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

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

The binding sites of Iron atom in the Cryo-Em Structure of Adna(D934A)-Adnb(D1014A) in Complex with Amppnp and Dna (pdb code 6ppr). 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 and Dna, PDB code: 6ppr:
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 and Dna


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 and Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1102 b:17.0 occ:1.00 FE1 A:SF41102 0.0 17.0 1.0 S3 A:SF41102 2.3 17.0 1.0 S4 A:SF41102 2.3 17.0 1.0 S2 A:SF41102 2.3 17.0 1.0 FE2 A:SF41102 2.7 17.0 1.0 FE4 A:SF41102 2.7 17.0 1.0 FE3 A:SF41102 2.7 17.0 1.0 SG A:CYS1030 3.1 19.0 1.0 CB A:CYS1030 3.6 19.0 1.0 S1 A:SF41102 3.9 17.0 1.0 O A:VAL1032 4.0 15.7 1.0 CA A:CYS1027 4.2 21.3 1.0 SG A:CYS1027 4.2 21.3 1.0 CD A:ARG810 4.4 14.7 1.0 CB A:CYS1027 4.5 21.3 1.0 NH1 A:ARG810 4.7 14.7 1.0 O A:GLY1026 4.7 21.5 1.0 O A:CYS1027 4.9 21.3 1.0 N A:CYS1027 4.9 21.3 1.0 CB A:ARG810 5.0 14.7 1.0

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


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 and Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1102 b:17.0 occ:1.00 FE2 A:SF41102 0.0 17.0 1.0 S4 A:SF41102 2.3 17.0 1.0 S3 A:SF41102 2.3 17.0 1.0 S1 A:SF41102 2.3 17.0 1.0 FE1 A:SF41102 2.7 17.0 1.0 FE4 A:SF41102 2.7 17.0 1.0 FE3 A:SF41102 2.7 17.0 1.0 SG A:CYS1036 3.0 12.0 1.0 CB A:CYS1036 3.3 12.0 1.0 S2 A:SF41102 3.9 17.0 1.0 O A:VAL1032 3.9 15.7 1.0 CA A:CYS1036 4.4 12.0 1.0 CD2 A:LEU809 4.8 12.4 1.0 SG A:CYS1030 4.8 19.0 1.0

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


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 and Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1102 b:17.0 occ:1.00 FE3 A:SF41102 0.0 17.0 1.0 S1 A:SF41102 2.3 17.0 1.0 S4 A:SF41102 2.3 17.0 1.0 S2 A:SF41102 2.3 17.0 1.0 FE1 A:SF41102 2.7 17.0 1.0 FE2 A:SF41102 2.7 17.0 1.0 FE4 A:SF41102 2.7 17.0 1.0 O A:ARG1022 3.1 18.7 1.0 SG A:CYS1027 3.1 21.3 1.0 S3 A:SF41102 3.9 17.0 1.0 C A:ARG1022 4.2 18.7 1.0 CB A:CYS1027 4.3 21.3 1.0 CA A:VAL1023 4.3 22.7 1.0 SG A:CYS1036 4.4 12.0 1.0 N A:ASN1024 4.7 21.8 1.0 N A:VAL1023 4.7 22.7 1.0 CA A:CYS1027 4.8 21.3 1.0 SG A:CYS807 4.8 19.1 1.0 CG2 A:VAL1023 5.0 22.7 1.0

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


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 and Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1102 b:17.0 occ:1.00 FE4 A:SF41102 0.0 17.0 1.0 S3 A:SF41102 2.3 17.0 1.0 S2 A:SF41102 2.3 17.0 1.0 S1 A:SF41102 2.3 17.0 1.0 FE1 A:SF41102 2.7 17.0 1.0 FE2 A:SF41102 2.7 17.0 1.0 FE3 A:SF41102 2.7 17.0 1.0 SG A:CYS807 3.0 19.1 1.0 CB A:CYS807 3.5 19.1 1.0 CB A:ARG810 3.6 14.7 1.0 S4 A:SF41102 3.9 17.0 1.0 N A:ARG810 4.0 14.7 1.0 O A:ARG1022 4.1 18.7 1.0 CA A:ARG810 4.2 14.7 1.0 CD A:ARG810 4.5 14.7 1.0 CG A:ARG810 4.5 14.7 1.0 C A:LEU809 4.9 12.4 1.0 CA A:CYS807 5.0 19.1 1.0 ND2 A:ASN1024 5.0 21.8 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