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Calcium in PDB 1sra: Structure of A Novel Extracellular CA2+-Binding Module in Bm-40(Slash)Sparc(Slash)Osteonectin

Protein crystallography data

The structure of Structure of A Novel Extracellular CA2+-Binding Module in Bm-40(Slash)Sparc(Slash)Osteonectin, PDB code: 1sra was solved by E.Hohenester, P.Maurer, C.Hohenadl, R.Timpl, J.N.Jansonius, J.Engel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.700, 55.200, 75.500, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 24.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of A Novel Extracellular CA2+-Binding Module in Bm-40(Slash)Sparc(Slash)Osteonectin (pdb code 1sra). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Structure of A Novel Extracellular CA2+-Binding Module in Bm-40(Slash)Sparc(Slash)Osteonectin, PDB code: 1sra:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 1sra

Go back to Calcium Binding Sites List in 1sra
Calcium binding site 1 out of 3 in the Structure of A Novel Extracellular CA2+-Binding Module in Bm-40(Slash)Sparc(Slash)Osteonectin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of A Novel Extracellular CA2+-Binding Module in Bm-40(Slash)Sparc(Slash)Osteonectin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:12.3
occ:1.00
 OD1 A:ASP222 2.1 14.5 1.0
O A:HOH408 2.2 20.6 1.0
O A:PRO225 2.4 14.3 1.0
OD1 A:ASP227 2.4 16.6 1.0
O A:TYR229 2.4 18.7 1.0
OE2 A:GLU234 2.6 11.9 1.0
OE1 A:GLU234 2.6 16.2 1.0
CD A:GLU234 2.9 12.0 1.0
CG A:ASP227 3.3 18.8 1.0
CG A:ASP222 3.4 13.9 1.0
C A:PRO225 3.6 18.6 1.0
C A:TYR229 3.6 19.6 1.0
OD2 A:ASP227 3.8 13.4 1.0
N A:ASP227 3.9 16.2 1.0
CA A:ASP222 4.1 15.8 1.0
OD2 A:ASP222 4.2 13.7 1.0
N A:TYR229 4.2 6.8 1.0
N A:PRO225 4.3 18.5 1.0
CB A:ASP222 4.3 18.1 1.0
N A:GLN223 4.4 14.4 1.0
CA A:ILE226 4.4 17.5 1.0
C A:ASP222 4.4 12.4 1.0
CG A:GLU234 4.4 14.5 1.0
N A:ILE226 4.5 11.7 1.0
CA A:TYR229 4.5 8.9 1.0
CB A:ASP227 4.5 10.5 1.0
O A:HOH406 4.5 19.9 1.0
N A:LEU230 4.5 16.5 1.0
C A:ILE226 4.5 20.8 1.0
N A:HIS224 4.5 11.4 1.0
C A:HIS224 4.6 14.4 1.0
CA A:PRO225 4.6 15.9 1.0
CA A:LEU230 4.6 13.7 1.0
CD A:PRO225 4.6 12.7 1.0
CA A:ASP227 4.7 13.8 1.0
N A:GLY228 4.8 17.7 1.0
CB A:TYR229 4.8 11.5 1.0
CG A:PRO225 4.9 10.3 1.0
O A:HIS224 4.9 15.1 1.0
CD2 A:LEU230 5.0 13.6 1.0

