Zinc in PDB 3a6l: E122Q Mutant Creatininase, Zn-Zn Type

All present enzymatic activity of E122Q Mutant Creatininase, Zn-Zn Type:
3.5.2.10;

The structure of E122Q Mutant Creatininase, Zn-Zn Type, PDB code: 3a6l 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 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	164.400, 164.400, 164.600, 90.00, 90.00, 120.00
R / Rfree (%)	23.5 / 25.9

The structure of E122Q Mutant Creatininase, Zn-Zn Type also contains other interesting chemical elements:

Chlorine

(Cl)

6 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the E122Q Mutant Creatininase, Zn-Zn Type (pdb code 3a6l). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the E122Q Mutant Creatininase, Zn-Zn Type, PDB code: 3a6l:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in the E122Q Mutant Creatininase, Zn-Zn Type


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, Zn-Zn Type within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn300 b:26.1 occ:1.00 OD2 A:ASP45 2.0 22.8 1.0 OE1 A:GLU34 2.0 20.4 1.0 ND1 A:HIS120 2.2 23.3 1.0 CD A:GLU34 2.9 22.6 1.0 CL A:CL302 3.0 36.6 1.0 CE1 A:HIS120 3.0 21.0 1.0 O A:HOH1157 3.0 47.7 1.0 CG A:ASP45 3.1 21.9 1.0 OE2 A:GLU34 3.2 23.1 1.0 CG A:HIS120 3.3 25.4 1.0 OD1 A:ASP45 3.6 21.4 1.0 CB A:HIS120 3.8 24.4 1.0 CA A:HIS120 3.8 25.4 1.0 ZN A:ZN301 3.8 24.9 1.0 NE2 A:HIS120 4.2 26.3 1.0 CG A:GLU34 4.2 20.2 1.0 N A:TYR121 4.3 29.6 1.0 CB A:ASP45 4.3 22.3 1.0 NE2 A:GLN122 4.4 47.2 1.0 CD2 A:HIS120 4.4 23.3 1.0 CB A:GLU34 4.4 20.7 1.0 CE1 A:HIS36 4.5 15.9 1.0 C A:HIS120 4.5 27.2 1.0 CE1 A:HIS178 4.5 33.8 1.0 NE2 A:HIS36 4.6 12.8 1.0 O A:GLY119 4.6 21.0 1.0 ND1 A:HIS178 4.6 35.2 1.0 CB A:ALA32 4.8 19.8 1.0 N A:HIS120 5.0 21.5 1.0

Zinc binding site 2 out of 12 in the E122Q Mutant Creatininase, Zn-Zn Type


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, Zn-Zn Type within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:24.9 occ:1.00 OD1 A:ASP45 2.1 21.4 1.0 NE2 A:HIS36 2.1 12.8 1.0 OE2 A:GLU183 2.2 26.1 1.0 OE1 A:GLU183 2.6 24.9 1.0 CD A:GLU183 2.7 26.9 1.0 CG A:ASP45 3.1 21.9 1.0 CE1 A:HIS36 3.1 15.9 1.0 CD2 A:HIS36 3.1 16.7 1.0 CL A:CL302 3.3 36.6 1.0 OD2 A:ASP45 3.3 22.8 1.0 ZN A:ZN300 3.8 26.1 1.0 O A:HOH1274 4.0 28.5 1.0 CG1 A:VAL44 4.1 17.3 1.0 OE1 A:GLU34 4.1 20.4 1.0 ND1 A:HIS178 4.2 35.2 1.0 ND1 A:HIS36 4.2 17.7 1.0 CG A:GLU183 4.2 26.4 1.0 CG A:HIS36 4.2 19.1 1.0 CE1 A:HIS178 4.3 33.8 1.0 CB A:ASP45 4.4 22.3 1.0 O A:GLY119 4.4 21.0 1.0 N A:ASP45 4.5 20.5 1.0 CB A:VAL44 4.6 21.8 1.0 CA A:ASP45 4.7 21.8 1.0

