Zinc in PDB 1m08: Crystal Structure of the Unbound Nuclease Domain of COLE7

The structure of Crystal Structure of the Unbound Nuclease Domain of COLE7, PDB code: 1m08 was solved by Y.S.Cheng, K.C.Hsia, L.G.Doudeva, K.F.Chak, H.S.Yuan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.61 / 2.10
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	37.700, 39.200, 53.200, 96.80, 103.90, 91.40
R / Rfree (%)	18.7 / 24

The binding sites of Zinc atom in the Crystal Structure of the Unbound Nuclease Domain of COLE7 (pdb code 1m08). 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 the Unbound Nuclease Domain of COLE7, PDB code: 1m08:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the Unbound Nuclease Domain of COLE7


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 the Unbound Nuclease Domain of COLE7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn600 b:24.9 occ:1.00 O1 A:PO4601 1.8 27.3 1.0 ND1 A:HIS544 1.9 18.2 1.0 NE2 A:HIS573 2.0 26.5 1.0 NE2 A:HIS569 2.1 19.0 1.0 CE1 A:HIS544 2.8 19.2 1.0 P A:PO4601 2.9 29.5 1.0 CG A:HIS544 2.9 20.7 1.0 CD2 A:HIS569 3.0 20.3 1.0 CE1 A:HIS573 3.0 27.6 1.0 CD2 A:HIS573 3.0 25.7 1.0 O3 A:PO4601 3.2 35.2 1.0 CE1 A:HIS569 3.2 17.9 1.0 CB A:HIS544 3.4 19.4 1.0 O4 A:PO4601 3.6 34.6 1.0 CA A:HIS544 3.6 20.3 1.0 O A:HOH824 3.7 24.0 1.0 N A:HIS545 3.9 21.0 1.0 NE2 A:HIS544 3.9 20.1 1.0 CD2 A:HIS544 4.0 18.5 1.0 O2 A:PO4601 4.1 29.6 1.0 ND1 A:HIS573 4.1 25.6 1.0 CG A:HIS569 4.2 17.4 1.0 CG A:HIS573 4.2 28.9 1.0 ND1 A:HIS569 4.2 18.6 1.0 C A:HIS544 4.2 21.6 1.0 O A:HIS545 4.5 25.7 1.0 NZ B:LYS576 4.6 39.8 1.0 O A:LEU543 4.7 18.3 1.0 N A:HIS544 4.8 20.8 1.0 O A:HOH830 5.0 33.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Unbound Nuclease Domain of COLE7


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 the Unbound Nuclease Domain of COLE7 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn600 b:24.0 occ:1.00 O1 B:PO4601 1.9 26.5 1.0 ND1 B:HIS544 2.1 19.1 1.0 NE2 B:HIS569 2.1 15.8 1.0 NE2 B:HIS573 2.1 26.6 1.0 P B:PO4601 3.0 29.5 1.0 CD2 B:HIS569 3.0 14.1 1.0 CE1 B:HIS573 3.0 27.3 1.0 CG B:HIS544 3.0 17.9 1.0 CE1 B:HIS544 3.0 20.2 1.0 CE1 B:HIS569 3.1 13.5 1.0 CD2 B:HIS573 3.2 25.2 1.0 O3 B:PO4601 3.2 31.8 1.0 CB B:HIS544 3.3 17.8 1.0 O4 B:PO4601 3.4 33.4 1.0 O B:HOH707 3.5 21.4 1.0 CA B:HIS544 3.6 16.2 1.0 N B:HIS545 3.9 17.6 1.0 ND1 B:HIS573 4.1 26.2 1.0 CG B:HIS569 4.1 12.8 1.0 NE2 B:HIS544 4.2 19.7 1.0 CD2 B:HIS544 4.2 21.2 1.0 ND1 B:HIS569 4.2 12.1 1.0 O2 B:PO4601 4.2 30.0 1.0 C B:HIS544 4.2 17.1 1.0 CG B:HIS573 4.2 26.9 1.0 O B:HIS545 4.5 23.9 1.0 CE A:LYS576 4.6 40.2 1.0 O B:LEU543 4.7 16.4 1.0 N B:HIS544 4.8 16.7 1.0 NZ A:LYS576 4.9 38.9 1.0

Y.S.Cheng, K.C.Hsia, L.G.Doudeva, K.F.Chak, H.S.Yuan. The Crystal Structure of the Nuclease Domain of Colicin E7 Suggests A Mechanism For Binding to Double-Stranded Dna By the H-N-H Endonucleases J.Mol.Biol. V. 324 227 2002.
ISSN: ISSN 0022-2836
PubMed: 12441102
DOI: 10.1016/S0022-2836(02)01092-6