Zinc in PDB 3itc: Crystal Structure of SCO3058 with Bound Citrate and Glycerol

The structure of Crystal Structure of SCO3058 with Bound Citrate and Glycerol, PDB code: 3itc was solved by T.T.Nguyen, J.A.Cummings, C.-L.Tsai, D.P.Barondeau, F.M.Raushel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.70
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	97.287, 97.287, 104.411, 90.00, 90.00, 120.00
R / Rfree (%)	16.7 / 20.3

The binding sites of Zinc atom in the Crystal Structure of SCO3058 with Bound Citrate and Glycerol (pdb code 3itc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of SCO3058 with Bound Citrate and Glycerol, PDB code: 3itc:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of SCO3058 with Bound Citrate and Glycerol


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of SCO3058 with Bound Citrate and Glycerol within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:19.1 occ:1.00 OD1 A:ASP22 1.9 17.8 1.0 OE1 A:GLU123 2.0 17.1 1.0 O A:HOH505 2.0 17.8 1.0 NE2 A:HIS20 2.1 17.0 1.0 O1 A:GOL504 2.6 33.5 1.0 CD A:GLU123 2.8 17.5 1.0 CG A:ASP22 2.8 16.9 1.0 OE2 A:GLU123 2.9 16.7 1.0 OD2 A:ASP22 3.0 18.7 1.0 CE1 A:HIS20 3.1 16.0 1.0 CD2 A:HIS20 3.1 20.5 1.0 ZN A:ZN502 3.3 18.8 1.0 O2 A:GOL504 3.5 30.4 1.0 C1 A:GOL504 3.6 41.2 1.0 OD1 A:ASP320 3.7 18.7 1.0 OG A:SER66 3.9 18.5 1.0 C2 A:GOL504 4.2 35.9 1.0 NE2 A:HIS212 4.2 16.3 1.0 CG A:GLU123 4.2 17.7 1.0 ND1 A:HIS20 4.2 15.6 1.0 CB A:ASP22 4.2 19.7 1.0 CG A:HIS20 4.3 18.5 1.0 CE1 A:HIS212 4.5 20.1 1.0 CB A:TYR68 4.6 18.2 1.0 CB A:SER66 4.6 15.5 1.0 O1 A:CIT503 4.7 22.2 1.0 CB A:GLU123 4.7 18.4 1.0 CG A:TYR68 4.8 18.4 1.0 O5 A:CIT503 4.9 18.5 1.0 CG A:ASP320 4.9 21.1 1.0 CD2 A:TYR68 4.9 15.9 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of SCO3058 with Bound Citrate and Glycerol


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of SCO3058 with Bound Citrate and Glycerol within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:18.8 occ:1.00 O A:HOH505 1.9 17.8 1.0 NE2 A:HIS191 2.1 17.4 1.0 NE2 A:HIS212 2.1 16.3 1.0 O5 A:CIT503 2.2 18.5 1.0 OE2 A:GLU123 2.2 16.7 1.0 CE1 A:HIS212 3.0 20.1 1.0 CD2 A:HIS191 3.0 18.6 1.0 CE1 A:HIS191 3.1 18.8 1.0 CD2 A:HIS212 3.1 17.7 1.0 C6 A:CIT503 3.1 23.3 1.0 O1 A:CIT503 3.2 22.2 1.0 ZN A:ZN501 3.3 19.1 1.0 CD A:GLU123 3.3 17.5 1.0 O6 A:CIT503 3.8 21.9 1.0 OE1 A:GLU123 3.8 17.1 1.0 O2 A:GOL504 3.9 30.4 1.0 NH1 A:ARG223 3.9 20.2 1.0 NE2 A:HIS20 4.0 17.0 1.0 ND1 A:HIS212 4.0 18.7 1.0 O7 A:CIT503 4.1 23.3 1.0 OD1 A:ASP320 4.1 18.7 1.0 C3 A:CIT503 4.1 23.5 1.0 ND1 A:HIS191 4.2 19.0 1.0 CG A:HIS191 4.2 16.1 1.0 CG A:HIS212 4.2 18.8 1.0 C1 A:CIT503 4.3 32.4 1.0 NE2 A:HIS150 4.3 22.0 1.0 CD2 A:HIS150 4.3 20.0 1.0 CD2 A:HIS20 4.4 20.5 1.0 O1 A:GOL504 4.4 33.5 1.0 CG A:GLU123 4.5 17.7 1.0 OD2 A:ASP320 4.6 20.8 1.0 CE1 A:HIS20 4.6 16.0 1.0 CG A:ASP320 4.6 21.1 1.0 C2 A:CIT503 4.8 26.0 1.0 CZ A:ARG223 4.8 18.6 1.0 OD1 A:ASP22 4.9 17.8 1.0 NE A:ARG223 4.9 18.6 1.0

J.A.Cummings, T.T.Nguyen, A.A.Fedorov, P.Kolb, C.Xu, E.V.Fedorov, B.K.Shoichet, D.P.Barondeau, S.C.Almo, F.M.Raushel. Structure, Mechanism, and Substrate Profile For SCO3058: the Closest Bacterial Homologue to Human Renal Dipeptidase Biochemistry V. 49 611 2010.
ISSN: ISSN 0006-2960
PubMed: 20000809
DOI: 10.1021/BI901935Y