Zinc in PDB 3a6e: W174F Mutant Creatininase, Type I

All present enzymatic activity of W174F Mutant Creatininase, Type I:
3.5.2.10;

The structure of W174F Mutant Creatininase, Type I, PDB code: 3a6e was solved by Y.Nakajima, K.Yamashita, K.Ito, T.Yoshimoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	105.900, 59.700, 145.100, 90.00, 99.70, 90.00
R / Rfree (%)	19.6 / 22.9

The structure of W174F Mutant Creatininase, Type I also contains other interesting chemical elements:

Arsenic	(As)	6 atoms
Manganese	(Mn)	6 atoms

The binding sites of Zinc atom in the W174F Mutant Creatininase, Type I (pdb code 3a6e). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the W174F Mutant Creatininase, Type I, PDB code: 3a6e:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the W174F Mutant Creatininase, Type I


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of W174F Mutant Creatininase, Type I within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:18.0 occ:1.00 OE1 A:GLU183 2.1 15.7 1.0 O2 A:CAC302 2.1 21.6 1.0 OD1 A:ASP45 2.1 11.8 1.0 NE2 A:HIS36 2.1 10.9 1.0 CD A:GLU183 2.8 18.9 1.0 OE2 A:GLU183 2.8 15.7 1.0 CE1 A:HIS36 3.0 13.4 1.0 CG A:ASP45 3.1 13.0 1.0 CD2 A:HIS36 3.1 10.8 1.0 AS A:CAC302 3.3 27.5 1.0 OD2 A:ASP45 3.4 11.9 1.0 C2 A:CAC302 3.4 22.3 1.0 MN A:MN300 3.7 29.1 1.0 ND1 A:HIS178 3.9 14.0 1.0 O A:HOH1165 3.9 18.4 1.0 O1 A:CAC302 4.1 23.9 1.0 CE1 A:HIS178 4.2 13.7 1.0 ND1 A:HIS36 4.2 11.6 1.0 CG A:GLU183 4.2 18.4 1.0 CG1 A:VAL44 4.2 12.1 1.0 OE1 A:GLU34 4.2 14.5 1.0 CG A:HIS36 4.3 12.6 1.0 CB A:ASP45 4.4 10.5 1.0 O A:GLY119 4.5 12.7 1.0 N A:ASP45 4.6 13.3 1.0 CA A:ASP45 4.7 11.8 1.0 CB A:VAL44 4.7 14.5 1.0 C1 A:CAC302 4.9 22.8 1.0

Zinc binding site 2 out of 6 in the W174F Mutant Creatininase, Type I


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of W174F Mutant Creatininase, Type I within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:19.9 occ:1.00 O2 B:CAC303 2.1 23.9 1.0 OD1 B:ASP45 2.1 14.4 1.0 NE2 B:HIS36 2.1 11.5 1.0 OE1 B:GLU183 2.1 16.6 1.0 CD B:GLU183 2.8 17.8 1.0 OE2 B:GLU183 2.8 16.4 1.0 CG B:ASP45 3.0 14.5 1.0 CD2 B:HIS36 3.1 12.4 1.0 CE1 B:HIS36 3.1 13.9 1.0 OD2 B:ASP45 3.2 13.7 1.0 AS B:CAC303 3.3 27.6 1.0 C2 B:CAC303 3.4 26.4 1.0 MN B:MN300 3.7 30.7 1.0 ND1 B:HIS178 3.8 14.6 1.0 O B:HOH1189 3.9 18.3 1.0 CE1 B:HIS178 4.1 16.9 1.0 O1 B:CAC303 4.1 25.7 1.0 OE2 B:GLU34 4.2 15.5 1.0 ND1 B:HIS36 4.2 12.9 1.0 CG B:HIS36 4.2 12.9 1.0 CG1 B:VAL44 4.2 14.1 1.0 CG B:GLU183 4.3 16.6 1.0 CB B:ASP45 4.4 15.0 1.0 O B:GLY119 4.6 12.3 1.0 N B:ASP45 4.6 13.3 1.0 CB B:VAL44 4.6 14.1 1.0 CA B:ASP45 4.7 13.9 1.0 C1 B:CAC303 4.8 25.2 1.0

