Zinc in PDB 3ttd: Crystal Structure of E. Coli Hypf with Amp-Cpp and Carbamoyl Phosphate

The structure of Crystal Structure of E. Coli Hypf with Amp-Cpp and Carbamoyl Phosphate, PDB code: 3ttd was solved by S.Petkun, R.Shi, Y.Li, M.Cygler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	100.32 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.446, 77.730, 200.635, 90.00, 90.00, 90.00
R / Rfree (%)	16.2 / 21.4

The structure of Crystal Structure of E. Coli Hypf with Amp-Cpp and Carbamoyl Phosphate also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Crystal Structure of E. Coli Hypf with Amp-Cpp and Carbamoyl Phosphate (pdb code 3ttd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of E. Coli Hypf with Amp-Cpp and Carbamoyl Phosphate, PDB code: 3ttd:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of E. Coli Hypf with Amp-Cpp and Carbamoyl Phosphate


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 E. Coli Hypf with Amp-Cpp and Carbamoyl Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1 b:24.1 occ:1.00 SG A:CYS112 2.3 25.2 1.0 SG A:CYS131 2.4 23.4 1.0 SG A:CYS109 2.4 20.1 1.0 SG A:CYS134 2.4 21.0 1.0 CB A:CYS112 3.3 23.4 1.0 CB A:CYS131 3.4 23.2 1.0 N A:CYS131 3.5 23.3 1.0 CB A:CYS134 3.5 19.2 1.0 CB A:CYS109 3.7 20.6 1.0 N A:CYS109 4.0 19.7 1.0 CA A:CYS131 4.0 23.7 1.0 N A:CYS112 4.2 25.3 1.0 NE A:ARG172 4.2 30.9 1.0 C A:ASN130 4.2 23.6 1.0 N A:CYS134 4.2 21.8 1.0 CA A:CYS112 4.3 24.5 1.0 CA A:CYS109 4.4 19.8 1.0 CA A:CYS134 4.4 19.6 1.0 CA A:ASN130 4.6 23.0 1.0 C A:CYS131 4.6 23.6 1.0 O A:HOH974 4.7 34.5 1.0 NH2 A:ARG172 4.7 28.4 1.0 C A:HIS133 4.8 24.4 1.0 CB A:HIS133 4.9 26.7 1.0 N A:HIS133 4.9 25.3 1.0 O A:CYS131 5.0 23.9 1.0 C A:CYS134 5.0 18.6 1.0 O A:CYS109 5.0 19.8 1.0 C A:CYS109 5.0 20.9 1.0 CZ A:ARG172 5.0 30.6 1.0 O A:CYS134 5.0 17.7 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of E. Coli Hypf with Amp-Cpp and Carbamoyl Phosphate


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 E. Coli Hypf with Amp-Cpp and Carbamoyl Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2 b:37.4 occ:1.00 SG A:CYS184 2.3 30.6 1.0 SG A:CYS162 2.3 35.1 1.0 SG A:CYS181 2.5 28.8 1.0 SG A:CYS159 2.5 35.3 1.0 CB A:CYS162 3.2 35.0 1.0 CB A:CYS181 3.4 28.4 1.0 CB A:CYS184 3.5 30.9 1.0 CB A:CYS159 3.5 34.2 1.0 N A:CYS181 3.5 28.5 1.0 N A:CYS184 3.9 32.8 1.0 N A:CYS159 3.9 33.2 1.0 CA A:CYS181 4.0 28.4 1.0 CA A:CYS184 4.3 31.8 1.0 CA A:CYS159 4.3 34.6 1.0 CA A:CYS162 4.3 35.3 1.0 N A:CYS162 4.3 35.7 1.0 C A:ALA180 4.4 29.7 1.0 NH2 A:ARG122 4.4 35.9 1.0 NE A:ARG122 4.5 36.3 1.0 C A:CYS181 4.5 28.8 1.0 O A:CYS181 4.5 27.9 1.0 CB A:GLU183 4.6 36.5 1.0 C A:GLU183 4.9 34.6 1.0 CA A:ALA180 4.9 30.1 1.0 O A:CYS159 4.9 36.0 1.0 C A:CYS159 4.9 35.5 1.0 N A:GLU183 4.9 34.5 1.0 CZ A:ARG122 5.0 36.5 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of E. Coli Hypf with Amp-Cpp and Carbamoyl Phosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of E. Coli Hypf with Amp-Cpp and Carbamoyl Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn3 b:41.2 occ:1.00 NE2 A:HIS479 2.4 15.3 1.0 OD1 A:ASP727 2.4 17.9 1.0 OD1 A:ASP502 2.4 26.1 1.0 NE2 A:HIS475 2.6 17.3 1.0 O A:HOH36 2.7 21.0 1.0 CD2 A:HIS475 3.0 16.2 1.0 O A:HOH20 3.0 28.4 1.0 CE1 A:HIS479 3.2 13.3 1.0 CG A:ASP502 3.4 25.8 1.0 CG A:ASP727 3.4 22.0 1.0 CD2 A:HIS479 3.5 12.3 1.0 CB A:ASP502 3.8 22.4 1.0 OD2 A:ASP727 3.8 26.6 1.0 CE1 A:HIS475 3.8 19.4 1.0 O A:HOH996 4.3 31.3 1.0 CG A:HIS475 4.3 13.9 1.0 ND1 A:HIS479 4.4 16.2 1.0 CG A:HIS479 4.6 12.9 1.0 OD2 A:ASP502 4.6 33.5 1.0 ND1 A:HIS475 4.7 19.4 1.0 CB A:ASP727 4.8 18.4 1.0 N A:ASP727 4.8 18.5 1.0 CA A:ASP727 4.9 18.5 1.0

S.Petkun, R.Shi, Y.Li, A.Asinas, C.Munger, L.Zhang, M.Waclawek, B.Soboh, R.G.Sawers, M.Cygler. Structure of Hydrogenase Maturation Protein Hypf with Reaction Intermediates Shows Two Active Sites. Structure V. 19 1773 2011.
ISSN: ISSN 0969-2126
PubMed: 22153500
DOI: 10.1016/J.STR.2011.09.023