Zinc binding site 3 out of 12 in the E122Q Mutant Creatininase, Zn-Zn Type


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, Zn-Zn Type within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn300 b:25.6 occ:1.00 OD2 B:ASP45 2.0 18.8 1.0 ND1 B:HIS120 2.1 23.1 1.0 OE1 B:GLU34 2.2 19.1 1.0 CL B:CL302 2.9 34.3 1.0 CE1 B:HIS120 3.0 24.8 1.0 CD B:GLU34 3.0 20.1 1.0 CG B:ASP45 3.2 22.8 1.0 CG B:HIS120 3.3 23.1 1.0 OE2 B:GLU34 3.3 22.2 1.0 CB B:HIS120 3.7 23.9 1.0 OD1 B:ASP45 3.7 27.6 1.0 CA B:HIS120 3.8 25.3 1.0 ZN B:ZN301 3.8 23.6 1.0 NE2 B:HIS120 4.1 26.3 1.0 N B:TYR121 4.2 29.0 1.0 CG B:GLU34 4.3 20.2 1.0 CD2 B:HIS120 4.3 24.6 1.0 CB B:ASP45 4.4 21.2 1.0 CB B:GLU34 4.4 17.0 1.0 C B:HIS120 4.5 27.0 1.0 CE1 B:HIS178 4.5 25.5 1.0 CE1 B:HIS36 4.6 23.0 1.0 O B:GLY119 4.6 22.2 1.0 ND1 B:HIS178 4.7 27.2 1.0 CB B:ALA32 4.7 18.5 1.0 NE2 B:HIS36 4.8 21.6 1.0 N B:HIS120 5.0 23.1 1.0

Zinc binding site 4 out of 12 in the E122Q Mutant Creatininase, Zn-Zn Type


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, Zn-Zn Type within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:23.6 occ:1.00 OD1 B:ASP45 2.1 27.6 1.0 OE2 B:GLU183 2.1 31.0 1.0 NE2 B:HIS36 2.2 21.6 1.0 CD B:GLU183 2.8 29.3 1.0 OE1 B:GLU183 2.8 30.5 1.0 CE1 B:HIS36 3.0 23.0 1.0 CL B:CL302 3.0 34.3 1.0 CG B:ASP45 3.1 22.8 1.0 CD2 B:HIS36 3.3 20.1 1.0 OD2 B:ASP45 3.4 18.8 1.0 ZN B:ZN300 3.8 25.6 1.0 O B:HOH1071 3.9 27.1 1.0 OE1 B:GLU34 4.1 19.1 1.0 ND1 B:HIS178 4.1 27.2 1.0 CG1 B:VAL44 4.1 21.7 1.0 ND1 B:HIS36 4.2 20.0 1.0 CE1 B:HIS178 4.2 25.5 1.0 CG B:GLU183 4.3 27.8 1.0 CG B:HIS36 4.4 21.1 1.0 O B:GLY119 4.4 22.2 1.0 CB B:ASP45 4.5 21.2 1.0 N B:ASP45 4.6 22.2 1.0 CB B:VAL44 4.6 20.0 1.0 CA B:ASP45 4.7 22.1 1.0

Zinc binding site 5 out of 12 in the E122Q Mutant Creatininase, Zn-Zn Type


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, Zn-Zn Type within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn300 b:29.3 occ:1.00 OD2 C:ASP45 2.0 23.2 1.0 ND1 C:HIS120 2.1 23.8 1.0 OE1 C:GLU34 2.2 24.6 1.0 CE1 C:HIS120 2.9 22.9 1.0 CD C:GLU34 3.0 25.4 1.0 CL C:CL302 3.0 39.2 1.0 CG C:ASP45 3.1 24.7 1.0 CG C:HIS120 3.3 23.7 1.0 OE2 C:GLU34 3.3 25.5 1.0 OD1 C:ASP45 3.6 22.7 1.0 CB C:HIS120 3.8 25.1 1.0 CA C:HIS120 3.8 25.3 1.0 ZN C:ZN301 3.9 26.1 1.0 NE2 C:HIS120 4.1 23.8 1.0 N C:TYR121 4.2 28.3 1.0 CG C:GLU34 4.3 23.9 1.0 CB C:ASP45 4.3 24.8 1.0 CD2 C:HIS120 4.3 24.2 1.0 CB C:GLU34 4.4 22.0 1.0 CE1 C:HIS36 4.5 21.2 1.0 C C:HIS120 4.5 27.0 1.0 O C:GLY119 4.5 22.6 1.0 CE1 C:HIS178 4.6 23.4 1.0 NE2 C:HIS36 4.6 21.3 1.0 CB C:ALA32 4.6 22.4 1.0 ND1 C:HIS178 4.8 27.2 1.0 N C:HIS120 5.0 23.5 1.0

