Calcium in PDB 3lum: Structure of Ulilysin Mutant M290L

The structure of Structure of Ulilysin Mutant M290L, PDB code: 3lum was solved by C.Tallant, R.Garcia-Castellanos, 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)	46.28 / 1.70
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	97.310, 174.110, 124.690, 90.00, 90.00, 90.00
R / Rfree (%)	16.3 / 19.5

The structure of Structure of Ulilysin Mutant M290L also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Calcium atom in the Structure of Ulilysin Mutant M290L (pdb code 3lum). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 11 binding sites of Calcium where determined in the Structure of Ulilysin Mutant M290L, PDB code: 3lum:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 11 in the Structure of Ulilysin Mutant M290L


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 Mutant M290L within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca997 b:7.0 occ:1.00 O A:TRP240 2.2 5.6 1.0 O A:PRO249 2.3 9.2 1.0 O A:GLN262 2.3 7.1 1.0 O A:HOH413 2.4 8.9 1.0 OE2 A:GLU243 2.5 8.1 1.0 OE1 A:GLU243 2.5 7.6 1.0 O A:ALA263 2.5 8.3 1.0 CD A:GLU243 2.8 8.5 1.0 C A:ALA263 3.3 7.6 1.0 C A:TRP240 3.4 5.5 1.0 C A:PRO249 3.4 9.9 1.0 C A:GLN262 3.5 6.9 1.0 CA A:ALA263 3.5 7.2 1.0 N A:ALA263 4.0 7.5 1.0 CA A:TRP240 4.1 4.9 1.0 CB A:TRP240 4.2 4.8 1.0 CA A:CYS250 4.3 10.8 1.0 CG A:GLU243 4.3 8.1 1.0 N A:CYS250 4.3 10.2 1.0 O A:ARG252 4.3 8.6 1.0 O A:HOH331 4.4 10.4 1.0 CA A:PRO249 4.4 10.8 1.0 O A:HOH352 4.5 11.2 1.0 N A:GLY241 4.5 6.4 1.0 N A:ASP264 4.5 7.8 1.0 CA A:GLY241 4.7 6.8 1.0 C A:CYS250 4.7 10.4 1.0 CD1 A:TRP240 4.7 5.7 1.0 CA A:GLN262 4.7 7.1 1.0 N A:SER251 4.8 10.2 1.0 OD1 A:ASN261 4.8 9.6 1.0 N A:ARG252 4.8 9.1 1.0 N A:GLN262 4.9 7.5 1.0 CG A:TRP240 4.9 5.0 1.0 CB A:ALA263 4.9 8.0 1.0

Calcium binding site 2 out of 11 in the Structure of Ulilysin Mutant M290L


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 Mutant M290L within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca998 b:6.9 occ:1.00 OD1 A:ASP254 2.3 6.0 1.0 O A:THR259 2.4 6.8 1.0 O A:VAL256 2.5 7.1 1.0 O A:HOH554 2.5 15.0 1.0 O A:HOH359 2.5 8.9 1.0 O A:HOH354 2.5 6.8 1.0 OG1 A:THR259 2.6 4.9 1.0 O A:HOH409 2.6 6.9 1.0 C A:THR259 3.4 6.5 1.0 CG A:ASP254 3.4 6.0 1.0 C A:VAL256 3.6 6.6 1.0 CB A:THR259 3.6 4.9 1.0 OD2 A:ASP254 3.8 7.5 1.0 CA A:THR259 3.9 6.2 1.0 N A:THR259 4.1 5.4 1.0 N A:VAL256 4.1 6.7 1.0 CA A:VAL256 4.3 6.3 1.0 O A:PRO260 4.3 8.1 1.0 C A:PRO260 4.4 7.8 1.0 CB A:VAL256 4.5 6.1 1.0 N A:ASP254 4.5 6.8 1.0 N A:PRO260 4.5 7.2 1.0 O A:HOH491 4.5 17.6 1.0 O A:HOH407 4.5 19.0 1.0 O A:HOH593 4.5 22.8 1.0 N A:ASN261 4.6 7.5 1.0 CB A:ASP254 4.6 5.7 1.0 N A:ASP257 4.6 7.6 1.0 O A:HOH352 4.7 11.2 1.0 C A:ASP257 4.8 7.2 1.0 O A:ASP257 4.8 7.7 1.0 OG A:SER253 4.9 9.1 1.0 CA A:ASP257 4.9 7.5 1.0 CA A:PRO260 4.9 7.5 1.0 CG2 A:THR259 4.9 6.8 1.0 CA A:ASP254 4.9 6.0 1.0 O A:ILE239 4.9 6.5 1.0 N A:GLU255 5.0 6.7 1.0 CA A:ASN261 5.0 8.0 1.0

