Zinc in PDB 3a6j: E122Q Mutant Creatininase Complexed with Creatine

All present enzymatic activity of E122Q Mutant Creatininase Complexed with Creatine:
3.5.2.10;

The structure of E122Q Mutant Creatininase Complexed with Creatine, PDB code: 3a6j 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 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	102.200, 152.700, 166.900, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 21.2

The binding sites of Zinc atom in the E122Q Mutant Creatininase Complexed with Creatine (pdb code 3a6j). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the E122Q Mutant Creatininase Complexed with Creatine, PDB code: 3a6j:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the E122Q Mutant Creatininase Complexed with Creatine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of E122Q Mutant Creatininase Complexed with Creatine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:19.4 occ:1.00 OE1 A:GLU183 2.0 19.8 1.0 OD1 A:ASP45 2.0 17.5 1.0 NE2 A:HIS36 2.1 19.1 1.0 O8 A:CRN303 2.2 39.8 1.0 CD A:GLU183 2.7 18.5 1.0 OE2 A:GLU183 2.8 16.0 1.0 C7 A:CRN303 2.8 41.1 1.0 CG A:ASP45 2.9 18.0 1.0 CD2 A:HIS36 3.1 18.6 1.0 OD2 A:ASP45 3.1 18.7 1.0 CE1 A:HIS36 3.1 19.7 1.0 C5 A:CRN303 3.3 40.0 1.0 O9 A:CRN303 3.8 35.3 1.0 O A:HOH1049 3.9 19.7 1.0 ND1 A:HIS178 4.1 19.8 1.0 CG1 A:VAL44 4.2 18.2 1.0 CG A:GLU183 4.2 17.8 1.0 ND1 A:HIS36 4.2 18.7 1.0 CG A:HIS36 4.2 19.2 1.0 CE1 A:HIS178 4.2 18.5 1.0 CB A:ASP45 4.3 16.7 1.0 OE2 A:GLU34 4.4 18.2 1.0 O A:GLY119 4.5 15.2 1.0 N A:ASP45 4.5 16.3 1.0 CB A:VAL44 4.6 18.0 1.0 CA A:ASP45 4.6 16.9 1.0 N1 A:CRN303 4.8 39.7 1.0 O A:HOH1052 5.0 18.2 1.0

Zinc binding site 2 out of 6 in the E122Q Mutant Creatininase Complexed with Creatine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of E122Q Mutant Creatininase Complexed with Creatine within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:22.3 occ:1.00 OD1 B:ASP45 2.0 20.2 1.0 OE1 B:GLU183 2.0 19.6 1.0 NE2 B:HIS36 2.2 23.4 1.0 O8 B:CRN304 2.2 37.8 1.0 CD B:GLU183 2.8 20.6 1.0 OE2 B:GLU183 2.8 18.2 1.0 CG B:ASP45 2.9 20.3 1.0 C7 B:CRN304 2.9 41.9 1.0 OD2 B:ASP45 3.1 21.4 1.0 CD2 B:HIS36 3.1 22.2 1.0 CE1 B:HIS36 3.2 23.4 1.0 C5 B:CRN304 3.5 40.6 1.0 O9 B:CRN304 3.8 35.2 1.0 O B:HOH1080 3.8 19.5 1.0 ND1 B:HIS178 4.1 22.1 1.0 CG B:GLU183 4.2 21.1 1.0 CG1 B:VAL44 4.3 21.5 1.0 CE1 B:HIS178 4.3 22.2 1.0 CG B:HIS36 4.3 22.8 1.0 CB B:ASP45 4.3 20.4 1.0 ND1 B:HIS36 4.3 21.6 1.0 OE2 B:GLU34 4.4 21.1 1.0 O B:GLY119 4.4 16.7 1.0 N B:ASP45 4.5 20.0 1.0 CB B:VAL44 4.6 21.6 1.0 CA B:ASP45 4.6 19.5 1.0 N1 B:CRN304 4.7 39.0 1.0

Zinc binding site 3 out of 6 in the E122Q Mutant Creatininase Complexed with Creatine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of E122Q Mutant Creatininase Complexed with Creatine within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:22.3 occ:1.00 OD1 C:ASP45 2.1 19.1 1.0 OE1 C:GLU183 2.1 21.2 1.0 NE2 C:HIS36 2.2 19.9 1.0 O9 C:CRN305 2.2 42.0 1.0 CD C:GLU183 2.8 22.1 1.0 C7 C:CRN305 2.9 42.2 1.0 OE2 C:GLU183 2.9 21.1 1.0 CG C:ASP45 2.9 19.0 1.0 CE1 C:HIS36 3.1 20.6 1.0 OD2 C:ASP45 3.1 21.1 1.0 CD2 C:HIS36 3.2 20.7 1.0 C5 C:CRN305 3.2 40.4 1.0 O C:HOH1084 3.9 19.2 1.0 O8 C:CRN305 3.9 39.0 1.0 ND1 C:HIS178 4.1 22.2 1.0 CG1 C:VAL44 4.2 22.5 1.0 ND1 C:HIS36 4.2 21.6 1.0 CE1 C:HIS178 4.2 22.3 1.0 CG C:GLU183 4.2 20.6 1.0 CB C:ASP45 4.3 17.7 1.0 CG C:HIS36 4.3 20.0 1.0 OE2 C:GLU34 4.4 21.5 1.0 O C:GLY119 4.4 19.7 1.0 N C:ASP45 4.5 18.0 1.0 CB C:VAL44 4.6 20.7 1.0 N1 C:CRN305 4.7 39.2 1.0 CA C:ASP45 4.7 17.0 1.0

