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Calcium in PDB 2j83: Ulilysin Metalloprotease in Complex with Batimastat.

Protein crystallography data

The structure of Ulilysin Metalloprotease in Complex with Batimastat., PDB code: 2j83 was solved by R.Garcia-Castellanos, C.Tallant, A.Marrero, M.Sola, 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) 50.00 / 2.00
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 118.850, 60.730, 168.940, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 21.1

Other elements in 2j83:

The structure of Ulilysin Metalloprotease in Complex with Batimastat. also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Ulilysin Metalloprotease in Complex with Batimastat. (pdb code 2j83). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Ulilysin Metalloprotease in Complex with Batimastat., PDB code: 2j83:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 2j83

Go back to Calcium Binding Sites List in 2j83
Calcium binding site 1 out of 5 in the Ulilysin Metalloprotease in Complex with Batimastat.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Ulilysin Metalloprotease in Complex with Batimastat. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca997

b:13.4
occ:1.00
 O A:TRP240 2.2 13.6 1.0
O A:HOH2169 2.2 9.8 1.0
O A:PRO249 2.3 17.3 1.0
O A:GLN262 2.4 13.9 1.0
OE2 A:GLU243 2.4 15.2 1.0
O A:ALA263 2.4 15.1 1.0
OE1 A:GLU243 2.5 14.9 1.0
CD A:GLU243 2.8 15.8 1.0
C A:ALA263 3.3 15.0 1.0
C A:TRP240 3.4 13.8 1.0
C A:GLN262 3.5 14.2 1.0
C A:PRO249 3.5 17.2 1.0
CA A:ALA263 3.6 14.7 1.0
N A:ALA263 4.0 14.5 1.0
CA A:TRP240 4.1 13.8 1.0
CG A:GLU243 4.2 16.0 1.0
CB A:TRP240 4.2 13.7 1.0
O A:HOH2172 4.3 15.8 1.0
CA A:CYS250 4.3 17.2 1.0
N A:CYS250 4.3 17.1 1.0
O A:ARG252 4.4 17.8 1.0
N A:GLY241 4.4 14.0 1.0
O A:HOH2139 4.4 9.5 1.0
CA A:PRO249 4.5 17.6 1.0
N A:ASP264 4.5 14.9 1.0
CA A:GLY241 4.6 14.3 1.0
CD1 A:TRP240 4.7 13.5 1.0
C A:CYS250 4.8 17.1 1.0
CA A:GLN262 4.8 14.0 1.0
OD1 A:ASN261 4.8 15.7 1.0
N A:ARG252 4.9 17.1 1.0
N A:GLN262 4.9 14.2 1.0
CG A:TRP240 4.9 13.2 1.0
N A:SER251 4.9 16.8 1.0
CB A:GLU243 5.0 16.5 1.0

Calcium binding site 2 out of 5 in 2j83

Go back to Calcium Binding Sites List in 2j83
Calcium binding site 2 out of 5 in the Ulilysin Metalloprotease in Complex with Batimastat.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Ulilysin Metalloprotease in Complex with Batimastat. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca998

b:13.1
occ:1.00
 O A:VAL256 2.3 13.8 1.0
O A:THR259 2.4 13.8 1.0
OD2 A:ASP254 2.4 15.0 1.0
OG1 A:THR259 2.5 12.7 1.0
O A:HOH2165 2.5 4.7 1.0
O A:HOH2149 2.5 10.9 1.0
O A:HOH2164 2.5 17.2 1.0
O A:HOH2154 2.6 12.4 1.0
C A:THR259 3.4 13.5 1.0
CG A:ASP254 3.4 16.0 1.0
C A:VAL256 3.5 14.4 1.0
CB A:THR259 3.6 13.8 1.0
OD1 A:ASP254 3.8 15.3 1.0
CA A:THR259 3.9 13.4 1.0
N A:THR259 4.1 13.9 1.0
N A:VAL256 4.2 15.4 1.0
O A:PRO260 4.3 14.3 1.0
CA A:VAL256 4.3 15.0 1.0
C A:PRO260 4.4 14.1 1.0
N A:PRO260 4.5 13.7 1.0
CB A:VAL256 4.6 15.2 1.0
N A:ASP254 4.6 16.3 1.0
O A:HOH2167 4.6 24.0 1.0
N A:ASP257 4.6 14.6 1.0
O A:HOH2139 4.6 9.5 1.0
CB A:ASP254 4.6 15.8 1.0
N A:ASN261 4.7 13.9 1.0
C A:ASP257 4.7 14.7 1.0
OG A:SER253 4.7 18.1 1.0
O A:ASP257 4.8 14.6 1.0
CA A:ASP257 4.8 14.9 1.0
CG2 A:THR259 4.8 13.4 1.0
CA A:PRO260 4.9 13.8 1.0
O A:ILE239 4.9 14.2 1.0
N A:GLU255 5.0 16.2 1.0
CA A:ASP254 5.0 16.2 1.0

