Zinc in PDB 4lmg: Crystal Structure of AFT2 in Complex with Dna

The structure of Crystal Structure of AFT2 in Complex with Dna, PDB code: 4lmg was solved by C.B.Poor, R.Sanishvili, J.P.Schuermann, C.He, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.93 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.536, 127.453, 70.766, 90.00, 90.04, 90.00
R / Rfree (%)	18.9 / 23.6

The binding sites of Zinc atom in the Crystal Structure of AFT2 in Complex with Dna (pdb code 4lmg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of AFT2 in Complex with Dna, PDB code: 4lmg:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of AFT2 in Complex with Dna


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 AFT2 in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:37.3 occ:1.00 NE2 A:HIS135 2.0 36.3 1.0 ND1 A:HIS133 2.1 30.6 1.0 SG A:CYS109 2.3 35.4 1.0 SG A:CYS86 2.3 27.9 1.0 CE1 A:HIS133 2.9 28.0 1.0 CE1 A:HIS135 3.0 32.6 1.0 CD2 A:HIS135 3.0 40.2 1.0 CB A:CYS86 3.2 33.6 1.0 CG A:HIS133 3.2 33.4 1.0 CB A:CYS109 3.3 33.9 1.0 CB A:HIS133 3.7 43.5 1.0 O A:HOH302 3.9 28.2 1.0 CB A:PHE111 3.9 32.3 1.0 NE2 A:HIS133 4.1 32.8 1.0 ND1 A:HIS135 4.1 40.4 1.0 CG A:HIS135 4.1 44.1 1.0 CD2 A:HIS133 4.2 37.8 1.0 CA A:HIS133 4.3 53.0 1.0 O A:HOH305 4.5 24.5 1.0 CA A:CYS86 4.6 34.4 1.0 CG A:PHE111 4.6 28.3 1.0 CA A:CYS109 4.7 42.9 1.0 N A:SER134 4.9 48.7 1.0 CD1 A:PHE111 4.9 21.9 1.0 CD2 A:LEU137 4.9 34.3 1.0 N A:CYS86 5.0 20.5 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of AFT2 in Complex with Dna


