Iron in PDB 6fws: Structure of Ding in Complex with Ssdna and Adpbef

The structure of Structure of Ding in Complex with Ssdna and Adpbef, PDB code: 6fws was solved by K.Cheng, D.Wigley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	63.37 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	109.771, 119.751, 126.740, 90.00, 90.00, 90.00
R / Rfree (%)	21.9 / 25.6

The structure of Structure of Ding in Complex with Ssdna and Adpbef also contains other interesting chemical elements:

Fluorine	(F)	6 atoms
Magnesium	(Mg)	2 atoms

The binding sites of Iron atom in the Structure of Ding in Complex with Ssdna and Adpbef (pdb code 6fws). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Structure of Ding in Complex with Ssdna and Adpbef, PDB code: 6fws:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the Structure of Ding in Complex with Ssdna and Adpbef


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Ding in Complex with Ssdna and Adpbef within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe801 b:0.7 occ:1.00 FE1 A:SF4801 0.0 0.7 1.0 S3 A:SF4801 2.2 0.8 1.0 S4 A:SF4801 2.2 83.5 1.0 S2 A:SF4801 2.2 0.5 1.0 SG A:CYS120 2.8 73.8 1.0 CB A:CYS120 2.9 63.1 1.0 FE4 A:SF4801 3.0 0.3 1.0 FE2 A:SF4801 3.1 1.0 1.0 FE3 A:SF4801 3.1 0.4 1.0 CA A:CYS120 3.4 59.7 1.0 O A:HOH919 3.7 71.2 1.0 CD A:PRO121 3.7 65.9 1.0 N A:PRO121 3.8 68.2 1.0 S1 A:SF4801 3.8 0.9 1.0 C A:CYS120 3.8 64.7 1.0 CG A:ARG122 4.0 64.8 1.0 NH1 A:ARG122 4.0 77.5 1.0 N A:ARG122 4.3 56.7 1.0 CD A:ARG122 4.4 70.4 1.0 CZ A:ARG122 4.6 74.5 1.0 CB A:ARG122 4.7 69.9 1.0 O A:CYS120 4.7 63.9 1.0 NE A:ARG122 4.8 80.7 1.0 N A:CYS120 4.8 61.0 1.0 CA A:PRO121 4.9 65.6 1.0 CG A:PRO121 5.0 61.0 1.0

Iron binding site 2 out of 8 in the Structure of Ding in Complex with Ssdna and Adpbef


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Ding in Complex with Ssdna and Adpbef within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe801 b:1.0 occ:1.00 FE2 A:SF4801 0.0 1.0 1.0 S1 A:SF4801 2.2 0.9 1.0 S4 A:SF4801 2.2 83.5 1.0 S3 A:SF4801 2.2 0.8 1.0 FE4 A:SF4801 3.1 0.3 1.0 FE1 A:SF4801 3.1 0.7 1.0 FE3 A:SF4801 3.1 0.4 1.0 NH1 A:ARG122 3.2 77.5 1.0 S2 A:SF4801 3.8 0.5 1.0 O A:HOH919 4.4 71.2 1.0 CZ A:ARG122 4.5 74.5 1.0 CD A:ARG122 4.6 70.4 1.0 NE A:ARG122 5.0 80.7 1.0

Iron binding site 3 out of 8 in the Structure of Ding in Complex with Ssdna and Adpbef


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Ding in Complex with Ssdna and Adpbef within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe801 b:0.4 occ:1.00 FE3 A:SF4801 0.0 0.4 1.0 S4 A:SF4801 2.2 83.5 1.0 S2 A:SF4801 2.2 0.5 1.0 S1 A:SF4801 2.2 0.9 1.0 FE4 A:SF4801 3.1 0.3 1.0 FE2 A:SF4801 3.1 1.0 1.0 FE1 A:SF4801 3.1 0.7 1.0 NH2 A:ARG115 3.1 67.6 1.0 S3 A:SF4801 3.9 0.8 1.0 O A:HOH919 4.0 71.2 1.0 CZ A:ARG115 4.1 62.9 1.0 SG A:CYS205 4.4 78.3 1.0 NE A:ARG115 4.5 65.8 1.0 OG1 A:THR189 4.8 73.7 1.0 CB A:CYS205 4.9 62.2 1.0 NH1 A:ARG122 5.0 77.5 1.0 CB A:CYS120 5.0 63.1 1.0

Iron binding site 4 out of 8 in the Structure of Ding in Complex with Ssdna and Adpbef


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Ding in Complex with Ssdna and Adpbef within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe801 b:0.3 occ:1.00 FE4 A:SF4801 0.0 0.3 1.0 S3 A:SF4801 2.2 0.8 1.0 S2 A:SF4801 2.2 0.5 1.0 S1 A:SF4801 2.2 0.9 1.0 CB A:CYS205 2.9 62.2 1.0 SG A:CYS205 2.9 78.3 1.0 FE1 A:SF4801 3.0 0.7 1.0 FE2 A:SF4801 3.1 1.0 1.0 FE3 A:SF4801 3.1 0.4 1.0 CD A:PRO121 3.7 65.9 1.0 S4 A:SF4801 3.8 83.5 1.0 CG A:PRO121 4.3 61.0 1.0 CA A:CYS205 4.3 63.8 1.0 N A:PRO121 4.6 68.2 1.0 N A:CYS205 4.7 66.3 1.0

