4.6 22.5 1.0
CA A:ASP63 4.6 20.6 1.0
C A:ASP63 4.7 20.4 1.0
CA A:ASP65 4.7 18.1 1.0
N A:GLY66 4.8 16.2 1.0
CB A:GLU67 4.9 12.1 1.0
O A:HOH144 4.9 35.5 1.0
CG A:ASP69 4.9 13.7 1.0
C A:ASP65 4.9 17.4 1.0
OD2 A:ASP69 4.9 16.6 1.0
C A:CYS68 5.0 11.3 0.5
C A:CYS68 5.0 11.4 0.5

Calcium binding site 2 out of 4 in 3d0y

Go back to Calcium Binding Sites List in 3d0y
Calcium binding site 2 out of 4 in the Crystal Structure of S100B in the Calcium and Zinc Loaded State at pH 6.5


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 S100B in the Calcium and Zinc Loaded State at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca93

b:32.1
occ:1.00
O A:GLU21 2.2 14.1 1.0
O A:ASP23 2.3 21.8 1.0
O A:SER18 2.3 16.0 1.0
O A:LYS26 2.3 15.2 1.0
OE1 A:GLU31 2.4 18.0 1.0
OE2 A:GLU31 2.5 16.9 1.0
CD A:GLU31 2.8 14.4 1.0
C A:SER18 3.3 15.5 1.0
C A:ASP23 3.4 21.2 1.0
C A:GLU21 3.5 17.8 1.0
C A:LYS26 3.6 16.4 1.0
CA A:SER18 3.9 15.1 1.0
N A:GLU21 4.1 17.6 1.0
N A:ASP23 4.1 21.1 1.0
CG A:GLU31 4.3 17.1 1.0
CA A:ASP23 4.3 21.4 1.0
C A:GLY22 4.3 20.8 1.0
N A:LYS24 4.4 21.6 1.0
CA A:GLU21 4.4 18.2 1.0
N A:LYS28 4.4 17.1 1.0
N A:LEU27 4.5 15.9 1.0
N A:GLY19 4.5 15.8 1.0
N A:GLY22 4.5 19.0 1.0
N A:LYS26 4.5 16.9 1.0
CA A:LYS24 4.5 21.0 1.0
CA A:LEU27 4.5 17.1 1.0
CA A:LYS26 4.6 15.9 1.0
CB A:SER18 4.6 14.5 1.0
O A:TYR17 4.6 15.2 1.0
OE1 A:GLU67 4.7 18.0 1.0
CA A:GLY22 4.7 20.0 1.0
N A:ARG20 4.7 16.5 1.0
CB A:ASP23 4.7 21.2 1.0
O A:GLY22 4.8 20.8 1.0
C A:LYS24 4.8 20.7 1.0
C A:LEU27 4.8 16.8 1.0
CA A:GLY19 4.9 15.7 1.0
O A:HOH149 4.9 53.6 1.0
C A:GLY19 5.0 16.2 1.0

Calcium binding site 3 out of 4 in 3d0y

Go back to Calcium Binding Sites List in 3d0y
Calcium binding site 3 out of 4 in the Crystal Structure of S100B in the Calcium and Zinc Loaded State at pH 6.5


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 S100B in the Calcium and Zinc Loaded State at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca92

