Iron in PDB 9f6i: Human Dna Polymerase Epsilon Bound to T-C Mismatched Dna (Post- Insertion State)

All present enzymatic activity of Human Dna Polymerase Epsilon Bound to T-C Mismatched Dna (Post- Insertion State):
2.7.7.7;

The structure of Human Dna Polymerase Epsilon Bound to T-C Mismatched Dna (Post- Insertion State) also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Iron atom in the Human Dna Polymerase Epsilon Bound to T-C Mismatched Dna (Post- Insertion State) (pdb code 9f6i). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Human Dna Polymerase Epsilon Bound to T-C Mismatched Dna (Post- Insertion State), PDB code: 9f6i:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Human Dna Polymerase Epsilon Bound to T-C Mismatched Dna (Post- Insertion State)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Human Dna Polymerase Epsilon Bound to T-C Mismatched Dna (Post- Insertion State) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1301 b:21.4 occ:1.00 FE1 A:SF41301 0.0 21.4 1.0 S2 A:SF41301 2.3 21.4 1.0 S3 A:SF41301 2.3 21.4 1.0 S4 A:SF41301 2.3 21.4 1.0 SG A:CYS651 2.3 16.4 1.0 FE4 A:SF41301 2.7 21.4 1.0 FE3 A:SF41301 2.7 21.4 1.0 FE2 A:SF41301 2.7 21.4 1.0 CB A:CYS651 3.2 16.4 1.0 CA A:CYS651 3.6 16.4 1.0 S1 A:SF41301 3.9 21.4 1.0 N A:CYS651 4.3 16.4 1.0 CG2 A:VAL646 4.5 20.6 1.0 CG A:GLN664 4.5 17.9 1.0 CB A:CYS654 4.7 16.3 1.0 C A:CYS651 4.8 16.4 1.0 SG A:CYS747 4.9 17.9 1.0 SG A:CYS654 4.9 16.3 1.0 SG A:CYS663 4.9 17.9 1.0 CD A:GLN664 4.9 17.9 1.0 O A:CYS651 5.0 16.4 1.0

Iron binding site 2 out of 4 in the Human Dna Polymerase Epsilon Bound to T-C Mismatched Dna (Post- Insertion State)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Human Dna Polymerase Epsilon Bound to T-C Mismatched Dna (Post- Insertion State) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1301 b:21.4 occ:1.00 FE2 A:SF41301 0.0 21.4 1.0 S1 A:SF41301 2.3 21.4 1.0 S4 A:SF41301 2.3 21.4 1.0 S3 A:SF41301 2.3 21.4 1.0 SG A:CYS654 2.3 16.3 1.0 FE3 A:SF41301 2.7 21.4 1.0 FE4 A:SF41301 2.7 21.4 1.0 FE1 A:SF41301 2.7 21.4 1.0 CB A:CYS654 2.9 16.3 1.0 S2 A:SF41301 3.9 21.4 1.0 CA A:CYS654 4.4 16.3 1.0 CB A:PHE656 4.6 18.2 1.0 CA A:CYS651 4.7 16.4 1.0 SG A:CYS651 4.8 16.4 1.0 SG A:CYS663 4.9 17.9 1.0 N A:ASN657 4.9 19.1 1.0 SG A:CYS747 4.9 17.9 1.0 C A:CYS654 4.9 16.3 1.0

Iron binding site 3 out of 4 in the Human Dna Polymerase Epsilon Bound to T-C Mismatched Dna (Post- Insertion State)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Human Dna Polymerase Epsilon Bound to T-C Mismatched Dna (Post- Insertion State) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1301 b:21.4 occ:1.00 FE3 A:SF41301 0.0 21.4 1.0 S2 A:SF41301 2.3 21.4 1.0 S1 A:SF41301 2.3 21.4 1.0 S4 A:SF41301 2.3 21.4 1.0 SG A:CYS663 2.3 17.9 1.0 FE4 A:SF41301 2.7 21.4 1.0 FE2 A:SF41301 2.7 21.4 1.0 FE1 A:SF41301 2.7 21.4 1.0 CB A:CYS663 3.5 17.9 1.0 S3 A:SF41301 3.9 21.4 1.0 CG A:GLN664 4.4 17.9 1.0 SG A:CYS747 4.6 17.9 1.0 CA A:CYS663 4.7 17.9 1.0 SG A:CYS654 4.7 16.3 1.0 C A:CYS663 4.7 17.9 1.0 SG A:CYS651 4.9 16.4 1.0 N A:GLN664 5.0 17.9 1.0 O A:CYS663 5.0 17.9 1.0

Iron binding site 4 out of 4 in the Human Dna Polymerase Epsilon Bound to T-C Mismatched Dna (Post- Insertion State)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Human Dna Polymerase Epsilon Bound to T-C Mismatched Dna (Post- Insertion State) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1301 b:21.4 occ:1.00 FE4 A:SF41301 0.0 21.4 1.0 S1 A:SF41301 2.3 21.4 1.0 S3 A:SF41301 2.3 21.4 1.0 S2 A:SF41301 2.3 21.4 1.0 SG A:CYS747 2.3 17.9 1.0 FE3 A:SF41301 2.7 21.4 1.0 FE1 A:SF41301 2.7 21.4 1.0 FE2 A:SF41301 2.7 21.4 1.0 CB A:CYS747 3.4 17.9 1.0 S4 A:SF41301 3.9 21.4 1.0 CA A:CYS747 4.2 17.9 1.0 SG A:CYS663 4.7 17.9 1.0 SG A:CYS651 4.8 16.4 1.0 SG A:CYS654 4.9 16.3 1.0 CG1 A:VAL646 5.0 20.6 1.0 CG2 A:VAL646 5.0 20.6 1.0

J.J.Roske, J.T.P.Yeeles. Structural Basis For Processive Daughter-Strand Synthesis and Proofreading By the Human Leading-Strand Dna Polymerase Pol Epsilon. Nat.Struct.Mol.Biol. 2024.
ISSN: ESSN 1545-9985
DOI: 10.1038/S41594-024-01370-Y