Calcium binding site 2 out of 3 in 1sra

Go back to Calcium Binding Sites List in 1sra
Calcium binding site 2 out of 3 in the Structure of A Novel Extracellular CA2+-Binding Module in Bm-40(Slash)Sparc(Slash)Osteonectin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of A Novel Extracellular CA2+-Binding Module in Bm-40(Slash)Sparc(Slash)Osteonectin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:19.7
occ:1.00
 OD1 A:ASP257 2.3 16.0 1.0
OD1 A:ASP261 2.3 20.2 1.0
OE1 A:GLU268 2.4 18.3 1.0
OD1 A:ASP259 2.4 28.6 1.0
O A:HOH405 2.4 19.0 1.0
O A:TYR263 2.4 15.4 1.0
OE2 A:GLU268 2.7 23.4 1.0
CD A:GLU268 2.9 21.4 1.0
CG A:ASP261 3.3 15.2 1.0
CG A:ASP259 3.4 27.1 1.0
CG A:ASP257 3.4 18.3 1.0
C A:TYR263 3.6 13.8 1.0
OD2 A:ASP261 3.7 20.5 1.0
OD2 A:ASP259 3.8 27.8 1.0
N A:TYR263 4.2 12.9 1.0
OD2 A:ASP257 4.2 18.2 1.0
CA A:ASP257 4.2 16.6 1.0
N A:ASP261 4.2 24.4 1.0
O A:HOH421 4.3 28.8 1.0
N A:ASP259 4.4 37.3 1.0
CB A:ASP257 4.4 12.6 1.0
CG A:GLU268 4.4 15.0 1.0
CA A:ILE264 4.5 12.6 1.0
CA A:TYR263 4.5 12.8 1.0
N A:ILE264 4.5 14.3 1.0
N A:ALA265 4.5 15.0 1.0
CB A:ASP261 4.5 14.3 1.0
C A:ASP257 4.6 17.1 1.0
N A:ASN260 4.6 21.7 1.0
CB A:ASP259 4.6 28.9 1.0
N A:LEU258 4.7 17.2 1.0
CA A:ASP259 4.8 26.9 1.0
CA A:ASP261 4.8 20.7 1.0
N A:LYS262 4.8 23.1 1.0
CB A:TYR263 4.8 9.7 1.0
C A:ASP259 4.8 25.9 1.0
O A:HOH417 4.9 26.5 1.0
C A:ILE264 5.0 15.5 1.0

Calcium binding site 3 out of 3 in 1sra

Go back to Calcium Binding Sites List in 1sra
Calcium binding site 3 out of 3 in the Structure of A Novel Extracellular CA2+-Binding Module in Bm-40(Slash)Sparc(Slash)Osteonectin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of A Novel Extracellular CA2+-Binding Module in Bm-40(Slash)Sparc(Slash)Osteonectin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:49.0
occ:1.00
 O A:PRO241 2.3 32.5 1.0
OE1 A:GLU246 2.5 26.7 1.0
O A:ILE243 2.6 18.4 1.0
O A:HOH416 2.8 25.9 1.0
O A:HOH488 3.0 58.9 1.0
O A:HOH479 3.3 53.9 1.0
C A:PRO241 3.4 25.0 1.0
CD A:GLU246 3.5 24.1 1.0
C A:ILE243 3.6 17.7 1.0
N A:ILE243 3.8 32.2 1.0
C A:LEU242 4.1 35.3 1.0
O A:HOH493 4.1 60.2 1.0
O A:HOH498 4.2 60.8 1.0
CA A:PRO241 4.2 27.0 1.0
CA A:LEU242 4.2 38.9 1.0
OE2 A:GLU246 4.3 29.9 1.0
CA A:PRO244 4.3 18.6 1.0
N A:LEU242 4.3 27.4 1.0
N A:MET245 4.3 18.3 1.0
N A:PRO244 4.4 17.5 1.0
CA A:ILE243 4.4 28.4 1.0
N A:GLU246 4.4 17.8 1.0
O A:HOH445 4.4 39.3 1.0
CG A:GLU246 4.5 18.3 1.0
CB A:GLU246 4.5 14.9 1.0
C A:PRO244 4.6 25.7 1.0
O A:LEU242 4.7 32.1 1.0
O A:ALA240 4.8 21.2 1.0
O A:HOH472 5.0 50.4 1.0

Reference:

E.Hohenester, P.Maurer, C.Hohenadl, R.Timpl, J.N.Jansonius, J.Engel. Structure of A Novel Extracellular Ca(2+)-Binding Module in Bm-40. Nat.Struct.Biol. V. 3 67 1996.
ISSN: ISSN 1072-8368
PubMed: 8548457
DOI: 10.1038/NSB0196-67
Page generated: Thu Jul 11 22:48:46 2024

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