Zinc in PDB 3zfk: N-Terminal Truncated Nuclease Domain of Colicin E7

The structure of N-Terminal Truncated Nuclease Domain of Colicin E7, PDB code: 3zfk was solved by E.Toth, A.Czene, B.Gyurcsik, H.Otten, J.-C.N.Poulsen, S.Larsen, H.E.M.Christensen, K.Nagata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.099 / 1.70
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	55.400, 55.400, 73.200, 90.00, 90.00, 120.00
R / Rfree (%)	20 / 23.43

The structure of N-Terminal Truncated Nuclease Domain of Colicin E7 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Zinc atom in the N-Terminal Truncated Nuclease Domain of Colicin E7 (pdb code 3zfk). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the N-Terminal Truncated Nuclease Domain of Colicin E7, PDB code: 3zfk:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the N-Terminal Truncated Nuclease Domain of Colicin E7


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of N-Terminal Truncated Nuclease Domain of Colicin E7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:40.5 occ:1.00 HE2 A:HIS569 1.4 25.6 1.0 HE2 A:HIS573 1.5 39.4 1.0 ND1 A:HIS544 2.0 27.5 1.0 NE2 A:HIS569 2.2 21.4 1.0 O4 A:SO41136 2.2 19.7 1.0 NE2 A:HIS573 2.3 32.8 1.0 CE1 A:HIS544 2.8 29.6 1.0 HD2 A:HIS569 2.9 27.7 1.0 O3 A:SO41136 2.9 26.2 1.0 CD2 A:HIS569 2.9 23.1 1.0 HE1 A:HIS544 2.9 35.5 1.0 HA A:HIS544 3.0 24.3 1.0 S A:SO41136 3.0 26.1 1.0 CG A:HIS544 3.1 19.0 1.0 CD2 A:HIS573 3.1 37.1 1.0 HD2 A:HIS573 3.2 44.6 1.0 CE1 A:HIS569 3.3 22.4 1.0 CE1 A:HIS573 3.3 40.4 1.0 H A:HIS545 3.4 17.8 1.0 HB2 A:HIS544 3.4 26.9 1.0 CB A:HIS544 3.6 22.4 1.0 HE1 A:HIS573 3.6 48.5 1.0 HE1 A:HIS569 3.7 26.9 1.0 CA A:HIS544 3.7 20.2 1.0 O A:HOH2072 4.0 33.0 1.0 NE2 A:HIS544 4.0 25.0 1.0 N A:HIS545 4.0 14.8 1.0 O2 A:SO41136 4.0 33.2 1.0 O1 A:SO41136 4.0 38.3 1.0 CG A:HIS569 4.1 22.8 1.0 CD2 A:HIS544 4.1 22.4 1.0 ND1 A:HIS569 4.3 23.3 1.0 CG A:HIS573 4.3 38.2 1.0 C A:HIS544 4.4 14.4 1.0 ND1 A:HIS573 4.4 38.0 1.0 HB3 A:HIS544 4.5 26.9 1.0 O A:LEU543 4.6 20.0 1.0 O A:HIS545 4.7 20.4 1.0 HE2 A:HIS544 4.8 30.0 1.0 N A:HIS544 4.9 19.9 1.0 HB A:ILE572 5.0 52.5 1.0

Zinc binding site 2 out of 2 in the N-Terminal Truncated Nuclease Domain of Colicin E7


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of N-Terminal Truncated Nuclease Domain of Colicin E7 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:24.6 occ:1.00 ND1 B:HIS544 1.7 17.6 1.0 NE2 B:HIS569 2.1 20.6 1.0 NE2 B:HIS573 2.1 29.2 1.0 O1 B:SO41134 2.1 23.6 1.0 CE1 B:HIS544 2.5 33.8 1.0 HE1 B:HIS544 2.7 40.6 1.0 O3 B:SO41134 2.8 35.1 1.0 CG B:HIS544 2.8 20.9 1.0 CD2 B:HIS569 2.9 24.9 1.0 CD2 B:HIS573 2.9 34.3 1.0 HD2 B:HIS573 2.9 41.1 1.0 HD2 B:HIS569 3.0 29.9 1.0 S B:SO41134 3.0 27.6 1.0 HA B:HIS544 3.1 23.6 1.0 CE1 B:HIS569 3.2 18.0 1.0 CE1 B:HIS573 3.2 41.2 1.0 HB2 B:HIS544 3.3 27.5 1.0 CB B:HIS544 3.4 22.9 1.0 HE1 B:HIS569 3.5 21.6 1.0 H B:HIS545 3.5 19.0 1.0 HE1 B:HIS573 3.5 49.5 1.0 NE2 B:HIS544 3.7 20.8 1.0 CA B:HIS544 3.7 19.6 1.0 CD2 B:HIS544 3.9 25.3 1.0 O B:HOH2065 3.9 31.4 1.0 O4 B:SO41134 4.0 31.6 1.0 O2 B:SO41134 4.0 38.2 1.0 N B:HIS545 4.1 15.9 1.0 CG B:HIS569 4.1 21.1 1.0 CG B:HIS573 4.1 41.1 1.0 ND1 B:HIS569 4.2 21.6 1.0 ND1 B:HIS573 4.2 37.0 1.0 HB3 B:HIS544 4.4 27.5 1.0 C B:HIS544 4.4 14.4 1.0 HE2 B:HIS544 4.4 25.0 1.0 O B:LEU543 4.7 16.7 1.0 O B:HIS545 4.7 19.1 1.0 HD2 B:HIS544 4.7 30.4 1.0 HB B:ILE572 4.9 51.8 1.0 N B:HIS544 4.9 18.7 1.0 HD1 B:HIS569 5.0 26.0 1.0

A.Czene, E.Toth, E.Nemeth, H.Otten, J.-C.N.Poulsen, H.E.M.Christensen, L.Rulisek, K.Nagata, S.Larsen, B.Gyurcsik. Tracing the Reason of Inactivity of A Mutant Colicin E7 Metallonuclease: A Hint to An Alternative Catalytic Mechanism? To Be Published.