Zinc 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:

Calcium

(Ca)

11 atoms

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

Zinc binding site 1 out of 4 in the Structure of Ulilysin Mutant M290L


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Ulilysin Mutant M290L within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn999 b:6.7 occ:1.00 NE2 A:HIS238 2.0 4.2 1.0 NE2 A:HIS232 2.0 5.8 1.0 NE2 A:HIS228 2.0 6.4 1.0 O A:HOH1421 2.3 7.2 1.0 CE1 A:HIS238 2.9 5.7 1.0 CD2 A:HIS238 2.9 3.0 1.0 CE1 A:HIS232 3.0 5.8 1.0 CD2 A:HIS228 3.0 3.5 1.0 CE1 A:HIS228 3.0 5.2 1.0 CD2 A:HIS232 3.1 5.5 1.0 CE1 A:TYR292 3.9 9.0 1.0 ND1 A:HIS238 4.0 5.4 1.0 CG A:HIS238 4.1 4.8 1.0 ND1 A:HIS228 4.1 5.2 1.0 ND1 A:HIS232 4.1 3.6 1.0 CG A:HIS228 4.1 5.5 1.0 CG A:HIS232 4.2 3.9 1.0 OH A:TYR292 4.2 11.9 1.0 OE2 A:GLU229 4.3 12.0 1.0 OE1 A:GLU229 4.4 7.7 1.0 O A:HOH1434 4.4 18.7 1.0 O A:HOH495 4.5 19.1 1.0 CZ A:TYR292 4.5 9.4 1.0 N A:ARG501 4.5 28.5 1.0 CA A:ARG501 4.6 28.5 1.0 CD A:GLU229 4.7 8.0 1.0 CD1 A:TYR292 4.9 8.9 1.0 O A:HOH1375 5.0 29.5 1.0

Zinc binding site 2 out of 4 in the Structure of Ulilysin Mutant M290L


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Ulilysin Mutant M290L within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn999 b:6.2 occ:1.00 NE2 B:HIS238 2.0 3.9 1.0 NE2 B:HIS232 2.0 4.3 1.0 NE2 B:HIS228 2.0 4.6 1.0 O B:HOH1422 2.3 7.1 1.0 CD2 B:HIS238 2.9 4.1 1.0 CE1 B:HIS238 3.0 4.7 1.0 CD2 B:HIS228 3.0 3.1 1.0 CE1 B:HIS232 3.0 4.0 1.0 CE1 B:HIS228 3.0 4.8 1.0 CD2 B:HIS232 3.0 4.2 1.0 CE1 B:TYR292 3.9 7.4 1.0 ND1 B:HIS238 4.1 3.7 1.0 CG B:HIS238 4.1 4.3 1.0 ND1 B:HIS228 4.1 5.0 1.0 ND1 B:HIS232 4.1 3.9 1.0 CG B:HIS228 4.1 3.6 1.0 CG B:HIS232 4.2 3.6 1.0 OH B:TYR292 4.3 11.1 1.0 OE2 B:GLU229 4.3 9.8 1.0 O B:HOH1426 4.4 17.6 1.0 OE1 B:GLU229 4.5 8.4 1.0 O B:HOH805 4.5 20.9 1.0 N B:ARG501 4.5 31.9 1.0 CA B:ARG501 4.6 31.4 1.0 CZ B:TYR292 4.6 8.8 1.0 CD B:GLU229 4.7 7.8 1.0 CB B:ARG501 4.9 31.3 1.0 CD1 B:TYR292 4.9 7.5 1.0

Zinc binding site 3 out of 4 in the Structure of Ulilysin Mutant M290L


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Ulilysin Mutant M290L within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn999 b:6.5 occ:1.00 NE2 C:HIS238 2.0 3.7 1.0 NE2 C:HIS232 2.0 5.0 1.0 NE2 C:HIS228 2.0 4.5 1.0 O C:HOH1423 2.3 6.9 1.0 CD2 C:HIS228 2.9 3.6 1.0 CD2 C:HIS238 3.0 4.7 1.0 CE1 C:HIS232 3.0 4.9 1.0 CE1 C:HIS238 3.0 6.2 1.0 CD2 C:HIS232 3.0 6.1 1.0 CE1 C:HIS228 3.1 5.2 1.0 CE1 C:TYR292 4.0 7.8 1.0 ND1 C:HIS238 4.1 5.1 1.0 CG C:HIS238 4.1 3.4 1.0 CG C:HIS228 4.1 5.5 1.0 ND1 C:HIS232 4.1 4.3 1.0 ND1 C:HIS228 4.1 5.2 1.0 CG C:HIS232 4.2 5.3 1.0 OH C:TYR292 4.3 11.5 1.0 OE2 C:GLU229 4.3 10.0 1.0 OE1 C:GLU229 4.5 8.8 1.0 N C:ARG501 4.5 32.1 1.0 CA C:ARG501 4.6 32.2 1.0 O C:HOH864 4.6 24.6 1.0 CZ C:TYR292 4.6 9.3 1.0 CD C:GLU229 4.7 7.2 1.0 CD1 C:TYR292 4.9 5.3 1.0 O C:HOH784 5.0 23.6 1.0

Zinc binding site 4 out of 4 in the Structure of Ulilysin Mutant M290L


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Ulilysin Mutant M290L within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn999 b:5.9 occ:1.00 NE2 D:HIS238 2.0 4.3 1.0 NE2 D:HIS228 2.0 4.7 1.0 NE2 D:HIS232 2.1 4.0 1.0 O D:HOH1424 2.3 7.6 1.0 CD2 D:HIS238 3.0 4.4 1.0 CD2 D:HIS228 3.0 2.3 1.0 CE1 D:HIS238 3.0 4.8 1.0 CE1 D:HIS232 3.0 4.4 1.0 CE1 D:HIS228 3.0 6.2 1.0 CD2 D:HIS232 3.1 3.7 1.0 CE1 D:TYR292 3.9 8.1 1.0 ND1 D:HIS238 4.1 4.7 1.0 CG D:HIS238 4.1 4.3 1.0 ND1 D:HIS228 4.1 5.6 1.0 CG D:HIS228 4.1 4.0 1.0 ND1 D:HIS232 4.1 4.6 1.0 CG D:HIS232 4.2 3.9 1.0 OH D:TYR292 4.2 12.4 1.0 O D:HOH628 4.4 23.1 1.0 O D:HOH1429 4.4 16.9 1.0 OE2 D:GLU229 4.4 9.1 1.0 OE1 D:GLU229 4.5 9.1 1.0 N D:ARG501 4.5 31.8 1.0 CZ D:TYR292 4.5 8.7 1.0 CA D:ARG501 4.6 31.4 1.0 CD D:GLU229 4.8 7.6 1.0 CD1 D:TYR292 4.9 9.2 1.0 CB D:ARG501 5.0 30.8 1.0 O D:HOH1291 5.0 30.5 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