Zinc binding site 3 out of 6 in the W174F Mutant Creatininase, Type I


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of W174F Mutant Creatininase, Type I within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:23.4 occ:1.00 OD1 C:ASP45 2.1 18.3 1.0 O1 C:CAC304 2.1 26.1 1.0 OE1 C:GLU183 2.2 21.9 1.0 NE2 C:HIS36 2.2 15.0 1.0 OE2 C:GLU183 2.8 20.2 1.0 CD C:GLU183 2.8 21.6 1.0 CG C:ASP45 3.1 19.5 1.0 CD2 C:HIS36 3.1 16.6 1.0 CE1 C:HIS36 3.2 16.8 1.0 AS C:CAC304 3.3 31.8 1.0 OD2 C:ASP45 3.3 16.9 1.0 C1 C:CAC304 3.5 30.0 1.0 MN C:MN300 3.8 36.6 1.0 O C:HOH1234 3.9 21.2 1.0 ND1 C:HIS178 3.9 21.2 1.0 O2 C:CAC304 4.1 31.6 1.0 CE1 C:HIS178 4.2 22.6 1.0 CG1 C:VAL44 4.2 15.4 1.0 OE2 C:GLU34 4.2 17.4 1.0 ND1 C:HIS36 4.3 18.1 1.0 CG C:GLU183 4.3 22.5 1.0 CG C:HIS36 4.3 16.8 1.0 CB C:ASP45 4.4 17.4 1.0 O C:GLY119 4.6 18.6 1.0 N C:ASP45 4.6 16.0 1.0 CB C:VAL44 4.7 16.4 1.0 CA C:ASP45 4.7 17.4 1.0 C2 C:CAC304 5.0 29.8 1.0

Zinc binding site 4 out of 6 in the W174F Mutant Creatininase, Type I


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of W174F Mutant Creatininase, Type I within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:22.3 occ:1.00 OD1 D:ASP45 2.1 14.3 1.0 OE1 D:GLU183 2.1 15.9 1.0 NE2 D:HIS36 2.1 13.7 1.0 O1 D:CAC305 2.1 25.0 1.0 CD D:GLU183 2.8 19.0 1.0 OE2 D:GLU183 2.8 18.0 1.0 CG D:ASP45 3.0 15.2 1.0 CD2 D:HIS36 3.1 15.7 1.0 CE1 D:HIS36 3.1 17.2 1.0 AS D:CAC305 3.3 30.8 1.0 OD2 D:ASP45 3.3 14.8 1.0 C1 D:CAC305 3.5 27.1 1.0 MN D:MN300 3.6 32.8 1.0 ND1 D:HIS178 3.9 14.4 1.0 O D:HOH1184 3.9 18.9 1.0 O2 D:CAC305 4.1 29.6 1.0 CE1 D:HIS178 4.1 14.3 1.0 ND1 D:HIS36 4.2 15.0 1.0 CG D:GLU183 4.2 17.6 1.0 CG D:HIS36 4.2 15.9 1.0 OE2 D:GLU34 4.3 19.4 1.0 CG1 D:VAL44 4.3 13.3 1.0 CB D:ASP45 4.4 14.4 1.0 O D:GLY119 4.5 17.4 1.0 N D:ASP45 4.6 15.1 1.0 CA D:ASP45 4.7 14.9 1.0 CB D:VAL44 4.7 16.0 1.0 C2 D:CAC305 4.9 27.7 1.0

