Zinc in PDB 3a6h: W154A Mutant Creatininase

All present enzymatic activity of W154A Mutant Creatininase:
3.5.2.10;

The structure of W154A Mutant Creatininase, PDB code: 3a6h 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 (°)	106.800, 60.240, 146.200, 90.00, 100.30, 90.00
R / Rfree (%)	19.9 / 23.1

The structure of W154A Mutant Creatininase also contains other interesting chemical elements:

Manganese	(Mn)	6 atoms
Chlorine	(Cl)	6 atoms

The binding sites of Zinc atom in the W154A Mutant Creatininase (pdb code 3a6h). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the W154A Mutant Creatininase, PDB code: 3a6h:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the W154A Mutant Creatininase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of W154A Mutant Creatininase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:33.1 occ:1.00 OE1 A:GLU183 2.2 25.2 1.0 NE2 A:HIS36 2.2 13.9 1.0 OD1 A:ASP45 2.2 17.0 1.0 CD A:GLU183 2.9 23.0 1.0 OE2 A:GLU183 3.0 23.3 1.0 CG A:ASP45 3.2 17.4 1.0 CE1 A:HIS36 3.2 16.7 1.0 CD2 A:HIS36 3.2 16.0 1.0 CL A:CL302 3.3 33.3 1.0 OD2 A:ASP45 3.4 18.5 1.0 MN A:MN300 3.5 36.3 1.0 ND1 A:HIS178 3.8 19.7 1.0 CE1 A:HIS178 4.1 18.0 1.0 O A:HOH1234 4.1 25.7 1.0 OE2 A:GLU34 4.3 21.3 1.0 ND1 A:HIS36 4.3 14.9 1.0 CG A:GLU183 4.4 24.3 1.0 CG A:HIS36 4.4 17.2 1.0 O A:GLY119 4.4 23.6 1.0 CG1 A:VAL44 4.4 17.4 1.0 CB A:ASP45 4.5 17.8 1.0 N A:ASP45 4.8 19.0 1.0 CA A:ASP45 4.9 17.7 1.0 O A:HOH1001 4.9 19.7 1.0 CB A:VAL44 5.0 19.4 1.0

Zinc binding site 2 out of 6 in the W154A Mutant Creatininase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of W154A Mutant Creatininase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:33.8 occ:1.00 OE1 B:GLU183 2.1 23.3 1.0 OD1 B:ASP45 2.2 18.6 1.0 NE2 B:HIS36 2.2 16.2 1.0 CD B:GLU183 2.9 23.8 1.0 OE2 B:GLU183 3.0 22.9 1.0 CG B:ASP45 3.1 18.7 1.0 CD2 B:HIS36 3.1 15.3 1.0 CE1 B:HIS36 3.2 18.0 1.0 CL B:CL303 3.3 32.0 1.0 OD2 B:ASP45 3.3 18.0 1.0 MN B:MN300 3.6 39.0 1.0 O B:HOH1184 4.0 31.6 1.0 ND1 B:HIS178 4.0 22.5 1.0 CE1 B:HIS178 4.2 21.3 1.0 CG B:HIS36 4.3 16.4 1.0 ND1 B:HIS36 4.3 16.6 1.0 O B:GLY119 4.3 27.4 1.0 OE2 B:GLU34 4.3 21.3 1.0 CG B:GLU183 4.4 23.0 1.0 CG1 B:VAL44 4.4 17.1 1.0 CB B:ASP45 4.5 18.0 1.0 N B:ASP45 4.8 18.2 1.0 CA B:ASP45 4.8 18.4 1.0 CB B:VAL44 4.9 19.7 1.0

Zinc binding site 3 out of 6 in the W154A Mutant Creatininase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of W154A Mutant Creatininase within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:37.7 occ:1.00 OE1 C:GLU183 2.2 29.9 1.0 NE2 C:HIS36 2.2 21.9 1.0 OD2 C:ASP45 2.2 23.2 1.0 CD C:GLU183 2.9 27.2 1.0 OE2 C:GLU183 2.9 29.2 1.0 CE1 C:HIS36 3.2 22.3 1.0 CG C:ASP45 3.2 23.4 1.0 CD2 C:HIS36 3.2 21.8 1.0 CL C:CL304 3.3 29.4 1.0 OD1 C:ASP45 3.4 23.2 1.0 MN C:MN300 3.5 44.6 1.0 ND1 C:HIS178 3.8 27.3 1.0 O C:HOH1314 4.0 38.8 1.0 CE1 C:HIS178 4.1 26.9 1.0 ND1 C:HIS36 4.3 21.8 1.0 CG C:HIS36 4.3 22.0 1.0 CG C:GLU183 4.4 27.3 1.0 OE2 C:GLU34 4.4 23.6 1.0 O C:GLY119 4.4 32.3 1.0 CG1 C:VAL44 4.5 20.4 1.0 CB C:ASP45 4.6 21.2 1.0 N C:ASP45 4.8 20.9 1.0 CA C:ASP45 4.9 22.7 1.0 CB C:VAL44 5.0 22.1 1.0