Iron binding site 5 out of 8 in the Structure of Ding in Complex with Ssdna and Adpbef


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of Ding in Complex with Ssdna and Adpbef within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe801 b:0.4 occ:1.00 FE1 B:SF4801 0.0 0.4 1.0 S2 B:SF4801 2.2 0.6 1.0 S4 B:SF4801 2.2 0.2 1.0 S3 B:SF4801 2.2 0.6 1.0 NH2 B:ARG115 2.8 69.3 1.0 FE3 B:SF4801 3.1 0.9 1.0 FE2 B:SF4801 3.1 89.5 1.0 FE4 B:SF4801 3.1 84.8 1.0 CE2 B:PHE208 3.4 59.4 1.0 O B:HOH1056 3.6 40.8 1.0 S1 B:SF4801 3.8 92.4 1.0 CZ B:PHE208 4.0 46.6 1.0 CZ B:ARG115 4.1 68.0 1.0 CD2 B:PHE208 4.4 52.9 1.0 O B:HOH1052 4.5 61.1 1.0 O B:HOH1039 4.6 63.3 1.0 O B:HOH1054 4.8 54.9 1.0 NH1 B:ARG115 4.8 67.2 1.0 CB B:CYS205 4.8 60.1 1.0 NE B:ARG115 5.0 65.5 1.0 SG B:CYS205 5.0 88.0 1.0

Iron binding site 6 out of 8 in the Structure of Ding in Complex with Ssdna and Adpbef


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure of Ding in Complex with Ssdna and Adpbef within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe801 b:89.5 occ:1.00 FE2 B:SF4801 0.0 89.5 1.0 S3 B:SF4801 2.2 0.6 1.0 S1 B:SF4801 2.2 92.4 1.0 S4 B:SF4801 2.2 0.2 1.0 SG B:CYS120 2.8 54.3 1.0 O B:HOH1039 3.0 63.3 1.0 FE4 B:SF4801 3.1 84.8 1.0 FE1 B:SF4801 3.1 0.4 1.0 FE3 B:SF4801 3.2 0.9 1.0 CB B:CYS120 3.2 50.1 1.0 CA B:CYS120 3.6 43.7 1.0 S2 B:SF4801 3.8 0.6 1.0 CD B:PRO121 4.0 52.5 1.0 C B:CYS120 4.2 47.2 1.0 N B:PRO121 4.3 52.9 1.0 CB B:THR189 4.3 67.7 1.0 CG2 B:THR189 4.5 58.8 1.0 NH2 B:ARG115 4.7 69.3 1.0 N B:ARG122 4.8 48.0 1.0 N B:CYS120 4.9 42.7 1.0 OG1 B:THR189 4.9 78.2 1.0 CB B:ARG122 5.0 56.6 1.0 NH2 B:ARG122 5.0 67.1 1.0

Iron binding site 7 out of 8 in the Structure of Ding in Complex with Ssdna and Adpbef


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Structure of Ding in Complex with Ssdna and Adpbef within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe801 b:0.9 occ:1.00 FE3 B:SF4801 0.0 0.9 1.0 S1 B:SF4801 2.2 92.4 1.0 S2 B:SF4801 2.2 0.6 1.0 S4 B:SF4801 2.2 0.2 1.0 FE1 B:SF4801 3.1 0.4 1.0 FE4 B:SF4801 3.1 84.8 1.0 FE2 B:SF4801 3.2 89.5 1.0 S3 B:SF4801 3.8 0.6 1.0 O B:HOH1056 4.0 40.8 1.0 CD B:ARG122 4.2 64.0 1.0 O B:HOH1039 4.3 63.3 1.0 CG B:ARG122 4.5 58.7 1.0 O B:HOH1052 4.8 61.1 1.0

Iron binding site 8 out of 8 in the Structure of Ding in Complex with Ssdna and Adpbef


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Structure of Ding in Complex with Ssdna and Adpbef within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe801 b:84.8 occ:1.00 FE4 B:SF4801 0.0 84.8 1.0 S1 B:SF4801 2.2 92.4 1.0 S3 B:SF4801 2.2 0.6 1.0 S2 B:SF4801 2.2 0.6 1.0 CB B:CYS205 2.9 60.1 1.0 SG B:CYS205 2.9 88.0 1.0 FE2 B:SF4801 3.1 89.5 1.0 FE1 B:SF4801 3.1 0.4 1.0 FE3 B:SF4801 3.1 0.9 1.0 CD B:PRO121 3.5 52.5 1.0 S4 B:SF4801 3.8 0.2 1.0 CG B:PRO121 4.0 53.6 1.0 CA B:CYS205 4.0 58.6 1.0 O B:HOH1054 4.2 54.9 1.0 N B:PRO121 4.6 52.9 1.0 CE2 B:PHE208 4.7 59.4 1.0 CB B:PRO121 4.8 43.9 1.0 N B:CYS205 4.9 49.7 1.0 CD2 B:PHE208 4.9 52.9 1.0

K.Cheng, D.B.Wigley. Dna Translocation Mechanism of An Xpd Family Helicase. Elife V. 7 2018.
ISSN: ESSN 2050-084X
PubMed: 30520735
DOI: 10.7554/ELIFE.42400