Calcium binding site 3 out of 5 in 2j83

Go back to Calcium Binding Sites List in 2j83
Calcium binding site 3 out of 5 in the Ulilysin Metalloprotease in Complex with Batimastat.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Ulilysin Metalloprotease in Complex with Batimastat. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca997

b:13.1
occ:1.00
 O B:TRP240 2.2 15.2 1.0
O B:PRO249 2.3 17.0 1.0
O B:HOH2168 2.3 13.0 1.0
O B:GLN262 2.3 14.1 1.0
OE1 B:GLU243 2.4 14.1 1.0
O B:ALA263 2.4 13.9 1.0
OE2 B:GLU243 2.5 13.7 1.0
CD B:GLU243 2.7 15.4 1.0
C B:ALA263 3.3 13.8 1.0
C B:TRP240 3.4 15.1 1.0
C B:GLN262 3.4 14.3 1.0
C B:PRO249 3.4 16.9 1.0
CA B:ALA263 3.5 14.1 1.0
N B:ALA263 3.9 14.1 1.0
CA B:TRP240 4.1 15.0 1.0
CB B:TRP240 4.1 14.3 1.0
CG B:GLU243 4.2 15.6 1.0
O B:HOH2190 4.3 9.0 1.0
N B:CYS250 4.3 16.8 1.0
CA B:PRO249 4.3 17.4 1.0
CA B:CYS250 4.4 16.8 1.0
O B:ARG252 4.4 17.5 1.0
O B:HOH2155 4.4 10.9 1.0
N B:GLY241 4.5 15.2 1.0
N B:ASP264 4.5 13.8 1.0
CD1 B:TRP240 4.6 14.2 1.0
CA B:GLY241 4.7 15.4 1.0
CA B:GLN262 4.7 14.5 1.0
C B:CYS250 4.8 16.6 1.0
CG B:TRP240 4.8 14.2 1.0
OD1 B:ASN261 4.8 16.3 1.0
N B:GLN262 4.9 14.8 1.0
N B:ARG252 4.9 17.2 1.0
CB B:ALA263 4.9 14.1 1.0
N B:SER251 4.9 16.7 1.0
CB B:PRO249 5.0 17.1 1.0

Calcium binding site 4 out of 5 in 2j83

Go back to Calcium Binding Sites List in 2j83
Calcium binding site 4 out of 5 in the Ulilysin Metalloprotease in Complex with Batimastat.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Ulilysin Metalloprotease in Complex with Batimastat. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca998

b:11.9
occ:1.00
 OD2 B:ASP254 2.3 15.5 1.0
O B:THR259 2.4 14.2 1.0
O B:VAL256 2.4 16.3 1.0
OG1 B:THR259 2.5 12.8 1.0
O B:HOH2172 2.5 11.1 1.0
O B:HOH2185 2.5 10.5 1.0
O B:HOH2184 2.5 8.8 1.0
O B:HOH2173 2.6 13.5 1.0
CG B:ASP254 3.3 16.9 1.0
C B:THR259 3.4 14.2 1.0
C B:VAL256 3.5 16.7 1.0
CB B:THR259 3.6 14.0 1.0
OD1 B:ASP254 3.8 15.1 1.0
CA B:THR259 3.9 14.0 1.0
N B:VAL256 4.1 17.5 1.0
N B:THR259 4.1 14.1 1.0
O B:PRO260 4.2 15.4 1.0
CA B:VAL256 4.3 17.0 1.0
C B:PRO260 4.4 14.9 1.0
CB B:VAL256 4.5 16.8 1.0
N B:ASP254 4.5 17.3 1.0
N B:PRO260 4.6 14.6 1.0
CB B:ASP254 4.6 17.1 1.0
N B:ASP257 4.6 16.5 1.0
O B:HOH2155 4.7 10.9 1.0
O B:ASP257 4.7 16.2 1.0
C B:ASP257 4.7 16.1 1.0
O B:HOH2186 4.8 22.5 1.0
N B:ASN261 4.8 15.0 1.0
O B:HOH2178 4.8 26.5 1.0
CA B:ASP257 4.8 16.5 1.0
CG2 B:THR259 4.9 13.6 1.0
O B:ILE239 4.9 15.7 1.0
OG B:SER253 4.9 16.7 1.0
CA B:ASP254 4.9 17.3 1.0
CA B:PRO260 5.0 14.8 1.0
N B:GLU255 5.0 17.7 1.0

Calcium binding site 5 out of 5 in 2j83

Go back to Calcium Binding Sites List in 2j83
Calcium binding site 5 out of 5 in the Ulilysin Metalloprotease in Complex with Batimastat.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Ulilysin Metalloprotease in Complex with Batimastat. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2326

b:14.3
occ:1.00
 O A:HOH2119 2.3 11.5 1.0
OD2 B:ASP152 2.3 13.2 1.0
OD2 A:ASP152 2.3 14.3 1.0
O B:HOH2141 2.4 18.5 1.0
O B:HOH2092 2.4 29.1 1.0
O A:HOH2075 2.5 20.0 1.0
CG B:ASP152 3.5 15.1 1.0
CG A:ASP152 3.5 13.8 1.0
CB B:ASP152 4.1 14.8 1.0
CB A:ASP152 4.2 13.9 1.0
O A:HOH2113 4.2 9.6 1.0
O B:HOH2130 4.2 12.2 1.0
O B:SER151 4.3 15.6 1.0
O A:SER151 4.3 14.5 1.0
OD1 A:ASP152 4.4 13.3 1.0
OD1 B:ASP152 4.4 13.8 1.0
CG2 B:THR200 4.6 12.9 1.0
C B:SER151 4.6 15.7 1.0
C A:SER151 4.7 14.7 1.0
OG1 A:THR200 4.7 14.3 1.0
OG1 B:THR200 4.7 13.6 1.0
CG2 A:THR200 4.8 14.2 1.0
O B:THR150 4.8 16.4 1.0
O A:THR150 4.8 16.1 1.0
CB B:THR200 4.9 13.4 1.0

Reference:

R.Garcia-Castellanos, C.Tallant, A.Marrero, M.Sola, U.Baumann, F.X.Gomis-Ruth. Substrate Specificity of A Metalloprotease of the Pappalysin Family Revealed By An Inhibitor and A Product Complex. Arch.Biochem.Biophys. V. 457 57 2007.
ISSN: ISSN 0003-9861
PubMed: 17097044
DOI: 10.1016/J.ABB.2006.10.004
Page generated: Fri Jul 12 13:31:50 2024

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