Zinc binding site 6 out of 12 in the E122Q Mutant Creatininase, Zn-Zn Type


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, Zn-Zn Type within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:26.1 occ:1.00 OE1 C:GLU183 2.1 28.0 1.0 NE2 C:HIS36 2.2 21.3 1.0 OD1 C:ASP45 2.2 22.7 1.0 OE2 C:GLU183 2.6 27.9 1.0 CD C:GLU183 2.7 29.4 1.0 CG C:ASP45 3.1 24.7 1.0 CE1 C:HIS36 3.1 21.2 1.0 CD2 C:HIS36 3.2 21.4 1.0 CL C:CL302 3.2 39.2 1.0 OD2 C:ASP45 3.3 23.2 1.0 ZN C:ZN300 3.9 29.3 1.0 O C:HOH1152 3.9 37.9 1.0 CG1 C:VAL44 4.0 23.5 1.0 OE1 C:GLU34 4.1 24.6 1.0 CG C:GLU183 4.1 28.6 1.0 ND1 C:HIS36 4.2 21.7 1.0 ND1 C:HIS178 4.3 27.2 1.0 CG C:HIS36 4.3 22.1 1.0 CE1 C:HIS178 4.3 23.4 1.0 CB C:ASP45 4.4 24.8 1.0 O C:GLY119 4.5 22.6 1.0 N C:ASP45 4.6 23.1 1.0 CB C:VAL44 4.6 25.4 1.0 CA C:ASP45 4.7 24.6 1.0

Zinc binding site 7 out of 12 in the E122Q Mutant Creatininase, Zn-Zn Type


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of E122Q Mutant Creatininase, Zn-Zn Type within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn300 b:25.8 occ:1.00 OD2 D:ASP45 2.1 16.6 1.0 OE1 D:GLU34 2.1 27.1 1.0 ND1 D:HIS120 2.2 25.4 1.0 CE1 D:HIS120 3.0 27.7 1.0 CD D:GLU34 3.0 24.3 1.0 CL D:CL302 3.0 34.6 1.0 CG D:ASP45 3.2 20.9 1.0 CG D:HIS120 3.3 25.6 1.0 OE2 D:GLU34 3.4 25.7 1.0 OD1 D:ASP45 3.7 24.2 1.0 CB D:HIS120 3.8 26.2 1.0 CA D:HIS120 3.8 26.9 1.0 ZN D:ZN301 3.8 25.7 1.0 NE2 D:HIS120 4.2 25.7 1.0 CG D:GLU34 4.3 21.1 1.0 N D:TYR121 4.3 28.6 1.0 CD2 D:HIS120 4.4 28.0 1.0 CB D:ASP45 4.4 20.9 1.0 CB D:GLU34 4.4 20.0 1.0 CE1 D:HIS36 4.4 25.7 1.0 CE1 D:HIS178 4.5 22.9 1.0 C D:HIS120 4.5 27.2 1.0 OE1 D:GLN122 4.5 50.7 1.0 O D:GLY119 4.5 24.3 1.0 CB D:ALA32 4.6 17.2 1.0 NE2 D:HIS36 4.7 23.0 1.0 ND1 D:HIS178 4.7 24.0 1.0 N D:HIS120 5.0 25.3 1.0