Zinc binding site 4 out of 6 in the E122Q Mutant Creatininase Complexed with Creatine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of E122Q Mutant Creatininase Complexed with Creatine within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:23.7 occ:1.00 OE1 D:GLU183 2.0 24.7 1.0 OD1 D:ASP45 2.1 24.7 1.0 O D:HOH1001 2.1 24.4 1.0 NE2 D:HIS36 2.2 23.0 1.0 CD D:GLU183 2.7 22.4 1.0 OE2 D:GLU183 2.8 21.3 1.0 CG D:ASP45 3.0 22.2 1.0 CD2 D:HIS36 3.1 20.1 1.0 OD2 D:ASP45 3.2 25.0 1.0 CE1 D:HIS36 3.2 21.5 1.0 O D:HOH1349 3.9 23.4 1.0 ND1 D:HIS178 4.0 20.4 1.0 O D:HOH1434 4.0 34.0 1.0 O D:HOH1078 4.1 20.8 1.0 CG D:GLU183 4.2 24.1 1.0 CG1 D:VAL44 4.2 21.5 1.0 CE1 D:HIS178 4.2 19.6 1.0 CG D:HIS36 4.3 21.9 1.0 ND1 D:HIS36 4.3 21.4 1.0 CB D:ASP45 4.4 21.3 1.0 O D:GLY119 4.4 20.8 1.0 OE2 D:GLU34 4.5 23.6 1.0 N D:ASP45 4.6 20.9 1.0 CB D:VAL44 4.6 20.8 1.0 CA D:ASP45 4.7 20.1 1.0

Zinc binding site 5 out of 6 in the E122Q Mutant Creatininase Complexed with Creatine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of E122Q Mutant Creatininase Complexed with Creatine within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn301 b:23.8 occ:1.00 OD1 E:ASP45 2.0 23.7 1.0 OE1 E:GLU183 2.1 23.1 1.0 NE2 E:HIS36 2.1 20.8 1.0 O8 E:CRN306 2.3 48.6 1.0 OE2 E:GLU183 2.7 22.6 1.0 CD E:GLU183 2.8 22.9 1.0 C7 E:CRN306 2.9 48.2 1.0 CG E:ASP45 2.9 23.7 1.0 OD2 E:ASP45 3.1 24.6 1.0 CE1 E:HIS36 3.1 21.2 1.0 CD2 E:HIS36 3.1 20.8 1.0 C5 E:CRN306 3.2 46.0 1.0 O9 E:CRN306 3.8 44.0 1.0 O E:HOH1144 3.8 22.1 1.0 ND1 E:HIS178 4.1 18.9 1.0 CG1 E:VAL44 4.1 21.5 1.0 ND1 E:HIS36 4.2 19.6 1.0 CG E:GLU183 4.2 23.7 1.0 CB E:ASP45 4.3 21.5 1.0 CG E:HIS36 4.3 19.4 1.0 CE1 E:HIS178 4.3 17.6 1.0 OE2 E:GLU34 4.4 19.6 1.0 O E:GLY119 4.4 19.4 1.0 N E:ASP45 4.5 21.2 1.0 CB E:VAL44 4.6 21.6 1.0 CA E:ASP45 4.7 20.1 1.0 N1 E:CRN306 4.7 44.2 1.0

Zinc binding site 6 out of 6 in the E122Q Mutant Creatininase Complexed with Creatine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of E122Q Mutant Creatininase Complexed with Creatine within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn301 b:21.6 occ:1.00 OD1 F:ASP45 2.0 19.6 1.0 OE2 F:GLU183 2.0 19.3 1.0 NE2 F:HIS36 2.1 18.6 1.0 O8 F:CRN307 2.3 44.9 1.0 CD F:GLU183 2.8 21.1 1.0 CG F:ASP45 2.9 20.2 1.0 OE1 F:GLU183 2.9 20.6 1.0 C7 F:CRN307 3.0 42.0 1.0 CD2 F:HIS36 3.1 20.5 1.0 OD2 F:ASP45 3.1 21.1 1.0 C5 F:CRN307 3.1 40.0 1.0 CE1 F:HIS36 3.1 19.8 1.0 O F:HOH1079 3.8 18.9 1.0 ND1 F:HIS178 4.1 21.6 1.0 O9 F:CRN307 4.1 38.7 1.0 CG1 F:VAL44 4.1 20.2 1.0 ND1 F:HIS36 4.2 18.5 1.0 CE1 F:HIS178 4.2 22.0 1.0 CG F:GLU183 4.2 20.1 1.0 CG F:HIS36 4.2 18.2 1.0 CB F:ASP45 4.3 19.3 1.0 OE2 F:GLU34 4.4 20.9 1.0 O F:GLY119 4.4 18.4 1.0 N F:ASP45 4.5 18.8 1.0 N1 F:CRN307 4.6 36.0 1.0 CB F:VAL44 4.6 18.6 1.0 CA F:ASP45 4.6 17.9 1.0 O F:HOH1047 4.9 18.5 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