Zinc binding site 5 out of 6 in the W174F Mutant Creatininase, Type I


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of W174F Mutant Creatininase, Type I within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn301 b:27.2 occ:1.00 NE2 E:HIS36 2.1 21.8 1.0 OE1 E:GLU183 2.1 31.8 1.0 OD1 E:ASP45 2.2 23.7 1.0 O2 E:CAC306 2.2 35.5 1.0 OE2 E:GLU183 2.7 30.5 1.0 CD E:GLU183 2.8 31.5 1.0 CE1 E:HIS36 3.1 21.8 1.0 CG E:ASP45 3.1 22.1 1.0 CD2 E:HIS36 3.1 22.7 1.0 OD2 E:ASP45 3.4 22.6 1.0 AS E:CAC306 3.4 40.5 1.0 C2 E:CAC306 3.5 39.6 1.0 MN E:MN300 3.8 41.4 1.0 ND1 E:HIS178 3.9 29.8 1.0 O E:HOH1305 3.9 23.0 1.0 CG1 E:VAL44 4.1 21.4 1.0 CE1 E:HIS178 4.2 27.8 1.0 ND1 E:HIS36 4.2 22.7 1.0 CG E:GLU183 4.2 30.7 1.0 CG E:HIS36 4.3 22.8 1.0 O1 E:CAC306 4.3 40.4 1.0 OE2 E:GLU34 4.4 22.0 1.0 CB E:ASP45 4.4 19.3 1.0 O E:GLY119 4.5 19.6 1.0 N E:ASP45 4.5 20.0 1.0 CB E:VAL44 4.6 19.8 1.0 CA E:ASP45 4.7 19.6 1.0 C1 E:CAC306 5.0 38.4 1.0

Zinc binding site 6 out of 6 in the W174F Mutant Creatininase, Type I


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of W174F Mutant Creatininase, Type I within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn301 b:26.1 occ:1.00 NE2 F:HIS36 2.1 19.4 1.0 OD1 F:ASP45 2.2 23.0 1.0 OE2 F:GLU183 2.2 27.0 1.0 O2 F:CAC307 2.3 35.3 1.0 OE1 F:GLU183 2.7 25.1 1.0 CD F:GLU183 2.8 26.2 1.0 CE1 F:HIS36 3.1 19.9 1.0 CD2 F:HIS36 3.1 19.5 1.0 CG F:ASP45 3.1 22.2 1.0 OD2 F:ASP45 3.4 21.5 1.0 C2 F:CAC307 3.4 37.3 1.0 AS F:CAC307 3.4 39.5 1.0 MN F:MN300 3.8 45.8 1.0 ND1 F:HIS178 3.9 23.3 1.0 O F:HOH1290 4.0 22.2 1.0 CG1 F:VAL44 4.1 23.5 1.0 CE1 F:HIS178 4.2 19.5 1.0 ND1 F:HIS36 4.2 20.0 1.0 CG F:HIS36 4.2 19.4 1.0 CG F:GLU183 4.3 27.0 1.0 O1 F:CAC307 4.3 39.1 1.0 OE2 F:GLU34 4.4 21.9 1.0 CB F:ASP45 4.5 20.0 1.0 O F:GLY119 4.6 21.0 1.0 N F:ASP45 4.6 19.8 1.0 CB F:VAL44 4.6 20.3 1.0 CA F:ASP45 4.7 19.4 1.0 C1 F:CAC307 5.0 37.8 1.0 O F:HOH1148 5.0 17.0 1.0

K.Yamashita, Y.Nakajima, H.Matsushita, Y.Nishiya, R.Yamazawa, Y.F.Wu, F.Matsubara, H.Oyama, K.Ito, T.Yoshimoto. Substitution of GLU122 By Glutamine Revealed the Function of the Second Water Molecule As A Proton Donor in the Binuclear Metal Enzyme Creatininase J.Mol.Biol. V. 396 1081 2010.
ISSN: ISSN 0022-2836
PubMed: 20043918
DOI: 10.1016/J.JMB.2009.12.045