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Calcium in PDB 2cki: Structure of Ulilysin, A Member of the Pappalysin Family of Metzincin Metalloendopeptidases.

Protein crystallography data

The structure of Structure of Ulilysin, A Member of the Pappalysin Family of Metzincin Metalloendopeptidases., PDB code: 2cki was solved by C.Tallant, R.Garcia-Castellanos, J.Seco, U.Baumann, F.X.Gomis-Ruth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.00 / 1.70
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 49.564, 126.148, 87.406, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 24.1

Other elements in 2cki:

The structure of Structure of Ulilysin, A Member of the Pappalysin Family of Metzincin Metalloendopeptidases. also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Ulilysin, A Member of the Pappalysin Family of Metzincin Metalloendopeptidases. (pdb code 2cki). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Structure of Ulilysin, A Member of the Pappalysin Family of Metzincin Metalloendopeptidases., PDB code: 2cki:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 2cki

Go back to Calcium Binding Sites List in 2cki
Calcium binding site 1 out of 5 in the Structure of Ulilysin, A Member of the Pappalysin Family of Metzincin Metalloendopeptidases.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Ulilysin, A Member of the Pappalysin Family of Metzincin Metalloendopeptidases. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca997

b:13.5
occ:1.00
 O A:TRP240 2.3 15.5 1.0
O A:PRO249 2.3 19.4 1.0
O A:HOH2243 2.4 12.3 1.0
O A:GLN262 2.4 16.0 1.0
OE2 A:GLU243 2.4 17.5 1.0
O A:ALA263 2.4 15.8 1.0
OE1 A:GLU243 2.4 16.9 1.0
CD A:GLU243 2.7 18.0 1.0
C A:ALA263 3.3 16.4 1.0
C A:TRP240 3.4 15.3 1.0
C A:PRO249 3.5 20.4 1.0
C A:GLN262 3.5 16.0 1.0
CA A:ALA263 3.6 16.3 1.0
N A:ALA263 4.0 16.1 1.0
CA A:TRP240 4.1 15.5 1.0
CB A:TRP240 4.2 14.9 1.0
CG A:GLU243 4.2 18.6 1.0
CA A:PRO249 4.3 20.6 1.0
O A:ARG252 4.4 19.3 1.0
CA A:CYS250 4.4 20.4 1.0
N A:CYS250 4.4 19.6 1.0
O A:HOH2213 4.4 9.4 1.0
O A:HOH2247 4.4 15.3 1.0
N A:GLY241 4.5 15.8 1.0
N A:ASP264 4.5 15.9 1.0
C A:CYS250 4.7 19.8 1.0
CA A:GLY241 4.8 16.9 1.0
CD1 A:TRP240 4.8 15.5 1.0
CA A:GLN262 4.8 15.9 1.0
N A:SER251 4.8 18.9 1.0
OD1 A:ASN261 4.8 16.9 1.0
N A:ARG252 4.9 18.8 1.0
N A:GLN262 4.9 15.9 1.0
CB A:PRO249 4.9 20.8 1.0
CG A:TRP240 4.9 15.0 1.0

Calcium binding site 2 out of 5 in 2cki

Go back to Calcium Binding Sites List in 2cki
Calcium binding site 2 out of 5 in the Structure of Ulilysin, A Member of the Pappalysin Family of Metzincin Metalloendopeptidases.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Ulilysin, A Member of the Pappalysin Family of Metzincin Metalloendopeptidases. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca998