Calcium binding site 3 out of 11 in the Structure of Ulilysin Mutant M290L


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 Mutant M290L within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1401 b:6.1 occ:1.00 O A:HOH466 2.3 15.1 1.0 OD2 A:ASP152 2.3 5.5 1.0 OD2 C:ASP152 2.4 5.6 1.0 O C:HOH497 2.4 15.1 1.0 O A:HOH400 2.4 8.8 1.0 O A:HOH397 2.5 9.1 1.0 CG A:ASP152 3.5 4.3 1.0 CG C:ASP152 3.5 5.5 1.0 CB A:ASP152 4.2 5.0 1.0 O A:HOH348 4.2 8.0 1.0 O C:HOH372 4.2 6.7 1.0 CB C:ASP152 4.2 4.9 1.0 O C:SER151 4.3 5.4 1.0 O A:SER151 4.4 6.2 1.0 OD1 A:ASP152 4.5 5.7 1.0 OD1 C:ASP152 4.5 4.6 1.0 C A:SER151 4.7 5.8 1.0 C C:SER151 4.7 5.9 1.0 O A:THR150 4.7 7.3 1.0 OG1 C:THR200 4.7 4.7 1.0 OG1 A:THR200 4.7 5.4 1.0 O C:THR150 4.8 7.4 1.0 CG2 C:THR200 4.9 3.8 1.0 O A:HOH953 4.9 25.5 1.0 CG2 A:THR200 4.9 4.7 1.0

Calcium binding site 4 out of 11 in the Structure of Ulilysin Mutant M290L


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 Mutant M290L within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca997 b:5.8 occ:1.00 O B:TRP240 2.3 5.1 1.0 O B:PRO249 2.3 7.8 1.0 O B:GLN262 2.4 4.8 1.0 O B:HOH354 2.5 6.2 1.0 OE2 B:GLU243 2.5 7.0 1.0 OE1 B:GLU243 2.5 5.5 1.0 O B:ALA263 2.5 4.9 1.0 CD B:GLU243 2.8 6.4 1.0 C B:ALA263 3.3 5.0 1.0 C B:TRP240 3.4 4.2 1.0 C B:PRO249 3.5 8.4 1.0 C B:GLN262 3.5 4.6 1.0 CA B:ALA263 3.6 4.7 1.0 N B:ALA263 4.0 4.4 1.0 CA B:TRP240 4.1 4.2 1.0 CB B:TRP240 4.2 3.0 1.0 CA B:CYS250 4.3 8.1 1.0 CG B:GLU243 4.3 7.2 1.0 N B:CYS250 4.3 7.6 1.0 O B:ARG252 4.3 9.1 1.0 CA B:PRO249 4.4 9.4 1.0 O B:HOH324 4.4 9.9 1.0 O B:HOH338 4.4 7.1 1.0 N B:GLY241 4.5 5.1 1.0 N B:ASP264 4.6 4.9 1.0 C B:CYS250 4.7 7.7 1.0 CD1 B:TRP240 4.7 5.4 1.0 CA B:GLY241 4.7 4.7 1.0 CA B:GLN262 4.7 4.5 1.0 OD1 B:ASN261 4.8 7.4 1.0 N B:SER251 4.8 7.7 1.0 N B:GLN262 4.9 4.2 1.0 CG B:TRP240 4.9 4.3 1.0 N B:ARG252 4.9 7.1 1.0 SG B:CYS277 4.9 8.7 1.0 CB B:ALA263 5.0 5.3 1.0 CB B:PRO249 5.0 9.4 1.0

