Zinc in PDB 3a6f: W174F Mutant Creatininase, Type II

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

The structure of W174F Mutant Creatininase, Type II, PDB code: 3a6f 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 / 1.78
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	164.300, 164.300, 163.900, 90.00, 90.00, 120.00
R / Rfree (%)	23.5 / 25.7

The structure of W174F Mutant Creatininase, Type II 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 II (pdb code 3a6f). 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 II, PDB code: 3a6f:
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 II


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 II within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:27.9 occ:1.00 NE2 A:HIS36 2.1 17.5 1.0 OE1 A:GLU183 2.1 22.9 1.0 OD1 A:ASP45 2.2 24.3 1.0 O1 A:CAC303 2.2 39.4 1.0 OE2 A:GLU183 2.7 24.3 1.0 CD A:GLU183 2.7 24.2 1.0 CE1 A:HIS36 3.0 18.4 1.0 CG A:ASP45 3.1 19.8 1.0 CD2 A:HIS36 3.2 16.7 1.0 OD2 A:ASP45 3.3 19.4 1.0 AS A:CAC303 3.4 40.5 1.0 C1 A:CAC303 3.6 38.5 1.0 MN A:MN300 3.8 34.8 1.0 O A:HOH1113 4.0 22.9 1.0 ND1 A:HIS178 4.0 25.3 1.0 ND1 A:HIS36 4.1 18.7 1.0 CG A:GLU183 4.2 22.1 1.0 CG1 A:VAL44 4.2 19.4 1.0 O2 A:CAC303 4.2 40.9 1.0 CE1 A:HIS178 4.3 24.8 1.0 CG A:HIS36 4.3 17.0 1.0 OE1 A:GLU34 4.4 23.1 1.0 CB A:ASP45 4.4 17.2 1.0 N A:ASP45 4.6 17.9 1.0 CB A:VAL44 4.6 18.7 1.0 O A:GLY119 4.6 21.8 1.0 CA A:ASP45 4.8 18.1 1.0 O A:HOH1015 5.0 16.9 1.0

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


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 II within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:26.1 occ:1.00 OD1 B:ASP45 2.1 14.6 1.0 OE1 B:GLU183 2.1 25.2 1.0 NE2 B:HIS36 2.2 17.5 1.0 O1 B:CAC303 2.3 30.5 1.0 OE2 B:GLU183 2.6 24.6 1.0 CD B:GLU183 2.7 22.1 1.0 CG B:ASP45 3.1 19.0 1.0 CE1 B:HIS36 3.1 18.6 1.0 CD2 B:HIS36 3.1 19.7 1.0 AS B:CAC303 3.3 35.7 1.0 C1 B:CAC303 3.3 33.8 1.0 OD2 B:ASP45 3.4 22.6 1.0 MN B:MN300 3.7 39.6 1.0 ND1 B:HIS178 3.9 20.4 1.0 O B:HOH1100 4.0 22.6 1.0 O2 B:CAC303 4.1 30.8 1.0 CG B:GLU183 4.1 24.4 1.0 CE1 B:HIS178 4.2 20.7 1.0 ND1 B:HIS36 4.2 18.4 1.0 OE2 B:GLU34 4.3 17.8 1.0 CG B:HIS36 4.3 17.7 1.0 CG1 B:VAL44 4.4 20.7 1.0 CB B:ASP45 4.4 17.0 1.0 O B:GLY119 4.5 21.9 1.0 N B:ASP45 4.7 16.4 1.0 CA B:ASP45 4.7 17.5 1.0 CB B:VAL44 4.8 19.8 1.0 CB B:GLU183 5.0 20.9 1.0 C2 B:CAC303 5.0 35.5 1.0

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


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 II within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:25.3 occ:1.00 OE2 C:GLU183 2.1 18.4 1.0 OD1 C:ASP45 2.1 18.9 1.0 O2 C:CAC303 2.1 37.3 1.0 NE2 C:HIS36 2.2 20.0 1.0 CD C:GLU183 2.8 19.9 1.0 OE1 C:GLU183 2.8 19.1 1.0 CG C:ASP45 3.1 19.5 1.0 CD2 C:HIS36 3.1 19.1 1.0 CE1 C:HIS36 3.1 18.9 1.0 AS C:CAC303 3.4 37.5 1.0 OD2 C:ASP45 3.4 15.6 1.0 C2 C:CAC303 3.7 38.0 1.0 MN C:MN300 3.7 31.9 1.0 O C:HOH1046 3.9 23.5 1.0 ND1 C:HIS178 4.0 20.7 1.0 O1 C:CAC303 4.1 40.0 1.0 CG1 C:VAL44 4.2 17.8 1.0 CG C:GLU183 4.2 18.4 1.0 ND1 C:HIS36 4.3 18.2 1.0 CE1 C:HIS178 4.3 19.4 1.0 CG C:HIS36 4.3 17.1 1.0 OE1 C:GLU34 4.3 25.6 1.0 O C:GLY119 4.4 19.9 1.0 CB C:ASP45 4.4 17.7 1.0 N C:ASP45 4.6 17.9 1.0 CA C:ASP45 4.7 17.2 1.0 CB C:VAL44 4.7 17.7 1.0 O C:HOH1026 4.9 14.8 1.0 C1 C:CAC303 5.0 35.4 1.0

