Zinc in PDB 1v7z: Creatininase-Product Complex

All present enzymatic activity of Creatininase-Product Complex:
3.5.2.10;

The structure of Creatininase-Product Complex, PDB code: 1v7z was solved by T.Yoshimoto, N.Tanaka, N.Kanada, T.Inoue, Y.Nakajima, M.Haratake, K.T.Nakamura, Y.Xu, K.Ito, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	102.186, 152.211, 167.119, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 19.8

The structure of Creatininase-Product Complex also contains other interesting chemical elements:

Manganese

(Mn)

6 atoms

The binding sites of Zinc atom in the Creatininase-Product Complex (pdb code 1v7z). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Creatininase-Product Complex, PDB code: 1v7z:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Creatininase-Product Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Creatininase-Product Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:20.5 occ:1.00 O8 A:CRN401 1.9 21.4 1.0 OD1 A:ASP45 2.0 18.0 1.0 OE1 A:GLU183 2.0 18.9 1.0 NE2 A:HIS36 2.0 18.4 1.0 CD A:GLU183 2.7 21.2 1.0 OE2 A:GLU183 2.8 20.8 1.0 C7 A:CRN401 2.8 27.0 1.0 CE1 A:HIS36 3.0 18.5 1.0 CG A:ASP45 3.0 17.6 1.0 CD2 A:HIS36 3.0 18.2 1.0 OD2 A:ASP45 3.2 19.3 1.0 C5 A:CRN401 3.4 26.4 1.0 MN A:MN300 3.6 18.0 1.0 O9 A:CRN401 3.8 25.0 1.0 ND1 A:HIS178 3.9 22.2 1.0 O A:HOH1002 4.0 18.8 1.0 CE1 A:HIS178 4.0 21.9 1.0 ND1 A:HIS36 4.1 18.7 1.0 CG1 A:VAL44 4.1 17.8 1.0 CG A:HIS36 4.2 18.8 1.0 CG A:GLU183 4.2 20.4 1.0 OE2 A:GLU34 4.2 17.1 1.0 CB A:ASP45 4.3 17.4 1.0 O A:GLY119 4.5 17.3 1.0 CB A:VAL44 4.5 18.0 1.0 N A:ASP45 4.6 17.5 1.0 CA A:ASP45 4.7 17.6 1.0 N1 A:CRN401 4.7 27.8 1.0 N3 A:CRN401 4.8 28.5 1.0 O A:HOH1082 4.9 16.8 1.0

Zinc binding site 2 out of 6 in the Creatininase-Product Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Creatininase-Product Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn3301 b:21.8 occ:1.00 OE1 B:GLU183 1.9 21.9 1.0 O8 B:CRN3401 2.0 22.4 1.0 NE2 B:HIS36 2.0 21.1 1.0 OD1 B:ASP45 2.0 17.5 1.0 CD B:GLU183 2.7 22.2 1.0 C7 B:CRN3401 2.8 29.7 1.0 OE2 B:GLU183 2.8 23.1 1.0 CE1 B:HIS36 2.9 20.4 1.0 CG B:ASP45 3.0 18.9 1.0 CD2 B:HIS36 3.1 20.6 1.0 OD2 B:ASP45 3.2 20.3 1.0 C5 B:CRN3401 3.3 30.6 1.0 MN B:MN3300 3.5 18.8 1.0 O9 B:CRN3401 3.8 28.6 1.0 O B:HOH1004 3.9 20.4 1.0 ND1 B:HIS178 3.9 22.9 1.0 ND1 B:HIS36 4.1 20.7 1.0 CG B:GLU183 4.1 22.5 1.0 OE2 B:GLU34 4.2 19.5 1.0 CG B:HIS36 4.2 20.1 1.0 CE1 B:HIS178 4.2 23.0 1.0 CG1 B:VAL44 4.2 19.8 1.0 CB B:ASP45 4.4 18.6 1.0 O B:GLY119 4.5 18.1 1.0 CB B:VAL44 4.6 19.5 1.0 N B:ASP45 4.6 18.5 1.0 N1 B:CRN3401 4.7 31.9 1.0 CA B:ASP45 4.7 18.5 1.0 N3 B:CRN3401 4.8 34.5 1.0 O B:HOH1013 5.0 18.0 1.0