Zinc binding site 8 out of 12 in the E122Q Mutant Creatininase, Zn-Zn Type


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of E122Q Mutant Creatininase, Zn-Zn Type within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:25.7 occ:1.00 NE2 D:HIS36 2.1 23.0 1.0 OD1 D:ASP45 2.1 24.2 1.0 OE1 D:GLU183 2.2 27.9 1.0 OE2 D:GLU183 2.7 30.6 1.0 CD D:GLU183 2.7 29.2 1.0 CE1 D:HIS36 2.9 25.7 1.0 CL D:CL302 3.1 34.6 1.0 CG D:ASP45 3.1 20.9 1.0 CD2 D:HIS36 3.2 23.4 1.0 OD2 D:ASP45 3.4 16.6 1.0 ZN D:ZN300 3.8 25.8 1.0 O D:HOH1457 3.9 37.1 1.0 ND1 D:HIS178 4.1 24.0 1.0 ND1 D:HIS36 4.1 23.2 1.0 CE1 D:HIS178 4.2 22.9 1.0 CG D:GLU183 4.2 27.9 1.0 OE1 D:GLU34 4.2 27.1 1.0 CG D:HIS36 4.3 23.1 1.0 CG1 D:VAL44 4.3 21.2 1.0 O D:GLY119 4.4 24.3 1.0 CB D:ASP45 4.5 20.9 1.0 N D:ASP45 4.6 23.8 1.0 CB D:VAL44 4.7 21.6 1.0 CA D:ASP45 4.7 22.7 1.0 O D:HOH1420 4.8 50.0 1.0

Zinc binding site 9 out of 12 in the E122Q Mutant Creatininase, Zn-Zn Type


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of E122Q Mutant Creatininase, Zn-Zn Type within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn300 b:26.1 occ:1.00 OD2 E:ASP45 2.0 22.5 1.0 OE1 E:GLU34 2.1 24.4 1.0 ND1 E:HIS120 2.2 25.1 1.0 CE1 E:HIS120 2.9 23.0 1.0 CL E:CL302 3.0 33.4 1.0 CD E:GLU34 3.0 26.7 1.0 CG E:ASP45 3.1 22.2 1.0 CG E:HIS120 3.3 25.0 1.0 OE2 E:GLU34 3.4 26.0 1.0 OD1 E:ASP45 3.6 18.4 1.0 ZN E:ZN301 3.8 25.0 1.0 CA E:HIS120 3.8 26.9 1.0 CB E:HIS120 3.8 25.3 1.0 NE2 E:HIS120 4.1 25.2 1.0 NE2 E:GLN122 4.2 46.7 1.0 CB E:ASP45 4.3 21.2 1.0 CG E:GLU34 4.3 25.6 1.0 CD2 E:HIS120 4.3 24.0 1.0 N E:TYR121 4.4 30.0 1.0 CE1 E:HIS178 4.4 28.6 1.0 NE2 E:HIS36 4.4 19.6 1.0 CB E:GLU34 4.5 25.0 1.0 CE1 E:HIS36 4.5 21.2 1.0 O E:GLY119 4.5 25.9 1.0 C E:HIS120 4.5 28.8 1.0 ND1 E:HIS178 4.5 30.6 1.0 CB E:ALA32 4.6 18.4 1.0 N E:HIS120 5.0 26.2 1.0

Zinc binding site 10 out of 12 in the E122Q Mutant Creatininase, Zn-Zn Type


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of E122Q Mutant Creatininase, Zn-Zn Type within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn301 b:25.0 occ:1.00 OD1 E:ASP45 2.0 18.4 1.0 NE2 E:HIS36 2.2 19.6 1.0 OE2 E:GLU183 2.2 27.5 1.0 OE1 E:GLU183 2.6 26.8 1.0 CD E:GLU183 2.7 28.6 1.0 CG E:ASP45 3.0 22.2 1.0 CD2 E:HIS36 3.1 21.3 1.0 CL E:CL302 3.2 33.4 1.0 CE1 E:HIS36 3.2 21.2 1.0 OD2 E:ASP45 3.3 22.5 1.0 O E:HOH1163 3.8 28.2 1.0 ZN E:ZN300 3.8 26.1 1.0 CG1 E:VAL44 3.9 24.9 1.0 ND1 E:HIS178 4.1 30.6 1.0 CE1 E:HIS178 4.1 28.6 1.0 CG E:GLU183 4.2 27.8 1.0 OE1 E:GLU34 4.2 24.4 1.0 CG E:HIS36 4.3 21.1 1.0 ND1 E:HIS36 4.3 23.8 1.0 CB E:ASP45 4.4 21.2 1.0 O E:GLY119 4.4 25.9 1.0 N E:ASP45 4.5 23.4 1.0 CB E:VAL44 4.6 27.8 1.0 CA E:ASP45 4.6 22.3 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