Zinc in PDB 1v9p: Crystal Structure of Nad+-Dependent Dna Ligase

All present enzymatic activity of Crystal Structure of Nad+-Dependent Dna Ligase:
6.5.1.2;

The structure of Crystal Structure of Nad+-Dependent Dna Ligase, PDB code: 1v9p was solved by J.Y.Lee, C.Chang, H.K.Song, J.Moon, J.K.Yang, H.K.Kim, S.K.Kwon, S.W.Suh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.93 / 2.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	89.210, 117.330, 97.480, 90.00, 115.09, 90.00
R / Rfree (%)	23.2 / 29.3

The binding sites of Zinc atom in the Crystal Structure of Nad+-Dependent Dna Ligase (pdb code 1v9p). 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 Nad+-Dependent Dna Ligase, PDB code: 1v9p:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Nad+-Dependent Dna Ligase


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 Nad+-Dependent Dna Ligase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:19.9 occ:1.00 SG A:CYS430 2.4 34.6 1.0 SG A:CYS412 2.5 17.9 1.0 SG A:CYS409 2.5 12.2 1.0 SG A:CYS425 2.6 37.1 1.0 CB A:CYS430 2.7 33.7 1.0 CB A:CYS412 3.4 22.8 1.0 CB A:CYS425 3.4 30.9 1.0 CB A:CYS409 3.5 17.3 1.0 CA A:CYS430 3.9 32.3 1.0 N A:CYS412 4.3 19.9 1.0 CB A:ASN427 4.4 28.8 1.0 CA A:CYS412 4.4 17.7 1.0 C A:GLU411 4.4 33.1 1.0 O A:GLU411 4.7 35.0 1.0 CB A:GLU411 4.7 48.0 1.0 C A:CYS430 4.8 29.6 1.0 CA A:CYS409 4.9 22.2 1.0 CA A:CYS425 4.9 28.3 1.0 N A:CYS430 4.9 34.0 1.0 CD A:LYS433 5.0 30.5 1.0 CA A:GLU411 5.0 35.2 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Nad+-Dependent Dna Ligase


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 Nad+-Dependent Dna Ligase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2701 b:29.2 occ:1.00 SG B:CYS2425 2.3 19.9 1.0 SG B:CYS2409 2.4 18.9 1.0 SG B:CYS2430 2.5 34.3 1.0 SG B:CYS2412 2.5 19.6 1.0 CB B:CYS2425 2.9 25.2 1.0 CB B:CYS2409 3.0 23.3 1.0 CB B:CYS2412 3.4 25.2 1.0 N B:CYS2412 3.5 35.5 1.0 CB B:CYS2430 3.5 29.8 1.0 CA B:CYS2412 4.0 33.4 1.0 CB B:GLU2411 4.2 50.0 1.0 CA B:CYS2425 4.4 25.3 1.0 C B:GLU2411 4.4 35.5 1.0 CA B:CYS2409 4.5 21.7 1.0 CA B:CYS2430 4.6 21.9 1.0 CG1 B:VAL2332 4.7 41.2 1.0 CA B:GLU2411 4.7 35.9 1.0 N B:GLU2411 4.7 33.5 1.0 C B:CYS2412 4.7 34.9 1.0 CB B:ASN2427 4.9 16.4 1.0 C B:CYS2409 4.9 21.9 1.0 N B:GLY2413 4.9 35.2 1.0

J.Y.Lee, C.Chang, H.K.Song, J.Moon, J.K.Yang, H.K.Kim, S.T.Kwon, S.W.Suh. Crystal Structure of Nad(+)-Dependent Dna Ligase: Modular Architecture and Functional Implications. Embo J. V. 19 1119 2000.
ISSN: ISSN 0261-4189
PubMed: 10698952
DOI: 10.1093/EMBOJ/19.5.1119