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


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 II within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:26.7 occ:1.00 OE1 D:GLU183 2.1 22.4 1.0 NE2 D:HIS36 2.1 18.2 1.0 OD1 D:ASP45 2.2 17.5 1.0 O2 D:CAC303 2.2 32.1 1.0 OE2 D:GLU183 2.7 22.8 1.0 CD D:GLU183 2.7 23.2 1.0 CD2 D:HIS36 3.0 19.5 1.0 CG D:ASP45 3.1 21.5 1.0 CE1 D:HIS36 3.2 18.6 1.0 C2 D:CAC303 3.2 33.1 1.0 AS D:CAC303 3.3 36.7 1.0 OD2 D:ASP45 3.4 24.1 1.0 MN D:MN300 3.8 40.0 1.0 ND1 D:HIS178 3.9 22.3 1.0 O D:HOH1149 4.0 25.7 1.0 CE1 D:HIS178 4.1 23.1 1.0 CG1 D:VAL44 4.2 18.8 1.0 CG D:GLU183 4.2 23.5 1.0 CG D:HIS36 4.2 19.9 1.0 O1 D:CAC303 4.2 34.5 1.0 ND1 D:HIS36 4.3 19.9 1.0 OE2 D:GLU34 4.4 20.5 1.0 CB D:ASP45 4.5 18.8 1.0 O D:GLY119 4.5 19.1 1.0 N D:ASP45 4.6 16.9 1.0 CB D:VAL44 4.6 20.0 1.0 CA D:ASP45 4.7 18.3 1.0 C1 D:CAC303 4.9 35.1 1.0

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


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 II within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn301 b:25.7 occ:1.00 NE2 E:HIS36 2.1 17.0 1.0 OE1 E:GLU183 2.1 19.2 1.0 OD1 E:ASP45 2.1 14.9 1.0 O2 E:CAC303 2.2 34.6 1.0 CD E:GLU183 2.8 20.6 1.0 OE2 E:GLU183 2.8 19.0 1.0 CE1 E:HIS36 3.0 15.9 1.0 CG E:ASP45 3.0 15.5 1.0 CD2 E:HIS36 3.1 14.8 1.0 OD2 E:ASP45 3.3 16.3 1.0 AS E:CAC303 3.4 36.3 1.0 C2 E:CAC303 3.6 34.9 1.0 MN E:MN300 3.8 33.8 1.0 O E:HOH1118 3.9 22.0 1.0 ND1 E:HIS178 4.0 19.0 1.0 CG1 E:VAL44 4.0 15.6 1.0 O1 E:CAC303 4.1 37.4 1.0 ND1 E:HIS36 4.1 16.1 1.0 CE1 E:HIS178 4.2 18.6 1.0 CG E:HIS36 4.2 16.3 1.0 OE1 E:GLU34 4.2 19.4 1.0 CG E:GLU183 4.2 19.6 1.0 CB E:ASP45 4.4 14.5 1.0 N E:ASP45 4.5 15.2 1.0 CB E:VAL44 4.6 15.6 1.0 O E:GLY119 4.6 18.6 1.0 CA E:ASP45 4.7 15.8 1.0 C1 E:CAC303 5.0 34.2 1.0

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


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 II within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn301 b:24.2 occ:1.00 OE1 F:GLU183 2.1 18.6 1.0 OD1 F:ASP45 2.1 17.7 1.0 NE2 F:HIS36 2.1 15.8 1.0 O2 F:CAC303 2.2 26.7 1.0 OE2 F:GLU183 2.6 19.1 1.0 CD F:GLU183 2.7 19.1 1.0 CG F:ASP45 3.0 17.1 1.0 CE1 F:HIS36 3.1 18.8 1.0 CD2 F:HIS36 3.2 18.3 1.0 C2 F:CAC303 3.2 30.6 1.0 OD2 F:ASP45 3.2 18.8 1.0 AS F:CAC303 3.3 35.0 1.0 MN F:MN300 3.7 36.1 1.0 ND1 F:HIS178 4.0 18.3 1.0 O F:HOH1122 4.0 23.2 1.0 CG F:GLU183 4.1 18.7 1.0 CG1 F:VAL44 4.2 18.6 1.0 CE1 F:HIS178 4.2 19.9 1.0 ND1 F:HIS36 4.2 19.4 1.0 O1 F:CAC303 4.2 31.7 1.0 OE2 F:GLU34 4.3 18.0 1.0 CG F:HIS36 4.3 17.9 1.0 CB F:ASP45 4.4 17.6 1.0 O F:GLY119 4.5 18.8 1.0 N F:ASP45 4.7 17.5 1.0 CA F:ASP45 4.7 17.6 1.0 C1 F:CAC303 4.8 32.9 1.0 CB F:VAL44 4.8 19.4 1.0 O F:HOH1006 4.9 19.5 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