b:31.7
occ:1.00
O B:ASP23 2.2 18.8 1.0
OE1 B:GLU31 2.3 11.9 1.0
O B:LYS26 2.4 12.4 1.0
O B:SER18 2.4 14.4 1.0
O B:HOH95 2.5 34.0 1.0
OE2 B:GLU31 2.5 15.0 1.0
O B:GLU21 2.6 19.3 1.0
CD B:GLU31 2.7 13.2 1.0
C B:ASP23 3.4 19.1 1.0
C B:SER18 3.4 13.9 1.0
C B:LYS26 3.6 13.1 1.0
C B:GLU21 3.7 19.3 1.0
CA B:SER18 3.9 13.1 1.0
N B:GLU21 4.1 18.3 1.0
N B:ASP23 4.1 20.3 1.0
CA B:ASP23 4.2 19.8 1.0
OE1 B:GLU67 4.2 22.8 1.0
CG B:GLU31 4.2 13.0 1.0
N B:LYS28 4.3 13.7 1.0
N B:LYS24 4.3 18.3 1.0
N B:LYS26 4.4 14.3 1.0
N B:LEU27 4.4 12.6 1.0
CA B:GLU21 4.5 20.0 1.0
CA B:LEU27 4.5 12.9 1.0
C B:GLY22 4.5 20.0 1.0
CA B:LYS24 4.5 16.7 1.0
CB B:ASP23 4.5 20.4 1.0
N B:GLY19 4.5 15.1 1.0
O B:TYR17 4.5 12.4 1.0
CA B:LYS26 4.6 14.0 1.0
CB B:SER18 4.6 13.4 1.0
CG B:LYS28 4.7 13.8 1.0
N B:ARG20 4.7 15.4 1.0
C B:LYS24 4.7 16.3 1.0
N B:GLY22 4.7 19.9 1.0
O B:HOH172 4.8 44.5 1.0
C B:LEU27 4.8 12.7 1.0
O B:GLY22 4.8 21.0 1.0
N B:HIS25 4.9 16.2 1.0
CB B:GLU21 4.9 20.1 1.0
NZ B:LYS28 4.9 20.6 1.0
CA B:GLY22 4.9 19.6 1.0
CA B:GLY19 5.0 14.7 1.0

Calcium binding site 4 out of 4 in 3d0y

Go back to Calcium Binding Sites List in 3d0y
Calcium binding site 4 out of 4 in the Crystal Structure of S100B in the Calcium and Zinc Loaded State at pH 6.5


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 S100B in the Calcium and Zinc Loaded State at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca93

b:36.0
occ:1.00
O B:HOH141 1.4 26.9 1.0
OD1 B:ASP61 1.9 21.0 1.0
OD1 B:ASP63 2.3 26.7 1.0
O B:GLU67 2.4 13.8 1.0
OD1 B:ASP65 2.5 20.9 1.0
OE1 B:GLU72 2.6 10.6 1.0
OE2 B:GLU72 2.7 11.0 1.0
CD B:GLU72 3.0 10.1 1.0
CG B:ASP61 3.1 23.0 1.0
CG B:ASP63 3.3 27.9 1.0
C B:GLU67 3.6 14.6 1.0
CG B:ASP65 3.6 22.6 1.0
CA B:ASP61 3.8 23.3 1.0
CB B:ASP61 3.8 23.3 1.0
OD2 B:ASP63 3.9 29.8 1.0
N B:ASP65 3.9 23.1 1.0
OD2 B:ASP61 4.0 21.2 1.0
N B:ASP63 4.1 25.2 1.0
OD2 B:ASP65 4.2 23.8 1.0
C B:ASP61 4.2 23.6 1.0
N B:GLU67 4.2 18.3 1.0
N B:GLY64 4.2 24.1 1.0
N B:ASN62 4.4 24.6 1.0
CA B:GLU67 4.4 16.1 1.0
CB B:ASP63 4.5 25.6 1.0
CG B:GLU72 4.5 8.4 1.0
N B:CYS68 4.5 13.1 1.0
CA B:ASP63 4.6 25.4 1.0
C B:ASP63 4.6 24.9 1.0
CB B:ASP65 4.6 22.2 1.0
CA B:CYS68 4.6 12.1 1.0
N B:GLY66 4.6 21.7 1.0
CA B:ASP65 4.6 22.6 1.0
N B:ASP69 4.7 11.1 1.0
O B:ASP61 4.7 23.5 1.0
C B:ASP65 4.9 22.0 1.0
C B:GLY64 4.9 23.6 1.0
CA B:GLY64 4.9 24.1 1.0
O B:HOH173 5.0 41.5 1.0

Reference:

T.Ostendorp, J.Diez, C.W.Heizmann, G.Fritz. The Crystal Structures of Human S100B in the Zinc- and Calcium-Loaded State at Three pH Values Reveal Zinc Ligand Swapping. Biochim.Biophys.Acta V.1813 1083 2011.
ISSN: ISSN 0006-3002
PubMed: 20950652
DOI: 10.1016/J.BBAMCR.2010.10.006
Page generated: Sat Dec 12 04:08:12 2020

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