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Zinc in PDB 1dgs: Crystal Structure of Nad+-Dependent Dna Ligase From T. Filiformis

Enzymatic activity of Crystal Structure of Nad+-Dependent Dna Ligase From T. Filiformis

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

Protein crystallography data

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

Resolution Low / High (Å) 20.00 / 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 (%) 22.8 / 29.8

Zinc Binding Sites:

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

Zinc binding site 1 out of 2 in 1dgs

Go back to Zinc Binding Sites List in 1dgs
Zinc binding site 1 out of 2 in the Crystal Structure of Nad+-Dependent Dna Ligase From T. Filiformis


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 From T. Filiformis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:20.9
occ:1.00
SG A:CYS427 2.4 34.0 1.0
SG A:CYS409 2.5 22.6 1.0
SG A:CYS422 2.5 32.8 1.0
SG A:CYS406 2.6 11.2 1.0
CB A:CYS427 2.9 36.7 1.0
CB A:CYS409 3.2 10.0 1.0
CB A:CYS422 3.6 20.8 1.0
CB A:CYS406 3.6 5.2 1.0
CA A:CYS427 4.0 31.3 1.0
N A:CYS409 4.2 15.8 1.0
CA A:CYS409 4.3 9.3 1.0
CB A:ASN424 4.3 25.5 1.0
C A:GLU408 4.4 22.0 1.0
O A:GLU408 4.6 35.0 1.0
C A:CYS427 4.9 18.5 1.0
CA A:CYS422 5.0 18.6 1.0
CB A:HIS411 5.0 31.7 1.0

Zinc binding site 2 out of 2 in 1dgs

Go back to Zinc Binding Sites List in 1dgs
Zinc binding site 2 out of 2 in the Crystal Structure of Nad+-Dependent Dna Ligase From T. Filiformis


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 From T. Filiformis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2701

b:33.4
occ:1.00
SG B:CYS2422 2.3 11.9 1.0
SG B:CYS2406 2.4 24.4 1.0
SG B:CYS2427 2.4 25.2 1.0
SG B:CYS2409 2.5 13.4 1.0
CB B:CYS2422 3.0 25.1 1.0
CB B:CYS2406 3.1 27.4 1.0
CB B:CYS2409 3.5 11.3 1.0
N B:CYS2409 3.5 33.4 1.0
CB B:CYS2427 3.6 26.8 1.0
CA B:CYS2409 4.0 23.8 1.0
CB B:GLU2408 4.2 63.1 1.0
C B:GLU2408 4.4 42.8 1.0
CA B:CYS2422 4.5 21.2 1.0
CA B:CYS2406 4.5 21.8 1.0
CA B:GLU2408 4.6 44.6 1.0
N B:GLU2408 4.6 38.5 1.0
CA B:CYS2427 4.7 29.1 1.0
CG2 B:VAL2329 4.8 24.6 1.0
C B:CYS2409 4.8 30.6 1.0
C B:CYS2406 4.8 20.0 1.0
CG1 B:VAL2329 4.8 17.9 1.0
O B:CYS2406 4.9 15.1 1.0
CB B:ASN2424 4.9 13.5 1.0
N B:GLY2410 5.0 33.9 1.0

Reference:

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
Page generated: Mon Jan 25 16:08:43 2021

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