Zinc in PDB 5fd3: Structure of LIN54 Tesmin Domain Bound to Dna

The structure of Structure of LIN54 Tesmin Domain Bound to Dna, PDB code: 5fd3 was solved by A.H.Marceau, J.G.Felthousen, P.D.Goetsch, H.Lee, S.M.Tripathi, S.Strome, L.Litovchick, S.M.Rubin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.00 / 2.42
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	39.320, 53.880, 67.120, 98.40, 102.53, 106.57
R / Rfree (%)	18.1 / 23.8

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Structure of LIN54 Tesmin Domain Bound to Dna (pdb code 5fd3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Structure of LIN54 Tesmin Domain Bound to Dna, PDB code: 5fd3:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in the Structure of LIN54 Tesmin Domain Bound to Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of LIN54 Tesmin Domain Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:48.4 occ:1.00 SG A:CYS527 2.1 44.8 1.0 SG A:CYS537 2.3 47.3 1.0 SG A:CYS532 2.4 39.6 1.0 SG A:CYS525 2.5 42.8 1.0 CB A:CYS532 3.2 32.4 1.0 CB A:CYS525 3.2 35.2 1.0 CB A:CYS527 3.2 59.5 1.0 CB A:CYS537 3.3 37.3 1.0 ZN A:ZN702 3.6 51.7 1.0 ZN A:ZN703 3.8 54.9 1.0 CA A:CYS532 3.8 41.3 1.0 CB A:CYS551 4.1 41.7 1.0 CA A:CYS537 4.2 49.6 1.0 SG A:CYS546 4.2 60.2 1.0 N A:CYS527 4.3 52.3 1.0 CA A:CYS527 4.4 55.4 1.0 N A:CYS532 4.5 46.3 1.0 SG A:CYS551 4.6 54.5 1.0 CA A:CYS525 4.6 47.7 1.0 C A:CYS537 4.9 55.6 1.0 C A:CYS525 4.9 57.5 1.0 CB A:CYS539 4.9 52.7 1.0 SG A:CYS539 4.9 65.3 1.0

Zinc binding site 2 out of 12 in the Structure of LIN54 Tesmin Domain Bound to Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of LIN54 Tesmin Domain Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn702 b:51.7 occ:1.00 SG A:CYS551 2.2 54.5 1.0 SG A:CYS532 2.4 39.6 1.0 SG A:CYS554 2.4 53.1 1.0 SG A:CYS546 2.6 60.2 1.0 CB A:CYS551 3.1 41.7 1.0 CB A:CYS532 3.2 32.4 1.0 CB A:CYS554 3.3 60.0 1.0 CB A:CYS546 3.4 66.8 1.0 ZN A:ZN701 3.6 48.4 1.0 ZN A:ZN703 3.7 54.9 1.0 SG A:CYS525 3.7 42.8 1.0 CA A:CYS554 4.2 55.2 1.0 CB A:ASN556 4.4 51.3 1.0 CA A:CYS551 4.5 41.5 1.0 CB A:CYS549 4.7 55.9 1.0 CA A:CYS532 4.7 41.3 1.0 O A:LEU531 4.8 49.6 1.0 CA A:CYS546 4.9 62.7 1.0 SG A:CYS549 5.0 59.5 1.0 SG A:CYS537 5.0 47.3 1.0 N A:CYS551 5.0 39.8 1.0

Zinc binding site 3 out of 12 in the Structure of LIN54 Tesmin Domain Bound to Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of LIN54 Tesmin Domain Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn703 b:54.9 occ:1.00 SG A:CYS539 2.3 65.3 1.0 SG A:CYS549 2.3 59.5 1.0 SG A:CYS525 2.3 42.8 1.0 SG A:CYS546 2.4 60.2 1.0 CB A:CYS546 3.1 66.8 1.0 CB A:CYS539 3.1 52.7 1.0 CB A:CYS525 3.3 35.2 1.0 CB A:CYS549 3.3 55.9 1.0 ZN A:ZN702 3.7 51.7 1.0 CA A:CYS546 3.8 62.7 1.0 ZN A:ZN701 3.8 48.4 1.0 N A:CYS525 3.9 60.7 1.0 CA A:CYS525 4.2 47.7 1.0 SG A:CYS551 4.2 54.5 1.0 SG A:CYS537 4.4 47.3 1.0 CA A:CYS539 4.6 50.7 1.0 N A:CYS546 4.7 54.8 1.0 CA A:CYS549 4.7 62.9 1.0 C A:CYS546 4.8 70.0 1.0 O A:CYS525 4.8 64.0 1.0 SG A:CYS532 4.8 39.6 1.0 C A:CYS525 4.8 57.5 1.0 N A:ASN547 4.9 75.9 1.0 N A:CYS539 4.9 54.6 1.0 ND2 A:ASN556 5.0 60.0 1.0