Calcium binding site 5 out of 11 in the Structure of Ulilysin Mutant M290L


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 Mutant M290L within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca998 b:5.0 occ:1.00 OD1 B:ASP254 2.3 5.2 1.0 O B:THR259 2.4 5.0 1.0 O B:HOH341 2.5 4.5 1.0 O B:VAL256 2.5 5.5 1.0 O B:HOH480 2.5 10.6 1.0 O B:HOH449 2.5 12.9 1.0 OG1 B:THR259 2.5 4.6 1.0 O B:HOH367 2.6 8.7 1.0 CG B:ASP254 3.3 5.9 1.0 C B:THR259 3.4 4.4 1.0 C B:VAL256 3.6 6.3 1.0 CB B:THR259 3.6 3.9 1.0 OD2 B:ASP254 3.7 5.9 1.0 CA B:THR259 3.9 4.2 1.0 N B:VAL256 4.1 6.0 1.0 N B:THR259 4.2 4.6 1.0 O B:HOH661 4.3 24.9 1.0 CA B:VAL256 4.3 6.1 1.0 O B:PRO260 4.4 5.3 1.0 C B:PRO260 4.4 4.5 1.0 N B:ASP254 4.5 6.5 1.0 CB B:VAL256 4.5 5.8 1.0 N B:PRO260 4.6 4.3 1.0 CB B:ASP254 4.6 6.4 1.0 O B:HOH621 4.6 18.9 1.0 O B:HOH338 4.6 7.1 1.0 N B:ASN261 4.6 4.4 1.0 N B:ASP257 4.7 6.7 1.0 O B:ASP257 4.8 6.3 1.0 O B:HOH389 4.8 12.9 1.0 C B:ASP257 4.8 5.9 1.0 OG B:SER253 4.8 8.0 1.0 CA B:ASP257 4.8 7.0 1.0 CA B:PRO260 4.9 4.8 1.0 O B:ILE239 4.9 5.3 1.0 CA B:ASP254 4.9 5.8 1.0 N B:GLU255 4.9 6.7 1.0 CA B:ASN261 5.0 4.9 1.0 CG2 B:THR259 5.0 3.3 1.0

Calcium binding site 6 out of 11 in the Structure of Ulilysin Mutant M290L


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of Ulilysin Mutant M290L within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1401 b:4.5 occ:0.50 OD2 B:ASP152 2.4 6.7 1.0 O B:HOH484 2.5 16.1 1.0 O B:HOH481 2.6 8.1 1.0 CG B:ASP152 3.6 5.0 1.0 O B:HOH357 4.1 8.4 1.0 CB B:ASP152 4.3 5.1 1.0 OD1 B:ASP152 4.5 4.8 1.0 O B:SER151 4.6 5.3 1.0 O B:HOH1354 4.6 26.6 0.5 OG1 B:THR200 4.6 5.5 1.0 CG2 B:THR200 4.9 5.3 1.0 C B:SER151 4.9 5.8 1.0 O B:THR150 4.9 7.6 1.0 CB B:THR200 5.0 4.4 1.0