b:14.6
occ:1.00
 O A:THR259 2.4 14.3 1.0
O A:HOH2240 2.4 17.9 1.0
O A:VAL256 2.4 15.1 1.0
O A:HOH2227 2.4 10.4 1.0
OD2 A:ASP254 2.4 13.8 1.0
O A:HOH2241 2.5 6.9 1.0
O A:HOH2231 2.5 11.2 1.0
OG1 A:THR259 2.6 13.6 1.0
C A:THR259 3.4 14.9 1.0
CG A:ASP254 3.4 16.4 1.0
C A:VAL256 3.6 15.7 1.0
CB A:THR259 3.7 15.3 1.0
OD1 A:ASP254 3.8 16.2 1.0
CA A:THR259 4.0 15.0 1.0
N A:THR259 4.2 15.8 1.0
N A:VAL256 4.2 15.7 1.0
O A:PRO260 4.3 15.5 1.0
CA A:VAL256 4.3 15.4 1.0
C A:PRO260 4.4 15.2 1.0
O A:HOH2233 4.4 24.2 1.0
N A:ASP254 4.5 17.3 1.0
CB A:VAL256 4.5 14.3 1.0
N A:PRO260 4.5 15.2 1.0
O A:HOH2242 4.6 21.2 1.0
N A:ASN261 4.6 15.8 1.0
O A:HOH2235 4.6 21.6 1.0
N A:ASP257 4.6 15.6 1.0
O A:HOH2213 4.7 9.4 1.0
CB A:ASP254 4.7 16.8 1.0
O A:ASP257 4.7 17.6 1.0
C A:ASP257 4.8 17.1 1.0
OG A:SER253 4.8 20.1 1.0
CA A:ASP257 4.8 17.0 1.0
CA A:PRO260 4.9 15.2 1.0
CA A:ASN261 4.9 16.1 1.0
CG2 A:THR259 4.9 14.5 1.0
N A:GLU255 5.0 16.9 1.0
O A:ILE239 5.0 16.2 1.0

Calcium binding site 3 out of 5 in 2cki

Go back to Calcium Binding Sites List in 2cki
Calcium binding site 3 out of 5 in the Structure of Ulilysin, A Member of the Pappalysin Family of Metzincin Metalloendopeptidases.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Ulilysin, A Member of the Pappalysin Family of Metzincin Metalloendopeptidases. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1403

b:11.5
occ:1.00
 O B:HOH2130 2.2 21.4 1.0
O A:HOH2139 2.2 19.9 1.0
O B:HOH2132 2.3 13.2 1.0
OD2 A:ASP152 2.4 15.8 1.0
OD2 B:ASP152 2.4 15.7 1.0
O B:HOH2184 2.4 14.1 1.0
CG B:ASP152 3.5 18.1 1.0
CG A:ASP152 3.5 17.6 1.0
O A:HOH2144 4.2 10.9 1.0
CB B:ASP152 4.2 15.6 1.0
CB A:ASP152 4.2 15.5 1.0
O B:SER151 4.2 16.6 1.0
O B:HOH2174 4.3 12.1 1.0
O A:SER151 4.3 16.3 1.0
OD1 B:ASP152 4.4 15.9 1.0
OD1 A:ASP152 4.4 17.6 1.0
C B:SER151 4.7 16.8 1.0
C A:SER151 4.7 16.8 1.0
O B:THR150 4.7 18.4 1.0
OG1 B:THR200 4.8 14.4 1.0
OG1 A:THR200 4.8 14.5 1.0
O A:THR150 4.8 18.2 1.0
CG2 A:THR200 4.8 13.7 1.0
CG2 B:THR200 4.9 14.7 1.0

Calcium binding site 4 out of 5 in 2cki

Go back to Calcium Binding Sites List in 2cki
Calcium binding site 4 out of 5 in the Structure of Ulilysin, A Member of the Pappalysin Family of Metzincin Metalloendopeptidases.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Ulilysin, A Member of the Pappalysin Family of Metzincin Metalloendopeptidases. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca997