Zinc binding site 4 out of 12 in the Structure of LIN54 Tesmin Domain Bound to Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of LIN54 Tesmin Domain Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn704 b:45.8 occ:1.00 SG A:CYS611 2.2 59.0 1.0 SG A:CYS599 2.3 46.0 1.0 SG A:CYS601 2.4 49.4 1.0 SG A:CYS606 2.4 41.7 1.0 CB A:CYS599 3.1 38.4 1.0 CB A:CYS611 3.1 53.4 1.0 CB A:CYS606 3.2 35.6 1.0 CB A:CYS601 3.3 30.4 1.0 ZN A:ZN705 3.6 46.8 1.0 ZN A:ZN706 3.7 55.4 1.0 SG A:CYS620 3.9 44.1 1.0 CA A:CYS606 3.9 33.1 1.0 CA A:CYS611 4.0 41.8 1.0 SG A:CYS626 4.3 52.1 1.0 N A:CYS601 4.3 45.2 1.0 CA A:CYS601 4.5 37.8 1.0 CA A:CYS599 4.5 50.9 1.0 N A:CYS606 4.6 32.2 1.0 CB A:CYS613 4.7 41.4 1.0 C A:CYS611 4.8 35.1 1.0 OG A:SER604 4.9 53.6 1.0 SG A:CYS613 4.9 49.5 1.0 N A:GLU612 4.9 35.8 1.0 C A:CYS599 4.9 49.5 1.0 CB A:CYS626 4.9 57.2 1.0

Zinc binding site 5 out of 12 in the Structure of LIN54 Tesmin Domain Bound to Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of LIN54 Tesmin Domain Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn705 b:46.8 occ:1.00 SG A:CYS626 2.1 52.1 1.0 SG A:CYS620 2.2 44.1 1.0 SG A:CYS629 2.4 44.8 1.0 SG A:CYS606 2.5 41.7 1.0 CB A:CYS626 3.1 57.2 1.0 CB A:CYS629 3.1 39.0 1.0 CB A:CYS620 3.2 49.0 1.0 CB A:CYS606 3.2 35.6 1.0 ZN A:ZN704 3.6 45.8 1.0 SG A:CYS599 3.7 46.0 1.0 ZN A:ZN706 3.8 55.4 1.0 CA A:CYS629 4.1 46.8 1.0 CA A:CYS626 4.5 61.9 1.0 CB A:ASN631 4.6 35.0 1.0 CA A:CYS620 4.7 55.0 1.0 CA A:CYS606 4.7 33.1 1.0 CB A:CYS624 4.8 46.1 1.0 SG A:CYS611 4.9 59.0 1.0 O A:ASN631 4.9 56.4 1.0

Zinc binding site 6 out of 12 in the Structure of LIN54 Tesmin Domain Bound to Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of LIN54 Tesmin Domain Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn706 b:55.4 occ:1.00 SG A:CYS613 2.2 49.5 1.0 SG A:CYS620 2.4 44.1 1.0 SG A:CYS624 2.4 54.5 1.0 SG A:CYS599 2.5 46.0 1.0 CB A:CYS613 3.2 41.4 1.0 CB A:CYS599 3.3 38.4 1.0 CB A:CYS620 3.3 49.0 1.0 CB A:CYS624 3.4 46.1 1.0 N A:CYS599 3.6 55.4 1.0 ZN A:ZN704 3.7 45.8 1.0 CA A:CYS620 3.7 55.0 1.0 ZN A:ZN705 3.8 46.8 1.0 SG A:CYS626 4.0 52.1 1.0 CA A:CYS599 4.0 50.9 1.0 SG A:CYS611 4.1 59.0 1.0 CA A:CYS613 4.5 40.8 1.0 C A:GLY598 4.6 65.9 1.0 N A:CYS620 4.6 55.2 1.0 CA A:CYS624 4.6 60.6 1.0 N A:CYS613 4.7 48.4 1.0 CA A:GLY598 4.7 76.0 1.0 N A:SER621 4.8 65.9 1.0 C A:CYS620 4.8 58.9 1.0 C A:CYS599 4.8 49.5 1.0 SG A:CYS606 4.9 41.7 1.0 O A:CYS599 4.9 53.6 1.0

Zinc binding site 7 out of 12 in the Structure of LIN54 Tesmin Domain Bound to Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of LIN54 Tesmin Domain Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn701 b:42.4 occ:1.00 SG B:CYS527 2.3 45.5 1.0 SG B:CYS537 2.4 50.6 1.0 SG B:CYS525 2.4 43.0 1.0 SG B:CYS532 2.5 39.2 1.0 CB B:CYS532 3.1 35.0 1.0 CB B:CYS525 3.1 37.8 1.0 CB B:CYS537 3.3 55.6 1.0 CB B:CYS527 3.4 53.4 1.0 ZN B:ZN702 3.6 45.4 1.0 CA B:CYS532 3.8 37.1 1.0 ZN B:ZN703 3.8 53.6 1.0 SG B:CYS546 3.9 55.3 1.0 CA B:CYS537 4.1 47.5 1.0 CB B:CYS551 4.3 39.7 1.0 N B:CYS527 4.5 42.8 1.0 SG B:CYS551 4.5 45.2 1.0 CA B:CYS525 4.6 44.1 1.0 CA B:CYS527 4.6 47.6 1.0 N B:CYS532 4.6 46.8 1.0 CB B:CYS539 4.8 40.0 1.0 SG B:CYS539 4.8 61.8 1.0 C B:CYS537 4.9 41.3 1.0 C B:CYS525 4.9 49.5 1.0

