Zinc in PDB 3cm5: Crystal Structure of Cell-Death Related Nuclease 4 (Crn-4) Bound with Mn

The structure of Crystal Structure of Cell-Death Related Nuclease 4 (Crn-4) Bound with Mn, PDB code: 3cm5 was solved by Y.-Y.Hsiao, H.S.Yuan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.81
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	125.132, 165.432, 64.589, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 23.9

The structure of Crystal Structure of Cell-Death Related Nuclease 4 (Crn-4) Bound with Mn also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Cell-Death Related Nuclease 4 (Crn-4) Bound with Mn (pdb code 3cm5). 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 Cell-Death Related Nuclease 4 (Crn-4) Bound with Mn, PDB code: 3cm5:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Cell-Death Related Nuclease 4 (Crn-4) Bound with Mn


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 Cell-Death Related Nuclease 4 (Crn-4) Bound with Mn within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn299 b:55.7 occ:1.00 SG A:CYS260 2.3 61.0 1.0 SG A:CYS270 2.3 60.7 1.0 SG A:CYS210 2.4 55.9 1.0 SG A:CYS263 2.5 62.5 1.0 CB A:CYS260 3.0 60.6 1.0 CB A:CYS210 3.1 54.3 1.0 CB A:CYS263 3.4 62.3 1.0 CB A:CYS270 3.5 61.9 1.0 N A:CYS210 3.9 52.6 1.0 N A:CYS263 4.0 62.4 1.0 CA A:CYS210 4.1 54.5 1.0 CA A:CYS263 4.2 62.3 1.0 NH2 A:ARG136 4.3 48.9 1.0 CA A:CYS260 4.5 60.6 1.0 CA A:CYS270 4.7 62.2 1.0 C A:CYS263 4.8 62.7 1.0 OG1 A:THR209 4.8 50.3 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Cell-Death Related Nuclease 4 (Crn-4) Bound with Mn


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 Cell-Death Related Nuclease 4 (Crn-4) Bound with Mn within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn299 b:33.4 occ:1.00 SG B:CYS270 2.2 36.6 1.0 SG B:CYS210 2.2 31.9 1.0 SG B:CYS263 2.2 41.6 1.0 SG B:CYS260 2.4 37.8 1.0 CB B:CYS210 3.1 32.7 1.0 CB B:CYS260 3.1 38.4 1.0 CB B:CYS270 3.2 41.6 1.0 CB B:CYS263 3.3 42.5 1.0 N B:CYS263 3.8 42.7 1.0 N B:CYS210 3.9 34.0 1.0 CA B:CYS210 4.1 33.6 1.0 CA B:CYS263 4.2 43.0 1.0 NH2 B:ARG136 4.3 40.7 1.0 CA B:CYS270 4.5 41.7 1.0 CA B:CYS260 4.6 38.9 1.0 CB B:TYR262 4.8 40.7 1.0 O B:HOH313 4.9 40.4 1.0 C B:CYS263 4.9 44.0 1.0 C B:TYR262 4.9 41.9 1.0 N B:ARG264 5.0 44.3 1.0 C B:THR209 5.0 34.1 1.0

Y.-Y.Hsiao, A.Nakagawa, Z.Shi, S.Mitani, D.Xue, H.S.Yuan. Crystal Structure of Crn-4: Implications For Domain Function in Apoptotic Dna Degradation Mol.Cell.Biol. V. 29 448 2009.
ISSN: ISSN 0270-7306
PubMed: 18981218
DOI: 10.1128/MCB.01006-08