Zinc binding site 3 out of 6 in the Creatininase-Product Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Creatininase-Product Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn4301 b:22.0 occ:1.00 O8 C:CRN4401 1.9 25.5 1.0 OE1 C:GLU183 2.0 19.2 1.0 OD1 C:ASP45 2.0 17.1 1.0 NE2 C:HIS36 2.1 21.8 1.0 C7 C:CRN4401 2.7 33.4 1.0 CD C:GLU183 2.8 21.8 1.0 OE2 C:GLU183 2.9 20.8 1.0 CG C:ASP45 3.0 18.3 1.0 CE1 C:HIS36 3.0 20.5 1.0 CD2 C:HIS36 3.1 21.5 1.0 C5 C:CRN4401 3.2 35.0 1.0 OD2 C:ASP45 3.2 18.4 1.0 MN C:MN4300 3.5 19.3 1.0 O9 C:CRN4401 3.7 32.3 1.0 ND1 C:HIS178 3.9 22.1 1.0 O C:HOH1006 4.0 22.0 1.0 ND1 C:HIS36 4.1 21.2 1.0 OE2 C:GLU34 4.2 19.4 1.0 CG1 C:VAL44 4.2 19.6 1.0 CE1 C:HIS178 4.2 21.2 1.0 CG C:GLU183 4.2 21.2 1.0 CG C:HIS36 4.2 21.2 1.0 CB C:ASP45 4.3 18.0 1.0 O C:GLY119 4.5 19.9 1.0 N1 C:CRN4401 4.6 37.5 1.0 N C:ASP45 4.6 18.3 1.0 CB C:VAL44 4.6 18.8 1.0 CA C:ASP45 4.7 18.1 1.0 O C:HOH1005 4.9 22.5 1.0

Zinc binding site 4 out of 6 in the Creatininase-Product Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Creatininase-Product Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn5301 b:23.4 occ:1.00 OE1 D:GLU183 1.9 24.7 1.0 NE2 D:HIS36 2.0 21.7 1.0 OD1 D:ASP45 2.0 19.6 1.0 O8 D:CRN5401 2.1 22.1 1.0 CD D:GLU183 2.7 25.0 1.0 C7 D:CRN5401 2.7 31.9 1.0 OE2 D:GLU183 2.8 24.3 1.0 CE1 D:HIS36 2.9 21.1 1.0 CG D:ASP45 3.0 21.6 1.0 CD2 D:HIS36 3.0 21.9 1.0 OD2 D:ASP45 3.2 21.6 1.0 C5 D:CRN5401 3.2 33.4 1.0 MN D:MN5300 3.5 20.4 1.0 O9 D:CRN5401 3.6 31.6 1.0 ND1 D:HIS178 3.9 23.8 1.0 O D:HOH1008 3.9 24.3 1.0 ND1 D:HIS36 4.0 21.9 1.0 CG1 D:VAL44 4.1 21.1 1.0 CG D:HIS36 4.1 22.6 1.0 CE1 D:HIS178 4.1 22.8 1.0 OE2 D:GLU34 4.1 19.2 1.0 CG D:GLU183 4.1 25.6 1.0 CB D:ASP45 4.3 20.2 1.0 O D:GLY119 4.4 19.7 1.0 CB D:VAL44 4.6 20.7 1.0 N D:ASP45 4.6 20.1 1.0 N1 D:CRN5401 4.6 34.9 1.0 CA D:ASP45 4.7 20.5 1.0 N3 D:CRN5401 4.9 38.6 1.0 O D:HOH1084 5.0 20.8 1.0

