Iron in PDB 6ppu: Cryo-Em Structure of Adnab-Amppnp-Dna Complex

All present enzymatic activity of Cryo-Em Structure of Adnab-Amppnp-Dna Complex:
3.6.4.12;

The structure of Cryo-Em Structure of Adnab-Amppnp-Dna Complex also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Iron atom in the Cryo-Em Structure of Adnab-Amppnp-Dna Complex (pdb code 6ppu). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Cryo-Em Structure of Adnab-Amppnp-Dna Complex, PDB code: 6ppu:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Cryo-Em Structure of Adnab-Amppnp-Dna Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cryo-Em Structure of Adnab-Amppnp-Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1102 b:18.0 occ:1.00 FE1 A:SF41102 0.0 18.0 1.0 S3 A:SF41102 2.3 18.0 1.0 S2 A:SF41102 2.3 18.0 1.0 S4 A:SF41102 2.3 18.0 1.0 FE4 A:SF41102 2.7 18.0 1.0 FE3 A:SF41102 2.7 18.0 1.0 FE2 A:SF41102 2.7 18.0 1.0 SG A:CYS1030 3.1 13.2 1.0 CB A:CYS1030 3.5 13.2 1.0 S1 A:SF41102 3.9 18.0 1.0 SG A:CYS1027 4.1 16.5 1.0 CA A:CYS1027 4.2 16.5 1.0 O A:GLY1026 4.4 18.5 1.0 CB A:CYS1027 4.5 16.5 1.0 NH1 A:ARG810 4.7 13.5 1.0 O A:VAL1032 4.8 15.0 1.0 CD A:ARG810 4.9 13.5 1.0 N A:CYS1027 5.0 16.5 1.0 CA A:CYS1030 5.0 13.2 1.0

Iron binding site 2 out of 4 in the Cryo-Em Structure of Adnab-Amppnp-Dna Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cryo-Em Structure of Adnab-Amppnp-Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1102 b:18.0 occ:1.00 FE2 A:SF41102 0.0 18.0 1.0 S1 A:SF41102 2.3 18.0 1.0 S4 A:SF41102 2.3 18.0 1.0 S3 A:SF41102 2.3 18.0 1.0 FE1 A:SF41102 2.7 18.0 1.0 FE4 A:SF41102 2.7 18.0 1.0 FE3 A:SF41102 2.7 18.0 1.0 SG A:CYS1036 3.1 9.6 1.0 CB A:CYS1036 3.5 9.6 1.0 O A:VAL1032 3.8 15.0 1.0 S2 A:SF41102 3.9 18.0 1.0 SG A:CYS1030 4.4 13.2 1.0 CA A:CYS1036 4.7 9.6 1.0 CD2 A:LEU809 4.7 15.5 1.0

Iron binding site 3 out of 4 in the Cryo-Em Structure of Adnab-Amppnp-Dna Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cryo-Em Structure of Adnab-Amppnp-Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1102 b:18.0 occ:1.00 FE3 A:SF41102 0.0 18.0 1.0 S1 A:SF41102 2.3 18.0 1.0 S4 A:SF41102 2.3 18.0 1.0 S2 A:SF41102 2.3 18.0 1.0 FE1 A:SF41102 2.7 18.0 1.0 FE2 A:SF41102 2.7 18.0 1.0 FE4 A:SF41102 2.7 18.0 1.0 O A:ARG1022 2.9 15.7 1.0 SG A:CYS1027 3.6 16.5 1.0 S3 A:SF41102 3.9 18.0 1.0 C A:ARG1022 4.0 15.7 1.0 SG A:CYS1036 4.2 9.6 1.0 CA A:VAL1023 4.2 13.2 1.0 N A:VAL1023 4.6 13.2 1.0 N A:ASN1024 4.7 16.8 1.0 SG A:CYS807 4.8 13.4 1.0 CG2 A:VAL1023 4.9 13.2 1.0 CB A:CYS1027 4.9 16.5 1.0

Iron binding site 4 out of 4 in the Cryo-Em Structure of Adnab-Amppnp-Dna Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cryo-Em Structure of Adnab-Amppnp-Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1102 b:18.0 occ:1.00 FE4 A:SF41102 0.0 18.0 1.0 S2 A:SF41102 2.3 18.0 1.0 S1 A:SF41102 2.3 18.0 1.0 S3 A:SF41102 2.3 18.0 1.0 FE1 A:SF41102 2.7 18.0 1.0 FE2 A:SF41102 2.7 18.0 1.0 FE3 A:SF41102 2.7 18.0 1.0 SG A:CYS807 3.0 13.4 1.0 CB A:CYS807 3.6 13.4 1.0 S4 A:SF41102 3.9 18.0 1.0 CB A:ARG810 4.0 13.5 1.0 N A:ARG810 4.3 13.5 1.0 O A:ARG1022 4.3 15.7 1.0 CA A:ARG810 4.5 13.5 1.0 CD A:ARG810 4.7 13.5 1.0 ND2 A:ASN1024 4.8 16.8 1.0 CG A:ARG810 4.8 13.5 1.0

N.Jia, M.C.Unciuleac, C.Xue, E.C.Greene, D.J.Patel, S.Shuman. Structures and Single-Molecule Analysis of Bacterial Motor Nuclease Adnab Illuminate the Mechanism of Dna Double-Strand Break Resection. Proc.Natl.Acad.Sci.Usa 2019.
ISSN: ESSN 1091-6490
PubMed: 31740608
DOI: 10.1073/PNAS.1913546116