Iron in PDB 6ppj: Cryo-Em Structure of Adna(D934A)-Adnb(D1014A) in Complex with Amppnp

All present enzymatic activity of Cryo-Em Structure of Adna(D934A)-Adnb(D1014A) in Complex with Amppnp:
3.6.4.12;

The binding sites of Iron atom in the Cryo-Em Structure of Adna(D934A)-Adnb(D1014A) in Complex with Amppnp (pdb code 6ppj). 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 Adna(D934A)-Adnb(D1014A) in Complex with Amppnp, PDB code: 6ppj:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Cryo-Em Structure of Adna(D934A)-Adnb(D1014A) in Complex with Amppnp


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 Adna(D934A)-Adnb(D1014A) in Complex with Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1101 b:21.1 occ:1.00 FE1 A:SF41101 0.0 21.1 1.0 S3 A:SF41101 2.3 21.1 1.0 S4 A:SF41101 2.3 21.1 1.0 S2 A:SF41101 2.3 21.1 1.0 FE4 A:SF41101 2.7 21.1 1.0 FE2 A:SF41101 2.7 21.1 1.0 FE3 A:SF41101 2.7 21.1 1.0 SG A:CYS1030 3.1 27.5 1.0 O A:VAL1032 3.5 21.5 1.0 CB A:CYS1030 3.7 27.5 1.0 S1 A:SF41101 3.9 21.1 1.0 CD A:ARG810 4.2 18.3 1.0 CA A:CYS1027 4.6 31.5 1.0 CG A:ARG810 4.6 18.3 1.0 O A:GLY1026 4.7 31.8 1.0 CB A:ARG810 4.7 18.3 1.0 C A:VAL1032 4.8 21.5 1.0 SG A:CYS1027 4.8 31.5 1.0 NE A:ARG810 4.9 18.3 1.0 NH1 A:ARG810 4.9 18.3 1.0 CB A:CYS1027 5.0 31.5 1.0

Iron binding site 2 out of 4 in the Cryo-Em Structure of Adna(D934A)-Adnb(D1014A) in Complex with Amppnp


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 Adna(D934A)-Adnb(D1014A) in Complex with Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1101 b:21.1 occ:1.00 FE2 A:SF41101 0.0 21.1 1.0 S4 A:SF41101 2.3 21.1 1.0 S1 A:SF41101 2.3 21.1 1.0 S3 A:SF41101 2.3 21.1 1.0 FE3 A:SF41101 2.7 21.1 1.0 FE1 A:SF41101 2.7 21.1 1.0 FE4 A:SF41101 2.7 21.1 1.0 SG A:CYS1036 3.0 21.0 1.0 CB A:CYS1036 3.3 21.0 1.0 O A:VAL1032 3.8 21.5 1.0 S2 A:SF41101 3.9 21.1 1.0 CA A:CYS1036 4.5 21.0 1.0 CD2 A:LEU809 4.5 17.1 1.0 C A:VAL1032 4.9 21.5 1.0

Iron binding site 3 out of 4 in the Cryo-Em Structure of Adna(D934A)-Adnb(D1014A) in Complex with Amppnp


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 Adna(D934A)-Adnb(D1014A) in Complex with Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1101 b:21.1 occ:1.00 FE3 A:SF41101 0.0 21.1 1.0 S1 A:SF41101 2.3 21.1 1.0 S4 A:SF41101 2.3 21.1 1.0 S2 A:SF41101 2.3 21.1 1.0 FE2 A:SF41101 2.7 21.1 1.0 FE4 A:SF41101 2.7 21.1 1.0 FE1 A:SF41101 2.7 21.1 1.0 SG A:CYS1027 3.0 31.5 1.0 O A:ARG1022 3.7 25.0 1.0 S3 A:SF41101 3.9 21.1 1.0 CB A:CYS1027 3.9 31.5 1.0 CA A:CYS1027 4.4 31.5 1.0 SG A:CYS1036 4.5 21.0 1.0 CA A:VAL1023 4.8 25.9 1.0 C A:ARG1022 4.8 25.0 1.0 SG A:CYS807 4.9 18.0 1.0 N A:ASN1024 4.9 27.6 1.0

Iron binding site 4 out of 4 in the Cryo-Em Structure of Adna(D934A)-Adnb(D1014A) in Complex with Amppnp


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 Adna(D934A)-Adnb(D1014A) in Complex with Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1101 b:21.1 occ:1.00 FE4 A:SF41101 0.0 21.1 1.0 S2 A:SF41101 2.3 21.1 1.0 S1 A:SF41101 2.3 21.1 1.0 S3 A:SF41101 2.3 21.1 1.0 FE3 A:SF41101 2.7 21.1 1.0 FE1 A:SF41101 2.7 21.1 1.0 FE2 A:SF41101 2.7 21.1 1.0 SG A:CYS807 3.0 18.0 1.0 CB A:CYS807 3.6 18.0 1.0 CB A:ARG810 3.7 18.3 1.0 S4 A:SF41101 3.9 21.1 1.0 N A:ARG810 4.1 18.3 1.0 O A:ARG1022 4.2 25.0 1.0 CA A:ARG810 4.4 18.3 1.0 CG A:ARG810 4.5 18.3 1.0 CD A:ARG810 4.5 18.3 1.0 CD2 A:LEU809 4.9 17.1 1.0 CB A:LEU809 5.0 17.1 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