Zinc binding site 5 out of 6 in the Creatininase-Product Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Creatininase-Product Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn6301 b:22.3 occ:1.00 OE1 E:GLU183 1.9 22.5 1.0 NE2 E:HIS36 2.0 21.5 1.0 OD1 E:ASP45 2.0 19.2 1.0 O8 E:CRN6401 2.0 21.9 1.0 CD E:GLU183 2.7 22.0 1.0 C7 E:CRN6401 2.7 31.0 1.0 OE2 E:GLU183 2.8 20.9 1.0 CE1 E:HIS36 2.9 20.9 1.0 CG E:ASP45 2.9 20.8 1.0 CD2 E:HIS36 3.0 21.7 1.0 OD2 E:ASP45 3.1 21.6 1.0 C5 E:CRN6401 3.2 31.9 1.0 MN E:MN6300 3.5 19.7 1.0 O9 E:CRN6401 3.6 30.2 1.0 ND1 E:HIS178 3.8 21.7 1.0 O E:HOH1010 3.9 20.5 1.0 ND1 E:HIS36 4.0 21.6 1.0 CG1 E:VAL44 4.1 20.3 1.0 CE1 E:HIS178 4.1 20.2 1.0 OE2 E:GLU34 4.1 18.4 1.0 CG E:HIS36 4.1 21.2 1.0 CG E:GLU183 4.1 22.8 1.0 CB E:ASP45 4.3 19.7 1.0 O E:GLY119 4.5 19.1 1.0 CB E:VAL44 4.6 20.1 1.0 N1 E:CRN6401 4.6 34.1 1.0 N E:ASP45 4.6 19.7 1.0 CA E:ASP45 4.7 19.9 1.0 N3 E:CRN6401 4.9 38.5 1.0 O E:HOH1039 5.0 20.4 1.0

Zinc binding site 6 out of 6 in the Creatininase-Product Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Creatininase-Product Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn7301 b:21.1 occ:1.00 OE1 F:GLU183 2.0 20.1 1.0 O8 F:CRN7401 2.0 25.3 1.0 OD1 F:ASP45 2.0 18.7 1.0 NE2 F:HIS36 2.0 19.3 1.0 CD F:GLU183 2.7 20.8 1.0 C7 F:CRN7401 2.8 33.2 1.0 OE2 F:GLU183 2.8 20.3 1.0 CE1 F:HIS36 2.9 19.5 1.0 CG F:ASP45 3.0 18.5 1.0 CD2 F:HIS36 3.1 22.4 1.0 OD2 F:ASP45 3.2 19.1 1.0 C5 F:CRN7401 3.3 34.7 1.0 MN F:MN7300 3.5 18.9 1.0 O9 F:CRN7401 3.8 31.3 1.0 ND1 F:HIS178 3.8 21.6 1.0 O F:HOH1012 3.9 20.8 1.0 ND1 F:HIS36 4.1 19.7 1.0 CE1 F:HIS178 4.1 21.7 1.0 OE2 F:GLU34 4.1 17.5 1.0 CG1 F:VAL44 4.1 19.3 1.0 CG F:GLU183 4.2 21.5 1.0 CG F:HIS36 4.2 20.3 1.0 CB F:ASP45 4.4 17.6 1.0 O F:GLY119 4.5 19.6 1.0 N1 F:CRN7401 4.6 36.2 1.0 N F:ASP45 4.6 17.7 1.0 CB F:VAL44 4.6 18.3 1.0 CA F:ASP45 4.7 17.6 1.0 N3 F:CRN7401 4.8 39.9 1.0 O F:HOH1019 5.0 17.4 1.0

T.Yoshimoto, N.Tanaka, N.Kanada, T.Inoue, Y.Nakajima, M.Haratake, K.T.Nakamura, Y.Xu, K.Ito. Crystal Structures of Creatininase Reveal the Substrate Binding Site and Provide An Insight Into the Catalytic Mechanism J.Mol.Biol. V. 337 399 2004.
ISSN: ISSN 0022-2836
PubMed: 15003455
DOI: 10.1016/J.JMB.2004.01.022