b:14.2
occ:1.00
 O B:TRP240 2.3 16.1 1.0
O B:PRO249 2.3 19.6 1.0
O B:HOH2216 2.3 10.5 1.0
O B:GLN262 2.4 15.4 1.0
OE1 B:GLU243 2.4 15.7 1.0
O B:ALA263 2.4 15.8 1.0
OE2 B:GLU243 2.5 16.4 1.0
CD B:GLU243 2.8 17.3 1.0
C B:ALA263 3.4 16.3 1.0
C B:TRP240 3.5 15.5 1.0
C B:PRO249 3.5 20.2 1.0
C B:GLN262 3.5 16.5 1.0
CA B:ALA263 3.7 16.5 1.0
N B:ALA263 4.1 16.2 1.0
CA B:TRP240 4.2 15.8 1.0
CG B:GLU243 4.3 17.3 1.0
CB B:TRP240 4.3 14.9 1.0
CA B:CYS250 4.3 20.2 1.0
N B:CYS250 4.4 19.6 1.0
CA B:PRO249 4.4 20.6 1.0
O B:ARG252 4.4 19.3 1.0
O B:HOH2240 4.4 14.5 1.0
O B:HOH2206 4.5 10.3 1.0
N B:GLY241 4.5 16.2 1.0
N B:ASP264 4.6 15.7 1.0
CD1 B:TRP240 4.7 17.0 1.0
C B:CYS250 4.7 19.6 1.0
CA B:GLY241 4.7 16.4 1.0
OD1 B:ASN261 4.8 17.9 1.0
CA B:GLN262 4.8 16.0 1.0
N B:SER251 4.8 19.1 1.0
N B:ARG252 4.9 18.7 1.0
N B:GLN262 4.9 16.2 1.0
CG B:TRP240 4.9 15.8 1.0

Calcium binding site 5 out of 5 in 2cki

Go back to Calcium Binding Sites List in 2cki
Calcium binding site 5 out of 5 in the Structure of Ulilysin, A Member of the Pappalysin Family of Metzincin Metalloendopeptidases.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of Ulilysin, A Member of the Pappalysin Family of Metzincin Metalloendopeptidases. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca998

b:13.7
occ:1.00
 OD2 B:ASP254 2.3 16.4 1.0
O B:HOH2224 2.3 11.7 1.0
O B:HOH2234 2.4 13.9 1.0
O B:HOH2235 2.4 10.8 1.0
O B:THR259 2.4 14.6 1.0
O B:VAL256 2.5 15.1 1.0
O B:HOH2219 2.5 9.7 1.0
OG1 B:THR259 2.6 14.5 1.0
CG B:ASP254 3.3 16.5 1.0
C B:THR259 3.5 14.8 1.0
C B:VAL256 3.6 15.8 1.0
CB B:THR259 3.7 15.5 1.0
OD1 B:ASP254 3.7 17.0 1.0
CA B:THR259 4.0 15.3 1.0
N B:VAL256 4.1 15.9 1.0
N B:THR259 4.2 16.4 1.0
O B:HOH2237 4.3 25.3 1.0
CA B:VAL256 4.3 15.0 1.0
O B:PRO260 4.4 15.4 1.0
C B:PRO260 4.4 15.4 1.0
N B:ASP254 4.4 16.9 1.0
O B:HOH2227 4.5 30.3 1.0
CB B:ASP254 4.6 16.6 1.0
N B:PRO260 4.6 15.7 1.0
CB B:VAL256 4.6 15.1 1.0
O B:HOH2206 4.6 10.3 1.0
N B:ASN261 4.7 15.7 1.0
N B:ASP257 4.7 15.5 1.0
O B:HOH2228 4.8 22.6 1.0
OG B:SER253 4.8 18.7 1.0
O B:ASP257 4.8 17.2 1.0
C B:ASP257 4.9 17.2 1.0
N B:GLU255 4.9 17.1 1.0
CA B:ASP257 4.9 17.1 1.0
O B:ILE239 4.9 15.7 1.0
CA B:ASP254 4.9 16.5 1.0
CG2 B:THR259 4.9 14.5 1.0
CA B:PRO260 4.9 15.1 1.0
CA B:ASN261 5.0 16.4 1.0

Reference:

C.Tallant, R.Garcia-Castellanos, J.Seco, U.Baumann, F.X.Gomis-Ruth. Molecular Analysis of Ulilysin, the Structural Prototype of A New Family of Metzincin Metalloproteases. J.Biol.Chem. V. 281 17920 2006.
ISSN: ISSN 0021-9258
PubMed: 16627477
DOI: 10.1074/JBC.M600907200
Page generated: Fri Jul 12 09:31:21 2024

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