Calcium binding site 7 out of 11 in the Structure of Ulilysin Mutant M290L


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of Ulilysin Mutant M290L within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca997 b:6.9 occ:1.00 O C:TRP240 2.3 4.8 1.0 O C:PRO249 2.3 8.6 1.0 O C:GLN262 2.3 5.4 1.0 O C:HOH349 2.5 7.8 1.0 O C:ALA263 2.5 5.2 1.0 OE1 C:GLU243 2.5 6.3 1.0 OE2 C:GLU243 2.5 7.6 1.0 CD C:GLU243 2.8 6.1 1.0 C C:ALA263 3.3 5.1 1.0 C C:TRP240 3.4 4.6 1.0 C C:PRO249 3.4 9.5 1.0 C C:GLN262 3.5 5.2 1.0 CA C:ALA263 3.6 5.5 1.0 N C:ALA263 4.0 4.7 1.0 CA C:TRP240 4.1 4.7 1.0 CB C:TRP240 4.2 3.8 1.0 CG C:GLU243 4.3 7.7 1.0 CA C:CYS250 4.3 9.0 1.0 N C:CYS250 4.3 8.7 1.0 O C:HOH332 4.3 10.0 1.0 O C:ARG252 4.4 9.5 1.0 CA C:PRO249 4.4 10.1 1.0 O C:HOH326 4.4 6.2 1.0 N C:GLY241 4.5 5.1 1.0 N C:ASP264 4.5 5.4 1.0 C C:CYS250 4.7 8.7 1.0 CA C:GLY241 4.7 5.3 1.0 CD1 C:TRP240 4.7 5.4 1.0 CA C:GLN262 4.7 5.2 1.0 N C:SER251 4.8 8.7 1.0 OD1 C:ASN261 4.8 7.0 1.0 N C:ARG252 4.9 8.3 1.0 N C:GLN262 4.9 5.2 1.0 CG C:TRP240 4.9 4.4 1.0 SG C:CYS277 5.0 9.4 1.0

Calcium binding site 8 out of 11 in the Structure of Ulilysin Mutant M290L


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of Ulilysin Mutant M290L within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca998 b:5.3 occ:1.00 OD1 C:ASP254 2.3 4.1 1.0 O C:THR259 2.4 6.1 1.0 O C:VAL256 2.4 5.4 1.0 O C:HOH355 2.4 4.9 1.0 O C:HOH567 2.5 10.5 1.0 O C:HOH365 2.5 12.8 1.0 OG1 C:THR259 2.6 5.6 1.0 O C:HOH404 2.6 8.4 1.0 CG C:ASP254 3.4 5.9 1.0 C C:THR259 3.4 5.4 1.0 C C:VAL256 3.6 5.4 1.0 CB C:THR259 3.6 5.0 1.0 OD2 C:ASP254 3.8 4.9 1.0 CA C:THR259 3.9 6.0 1.0 N C:THR259 4.1 5.7 1.0 N C:VAL256 4.1 5.9 1.0 O C:HOH647 4.3 22.6 1.0 CA C:VAL256 4.3 5.4 1.0 O C:PRO260 4.3 6.7 1.0 C C:PRO260 4.4 6.0 1.0 CB C:VAL256 4.5 5.0 1.0 N C:ASP254 4.5 7.0 1.0 O C:HOH523 4.5 18.9 1.0 N C:PRO260 4.6 6.0 1.0 N C:ASN261 4.6 6.5 1.0 CB C:ASP254 4.6 6.6 1.0 N C:ASP257 4.6 6.3 1.0 O C:HOH326 4.7 6.2 1.0 O C:ASP257 4.7 7.1 1.0 C C:ASP257 4.8 6.1 1.0 O C:HOH572 4.8 15.0 1.0 OG C:SER253 4.8 8.2 1.0 CA C:ASP257 4.8 6.7 1.0 O C:ILE239 4.9 5.0 1.0 CA C:PRO260 4.9 5.8 1.0 CA C:ASN261 4.9 5.9 1.0 CG2 C:THR259 4.9 5.7 1.0 CA C:ASP254 5.0 6.2 1.0 N C:GLU255 5.0 6.7 1.0