Zinc binding site 8 out of 12 in the Structure of LIN54 Tesmin Domain Bound to Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of LIN54 Tesmin Domain Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn702 b:45.4 occ:1.00 SG B:CYS551 2.0 45.2 1.0 SG B:CYS532 2.3 39.2 1.0 SG B:CYS546 2.4 55.3 1.0 SG B:CYS554 2.5 49.1 1.0 CB B:CYS551 3.1 39.7 1.0 CB B:CYS532 3.2 35.0 1.0 CB B:CYS554 3.3 35.6 1.0 CB B:CYS546 3.3 61.7 1.0 SG B:CYS525 3.5 43.0 1.0 ZN B:ZN701 3.6 42.4 1.0 ZN B:ZN703 3.7 53.6 1.0 CA B:CYS554 4.2 49.4 1.0 CB B:ASN556 4.4 52.7 1.0 CA B:CYS551 4.5 46.6 1.0 CA B:CYS532 4.6 37.1 1.0 CB B:CYS549 4.7 38.7 1.0 CA B:CYS546 4.7 58.2 1.0 O B:LEU531 4.7 45.4 1.0 N B:CYS551 4.9 46.2 1.0

Zinc binding site 9 out of 12 in the Structure of LIN54 Tesmin Domain Bound to Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of LIN54 Tesmin Domain Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn703 b:53.6 occ:1.00 SG B:CYS549 2.2 53.1 1.0 SG B:CYS539 2.3 61.8 1.0 SG B:CYS525 2.4 43.0 1.0 SG B:CYS546 2.5 55.3 1.0 CB B:CYS546 3.1 61.7 1.0 CB B:CYS549 3.2 38.7 1.0 CB B:CYS539 3.3 40.0 1.0 CB B:CYS525 3.4 37.8 1.0 CA B:CYS546 3.6 58.2 1.0 ZN B:ZN702 3.7 45.4 1.0 ZN B:ZN701 3.8 42.4 1.0 N B:CYS525 3.8 50.8 1.0 SG B:CYS551 4.2 45.2 1.0 CA B:CYS525 4.2 44.1 1.0 SG B:CYS537 4.4 50.6 1.0 CA B:CYS549 4.6 53.6 1.0 C B:CYS546 4.6 65.3 1.0 N B:CYS546 4.6 57.1 1.0 N B:ASN547 4.7 63.6 1.0 CA B:CYS539 4.7 41.5 1.0 O B:CYS525 4.8 55.8 1.0 C B:CYS525 4.9 49.5 1.0 SG B:CYS532 4.9 39.2 1.0 C B:PRO524 4.9 60.6 1.0 ND2 B:ASN556 5.0 61.0 1.0

Zinc binding site 10 out of 12 in the Structure of LIN54 Tesmin Domain Bound to Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of LIN54 Tesmin Domain Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn704 b:49.3 occ:1.00 SG B:CYS611 2.2 53.0 1.0 SG B:CYS601 2.2 52.5 1.0 SG B:CYS599 2.4 43.2 1.0 SG B:CYS606 2.7 53.5 1.0 CB B:CYS611 3.1 47.2 1.0 CB B:CYS599 3.1 42.1 1.0 CB B:CYS606 3.2 38.6 1.0 CB B:CYS601 3.4 41.9 1.0 ZN B:ZN706 3.6 53.2 1.0 ZN B:ZN705 3.6 50.9 1.0 CA B:CYS606 3.8 47.7 1.0 CA B:CYS611 3.9 43.1 1.0 SG B:CYS620 4.0 51.0 1.0 N B:CYS601 4.3 52.2 1.0 CA B:CYS601 4.5 48.2 1.0 SG B:CYS626 4.5 57.2 1.0 CA B:CYS599 4.6 49.4 1.0 CB B:CYS613 4.7 63.6 1.0 C B:CYS611 4.7 45.6 1.0 N B:GLU612 4.7 54.3 1.0 N B:CYS606 4.7 50.8 1.0 O B:HOH804 4.8 36.3 1.0 N B:CYS613 4.9 55.8 1.0 SG B:CYS613 4.9 62.7 1.0 C B:CYS599 5.0 52.1 1.0

A.H.Marceau, J.G.Felthousen, P.D.Goetsch, A.N.Iness, H.W.Lee, S.M.Tripathi, S.Strome, L.Litovchick, S.M.Rubin. Structural Basis For LIN54 Recognition of Chr Elements in Cell Cycle-Regulated Promoters. Nat Commun V. 7 12301 2016.
ISSN: ESSN 2041-1723
PubMed: 27465258
DOI: 10.1038/NCOMMS12301