Iron in PDB 5ean: Crystal Structure of DNA2 in Complex with A 5' Overhang Dna

All present enzymatic activity of Crystal Structure of DNA2 in Complex with A 5' Overhang Dna:
3.6.4.12;

The structure of Crystal Structure of DNA2 in Complex with A 5' Overhang Dna, PDB code: 5ean was solved by C.Zhou, S.Pourmal, N.P.Pavletich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.36
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	87.153, 118.488, 149.260, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 24.6

The structure of Crystal Structure of DNA2 in Complex with A 5' Overhang Dna also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Iron atom in the Crystal Structure of DNA2 in Complex with A 5' Overhang Dna (pdb code 5ean). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of DNA2 in Complex with A 5' Overhang Dna, PDB code: 5ean:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of DNA2 in Complex with A 5' Overhang Dna


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of DNA2 in Complex with A 5' Overhang Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1101 b:58.7 occ:1.00 FE1 A:SF41101 0.0 58.7 1.0 S2 A:SF41101 2.1 62.3 1.0 S3 A:SF41101 2.1 60.4 1.0 S4 A:SF41101 2.1 55.6 1.0 SG A:CYS137 2.3 57.9 1.0 FE3 A:SF41101 2.9 61.8 1.0 FE4 A:SF41101 2.9 67.2 1.0 FE2 A:SF41101 3.0 59.4 1.0 CB A:CYS137 3.4 58.5 1.0 S1 A:SF41101 3.7 61.9 1.0 N A:ARG140 3.9 53.6 1.0 CB A:ARG140 4.0 57.4 1.0 CG1 A:ILE388 4.1 69.7 1.0 CB A:ARG139 4.2 52.5 1.0 CD A:ARG139 4.4 53.9 1.0 CA A:ARG140 4.4 53.9 1.0 CG A:ARG139 4.6 52.0 1.0 CD1 A:ILE388 4.6 69.3 1.0 C A:ARG139 4.7 52.0 1.0 CA A:CYS137 4.8 58.6 1.0 CA A:ARG139 4.9 51.9 1.0 SG A:CYS394 5.0 74.9 1.0 SG A:CYS397 5.0 64.6 1.0

Iron binding site 2 out of 4 in the Crystal Structure of DNA2 in Complex with A 5' Overhang Dna


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of DNA2 in Complex with A 5' Overhang Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1101 b:59.4 occ:1.00 FE2 A:SF41101 0.0 59.4 1.0 S1 A:SF41101 2.1 61.9 1.0 S4 A:SF41101 2.1 55.6 1.0 S3 A:SF41101 2.2 60.4 1.0 SG A:CYS403 2.3 55.1 1.0 FE3 A:SF41101 2.9 61.8 1.0 FE4 A:SF41101 2.9 67.2 1.0 FE1 A:SF41101 3.0 58.7 1.0 CB A:CYS403 3.1 52.2 1.0 S2 A:SF41101 3.7 62.3 1.0 CD A:ARG139 4.0 53.9 1.0 CE A:MET423 4.0 81.6 1.0 NE A:ARG139 4.1 53.9 1.0 CG1 A:ILE387 4.5 59.8 1.0 CA A:CYS403 4.5 50.1 1.0 CG A:ARG139 4.7 52.0 1.0 SG A:CYS394 5.0 74.9 1.0

Iron binding site 3 out of 4 in the Crystal Structure of DNA2 in Complex with A 5' Overhang Dna


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of DNA2 in Complex with A 5' Overhang Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1101 b:61.8 occ:1.00 FE3 A:SF41101 0.0 61.8 1.0 S4 A:SF41101 2.1 55.6 1.0 S1 A:SF41101 2.1 61.9 1.0 S2 A:SF41101 2.1 62.3 1.0 SG A:CYS397 2.3 64.6 1.0 FE1 A:SF41101 2.9 58.7 1.0 FE2 A:SF41101 2.9 59.4 1.0 FE4 A:SF41101 3.0 67.2 1.0 CB A:CYS397 3.0 71.8 1.0 S3 A:SF41101 3.7 60.4 1.0 CB A:ARG140 4.2 57.4 1.0 CG A:ARG140 4.3 60.0 1.0 CA A:CYS397 4.5 74.6 1.0 CA A:ARG140 4.7 53.9 1.0 N A:ILE400 4.7 59.4 1.0 CA A:CYS394 4.7 76.9 1.0 CB A:GLN399 4.8 61.1 1.0 SG A:CYS137 4.8 57.9 1.0 C A:GLN399 4.8 59.4 1.0 CB A:CYS403 4.9 52.2 1.0 SG A:CYS403 5.0 55.1 1.0 CA A:ILE400 5.0 59.4 1.0

Iron binding site 4 out of 4 in the Crystal Structure of DNA2 in Complex with A 5' Overhang Dna


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of DNA2 in Complex with A 5' Overhang Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1101 b:67.2 occ:1.00 FE4 A:SF41101 0.0 67.2 1.0 S3 A:SF41101 2.1 60.4 1.0 S2 A:SF41101 2.2 62.3 1.0 S1 A:SF41101 2.2 61.9 1.0 SG A:CYS394 2.3 74.9 1.0 FE1 A:SF41101 2.9 58.7 1.0 FE2 A:SF41101 2.9 59.4 1.0 FE3 A:SF41101 3.0 61.8 1.0 CB A:CYS394 3.2 76.4 1.0 CA A:CYS394 3.5 76.9 1.0 S4 A:SF41101 3.7 55.6 1.0 CG1 A:ILE388 4.0 69.7 1.0 N A:CYS394 4.1 78.5 1.0 CE A:MET423 4.1 81.6 1.0 CD1 A:ILE388 4.4 69.3 1.0 C A:CYS394 4.7 79.7 1.0 CB A:CYS397 4.8 71.8 1.0 SD A:MET423 4.9 91.3 1.0 C A:THR393 4.9 79.2 1.0 SG A:CYS137 4.9 57.9 1.0 O A:CYS394 4.9 78.6 1.0 SG A:CYS397 5.0 64.6 1.0

C.Zhou, S.Pourmal, N.P.Pavletich. DNA2 Nuclease-Helicase Structure, Mechanism and Regulation By Rpa. Elife V. 4 2015.
ISSN: ESSN 2050-084X
PubMed: 26491943
DOI: 10.7554/ELIFE.09832