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 AFT2 in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:37.7 occ:1.00 NE2 B:HIS135 2.0 41.6 1.0 ND1 B:HIS133 2.1 28.3 1.0 SG B:CYS86 2.2 23.7 1.0 SG B:CYS109 2.3 36.8 1.0 CE1 B:HIS133 3.0 28.3 1.0 CD2 B:HIS135 3.0 42.4 1.0 CE1 B:HIS135 3.0 31.9 1.0 CG B:HIS133 3.1 38.3 1.0 CB B:CYS86 3.2 26.0 1.0 CB B:CYS109 3.4 31.8 1.0 CB B:HIS133 3.5 42.7 1.0 CB B:PHE111 3.9 35.4 1.0 O B:HOH302 3.9 26.2 1.0 CA B:HIS133 4.1 45.7 1.0 NE2 B:HIS133 4.1 32.0 1.0 ND1 B:HIS135 4.1 38.9 1.0 CG B:HIS135 4.1 43.1 1.0 CD2 B:HIS133 4.2 31.5 1.0 O B:HOH307 4.3 28.4 1.0 CA B:CYS86 4.6 31.2 1.0 CG B:PHE111 4.6 32.2 1.0 N B:SER134 4.7 46.7 1.0 CA B:CYS109 4.8 40.2 1.0 CD1 B:PHE111 4.8 29.2 1.0 C B:HIS133 4.9 47.0 1.0 N B:CYS86 5.0 22.5 1.0 N B:PHE111 5.0 47.4 1.0 CD2 B:LEU137 5.0 35.4 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of AFT2 in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of AFT2 in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:0.3 occ:1.00 OD2 B:ASP53 2.0 76.2 1.0 ND1 B:HIS55 2.0 73.2 1.0 O B:HOH301 2.1 75.3 1.0 CE1 B:HIS55 2.6 76.9 1.0 CG B:ASP53 2.7 77.4 1.0 OD1 B:ASP53 2.7 83.2 1.0 CG B:HIS55 3.3 68.4 1.0 NE2 B:HIS55 3.8 73.2 1.0 CB B:HIS55 3.9 62.9 1.0 CB B:ASP53 4.2 71.7 1.0 CD2 B:HIS55 4.2 70.9 1.0 N B:HIS55 4.8 54.0 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of AFT2 in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of AFT2 in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:45.7 occ:1.00 NE2 C:HIS135 2.0 53.4 1.0 ND1 C:HIS133 2.0 37.2 1.0 SG C:CYS86 2.3 26.1 1.0 SG C:CYS109 2.3 42.0 1.0 CE1 C:HIS133 2.8 34.8 1.0 CE1 C:HIS135 2.9 50.9 1.0 CD2 C:HIS135 3.1 47.2 1.0 CB C:CYS86 3.2 28.7 1.0 CG C:HIS133 3.2 39.7 1.0 CB C:CYS109 3.3 31.7 1.0 CB C:HIS133 3.7 40.8 1.0 CB C:PHE111 4.0 28.2 1.0 O C:HOH303 4.0 28.0 1.0 ND1 C:HIS135 4.0 47.1 1.0 NE2 C:HIS133 4.0 36.5 1.0 CG C:HIS135 4.2 42.8 1.0 CA C:HIS133 4.2 46.5 1.0 CD2 C:HIS133 4.2 37.5 1.0 O C:HOH305 4.2 34.6 1.0 CA C:CYS86 4.6 31.0 1.0 CG C:PHE111 4.6 27.9 1.0 N C:SER134 4.7 53.4 1.0 CD2 C:PHE111 4.8 21.8 1.0 CA C:CYS109 4.8 45.7 1.0 N C:CYS86 5.0 22.5 1.0 CD2 C:LEU137 5.0 25.6 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of AFT2 in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of AFT2 in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:38.1 occ:1.00 ND1 D:HIS133 2.0 26.2 1.0 NE2 D:HIS135 2.0 38.4 1.0 SG D:CYS86 2.3 23.4 1.0 SG D:CYS109 2.3 37.7 1.0 CE1 D:HIS133 2.9 31.6 1.0 CE1 D:HIS135 3.0 37.6 1.0 CD2 D:HIS135 3.0 38.7 1.0 CG D:HIS133 3.1 32.2 1.0 CB D:CYS86 3.2 24.5 1.0 CB D:CYS109 3.3 32.8 1.0 CB D:HIS133 3.6 30.6 1.0 CB D:PHE111 3.9 33.0 1.0 NE2 D:HIS133 4.1 30.7 1.0 O D:HOH307 4.1 27.5 1.0 ND1 D:HIS135 4.1 40.3 1.0 CG D:HIS135 4.1 41.0 1.0 CD2 D:HIS133 4.2 23.5 1.0 CA D:HIS133 4.2 41.8 1.0 O D:HOH311 4.3 30.1 1.0 CG D:PHE111 4.6 22.4 1.0 CA D:CYS86 4.6 24.0 1.0 CA D:CYS109 4.7 35.9 1.0 CD1 D:PHE111 4.7 24.2 1.0 N D:SER134 4.7 42.8 1.0 CD2 D:LEU137 4.8 38.0 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of AFT2 in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of AFT2 in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn202 b:69.3 occ:1.00 OD2 D:ASP53 2.0 52.8 1.0 ND1 D:HIS55 2.0 40.8 1.0 O D:HOH302 2.1 42.1 1.0 O D:HOH301 2.1 33.8 1.0 OD1 D:ASP53 2.5 59.8 1.0 CG D:ASP53 2.6 52.1 1.0 CE1 D:HIS55 2.8 38.2 1.0 CG D:HIS55 3.2 41.9 1.0 CB D:HIS55 3.7 31.9 1.0 NE2 D:HIS55 3.9 37.0 1.0 CB D:ASP53 4.1 49.0 1.0 O D:HOH344 4.1 54.2 1.0 CD2 D:HIS55 4.2 43.6 1.0 O D:HOH343 4.2 60.9 1.0 N D:HIS55 4.4 27.0 1.0 NZ C:LYS162 4.4 89.8 1.0 CA D:HIS55 4.7 31.9 1.0 O D:HOH341 4.9 49.8 1.0 N D:ARG54 4.9 29.9 1.0 CG D:ARG54 5.0 37.2 1.0 CA D:ASP53 5.0 49.5 1.0

C.B.Poor, S.V.Wegner, H.Li, A.C.Dlouhy, J.P.Schuermann, R.Sanishvili, J.R.Hinshaw, P.J.Riggs-Gelasco, C.E.Outten, C.He. Molecular Mechanism and Structure of the Saccharomyces Cerevisiae Iron Regulator AFT2. Proc.Natl.Acad.Sci.Usa V. 111 4043 2014.
ISSN: ISSN 0027-8424
PubMed: 24591629
DOI: 10.1073/PNAS.1318869111