Calcium binding site 9 out of 11 in the Structure of Ulilysin Mutant M290L


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Structure of Ulilysin Mutant M290L within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca997 b:7.0 occ:1.00 O D:TRP240 2.3 5.8 1.0 O D:PRO249 2.3 10.1 1.0 O D:GLN262 2.4 6.2 1.0 O D:HOH398 2.4 11.2 1.0 OE2 D:GLU243 2.4 6.6 1.0 O D:ALA263 2.5 7.0 1.0 OE1 D:GLU243 2.5 6.6 1.0 CD D:GLU243 2.8 6.7 1.0 C D:ALA263 3.3 7.0 1.0 C D:TRP240 3.4 5.6 1.0 C D:GLN262 3.5 5.9 1.0 C D:PRO249 3.5 10.9 1.0 CA D:ALA263 3.6 7.0 1.0 N D:ALA263 4.0 6.8 1.0 CA D:TRP240 4.1 5.0 1.0 CB D:TRP240 4.2 4.7 1.0 O D:ARG252 4.3 9.3 1.0 CG D:GLU243 4.3 7.8 1.0 CA D:CYS250 4.3 10.3 1.0 N D:CYS250 4.3 10.4 1.0 O D:HOH790 4.4 8.2 1.0 O D:HOH342 4.4 8.5 1.0 CA D:PRO249 4.4 11.6 1.0 N D:GLY241 4.5 6.4 1.0 N D:ASP264 4.5 6.8 1.0 CD1 D:TRP240 4.7 6.9 1.0 CA D:GLY241 4.7 6.2 1.0 CA D:GLN262 4.7 6.1 1.0 C D:CYS250 4.7 10.2 1.0 N D:SER251 4.8 9.6 1.0 N D:ARG252 4.8 8.8 1.0 OD1 D:ASN261 4.8 10.2 1.0 N D:GLN262 4.8 6.1 1.0 CG D:TRP240 4.9 4.3 1.0 CB D:ALA263 5.0 7.4 1.0

Calcium binding site 10 out of 11 in the Structure of Ulilysin Mutant M290L


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Structure of Ulilysin Mutant M290L within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca998 b:6.0 occ:1.00 OD1 D:ASP254 2.3 5.5 1.0 O D:THR259 2.4 5.8 1.0 O D:VAL256 2.5 6.2 1.0 O D:HOH387 2.5 14.6 1.0 O D:HOH326 2.5 7.7 1.0 O D:HOH346 2.5 8.1 1.0 O D:HOH369 2.5 6.5 1.0 OG1 D:THR259 2.5 4.2 1.0 CG D:ASP254 3.4 6.2 1.0 C D:THR259 3.4 5.7 1.0 C D:VAL256 3.6 6.6 1.0 CB D:THR259 3.6 5.4 1.0 OD2 D:ASP254 3.8 5.5 1.0 CA D:THR259 3.9 5.7 1.0 N D:VAL256 4.1 6.7 1.0 N D:THR259 4.1 5.1 1.0 CA D:VAL256 4.3 6.6 1.0 O D:PRO260 4.4 7.6 1.0 O D:HOH556 4.4 19.4 1.0 C D:PRO260 4.4 7.0 1.0 CB D:VAL256 4.5 6.1 1.0 N D:ASP254 4.5 7.9 1.0 N D:PRO260 4.5 6.7 1.0 O D:HOH738 4.6 21.8 1.0 CB D:ASP254 4.6 7.5 1.0 N D:ASN261 4.7 7.5 1.0 N D:ASP257 4.7 6.5 1.0 O D:HOH342 4.7 8.5 1.0 O D:ASP257 4.8 7.5 1.0 C D:ASP257 4.8 6.7 1.0 OG D:SER253 4.8 9.7 1.0 CA D:ASP257 4.9 6.8 1.0 CG2 D:THR259 4.9 6.1 1.0 O D:ILE239 4.9 5.8 1.0 CA D:PRO260 4.9 6.8 1.0 CA D:ASP254 4.9 6.9 1.0 N D:GLU255 5.0 7.3 1.0 CA D:ASN261 5.0 7.3 1.0

C.Tallant, R.Garcia-Castellanos, U.Baumann, F.X.Gomis-Ruth. On the Relevance of the Met-Turn Methionine in Metzincins. J.Biol.Chem. V. 285 13951 2010.
ISSN: ISSN 0021-9258
PubMed: 20202937
DOI: 10.1074/JBC.M109.083378