Zinc binding site 4 out of 6 in the W154A Mutant Creatininase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of W154A Mutant Creatininase within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:35.2 occ:1.00 OE1 D:GLU183 2.1 25.6 1.0 OD1 D:ASP45 2.2 20.1 1.0 NE2 D:HIS36 2.3 15.3 1.0 CD D:GLU183 3.0 23.9 1.0 OE2 D:GLU183 3.1 26.3 1.0 CG D:ASP45 3.2 19.5 1.0 CD2 D:HIS36 3.2 17.4 1.0 CE1 D:HIS36 3.2 17.4 1.0 CL D:CL305 3.2 35.1 1.0 OD2 D:ASP45 3.4 20.4 1.0 MN D:MN300 3.5 38.7 1.0 ND1 D:HIS178 3.7 22.0 1.0 O D:HOH1262 4.0 30.6 1.0 CE1 D:HIS178 4.0 23.1 1.0 O D:GLY119 4.3 26.2 1.0 OE2 D:GLU34 4.3 22.9 1.0 ND1 D:HIS36 4.4 17.8 1.0 CG1 D:VAL44 4.4 20.1 1.0 CG D:HIS36 4.4 18.5 1.0 CG D:GLU183 4.4 24.1 1.0 CB D:ASP45 4.5 19.7 1.0 N D:ASP45 4.8 19.4 1.0 CA D:ASP45 4.8 18.6 1.0 O D:HOH1004 4.9 17.8 1.0 CB D:VAL44 4.9 20.1 1.0

Zinc binding site 5 out of 6 in the W154A Mutant Creatininase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of W154A Mutant Creatininase within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn301 b:45.4 occ:1.00 NE2 E:HIS36 2.3 29.9 1.0 OD1 E:ASP45 2.3 30.3 1.0 OE1 E:GLU183 2.3 36.2 1.0 CD E:GLU183 3.0 37.4 1.0 OE2 E:GLU183 3.0 38.0 1.0 CG E:ASP45 3.1 27.9 1.0 CL E:CL306 3.2 37.7 1.0 CE1 E:HIS36 3.2 29.9 1.0 OD2 E:ASP45 3.2 28.6 1.0 CD2 E:HIS36 3.3 29.5 1.0 MN E:MN300 3.6 54.9 1.0 ND1 E:HIS178 3.8 36.7 1.0 CE1 E:HIS178 4.0 35.1 1.0 CG1 E:VAL44 4.3 27.8 1.0 ND1 E:HIS36 4.3 30.6 1.0 CG E:HIS36 4.4 30.0 1.0 OE2 E:GLU34 4.4 26.4 1.0 CG E:GLU183 4.5 37.4 1.0 O E:GLY119 4.5 30.5 1.0 CB E:ASP45 4.5 27.4 1.0 N E:ASP45 4.8 25.0 1.0 CA E:ASP45 4.9 25.3 1.0 CB E:VAL44 4.9 24.3 1.0

Zinc binding site 6 out of 6 in the W154A Mutant Creatininase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of W154A Mutant Creatininase within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn301 b:45.7 occ:1.00 NE2 F:HIS36 2.2 27.9 1.0 OD2 F:ASP45 2.3 29.1 1.0 OE1 F:GLU183 2.3 32.8 1.0 OE2 F:GLU183 3.0 33.5 1.0 CD F:GLU183 3.0 33.5 1.0 CE1 F:HIS36 3.0 27.1 1.0 CG F:ASP45 3.2 28.7 1.0 CL F:CL307 3.2 47.7 1.0 CD2 F:HIS36 3.3 28.7 1.0 OD1 F:ASP45 3.3 29.5 1.0 MN F:MN300 3.6 52.1 1.0 ND1 F:HIS178 3.9 35.1 1.0 CE1 F:HIS178 4.2 32.5 1.0 O F:HOH1753 4.2 40.1 1.0 ND1 F:HIS36 4.2 30.9 1.0 O F:GLY119 4.4 32.4 1.0 CG F:HIS36 4.4 29.4 1.0 CG F:GLU183 4.5 32.5 1.0 CG1 F:VAL44 4.5 29.4 1.0 OE2 F:GLU34 4.5 28.7 1.0 CB F:ASP45 4.5 27.1 1.0 N F:ASP45 4.8 25.8 1.0 CB F:VAL44 4.8 26.7 1.0 CA F:ASP45 4.9 25.5 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