Iron in PDB 9f6d: Human Dna Polymerase Epsilon Bound to Dna and Pcna (Open Conformation)

All present enzymatic activity of Human Dna Polymerase Epsilon Bound to Dna and Pcna (Open Conformation):
2.7.7.7;

The structure of Human Dna Polymerase Epsilon Bound to Dna and Pcna (Open Conformation) also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Iron atom in the Human Dna Polymerase Epsilon Bound to Dna and Pcna (Open Conformation) (pdb code 9f6d). 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 Dna and Pcna (Open Conformation), PDB code: 9f6d:
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 Dna and Pcna (Open Conformation)


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 Dna and Pcna (Open Conformation) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1301 b:32.1 occ:1.00 FE1 A:SF41301 0.0 32.1 1.0 S2 A:SF41301 2.3 32.1 1.0 S4 A:SF41301 2.3 32.1 1.0 S3 A:SF41301 2.3 32.1 1.0 SG A:CYS651 2.3 36.5 1.0 FE2 A:SF41301 2.7 32.1 1.0 FE3 A:SF41301 2.7 32.1 1.0 FE4 A:SF41301 2.7 32.1 1.0 CB A:CYS651 3.5 36.5 1.0 S1 A:SF41301 3.9 32.1 1.0 CA A:CYS651 4.0 36.5 1.0 CG2 A:VAL646 4.5 33.2 1.0 SG A:CYS747 4.5 31.7 1.0 CG A:GLN664 4.6 19.8 1.0 NE2 A:GLN664 4.6 19.8 1.0 CB A:CYS654 4.7 28.2 1.0 N A:CYS651 4.7 36.5 1.0 SG A:CYS663 4.8 22.8 1.0 CB A:CYS747 4.8 31.7 1.0 SG A:CYS654 4.9 28.2 1.0

Iron binding site 2 out of 4 in the Human Dna Polymerase Epsilon Bound to Dna and Pcna (Open Conformation)


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 Dna and Pcna (Open Conformation) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1301 b:32.1 occ:1.00 FE2 A:SF41301 0.0 32.1 1.0 S1 A:SF41301 2.3 32.1 1.0 S3 A:SF41301 2.3 32.1 1.0 S4 A:SF41301 2.3 32.1 1.0 SG A:CYS654 2.3 28.2 1.0 CB A:CYS654 2.7 28.2 1.0 FE3 A:SF41301 2.7 32.1 1.0 FE4 A:SF41301 2.7 32.1 1.0 FE1 A:SF41301 2.7 32.1 1.0 S2 A:SF41301 3.9 32.1 1.0 CA A:CYS654 4.2 28.2 1.0 CB A:PHE656 4.4 34.9 1.0 N A:ASN657 4.6 38.3 1.0 C A:CYS654 4.7 28.2 1.0 SG A:CYS651 4.7 36.5 1.0 O A:CYS654 4.8 28.2 1.0 SG A:CYS663 4.8 22.8 1.0 C A:PHE656 4.9 34.9 1.0 CA A:CYS651 4.9 36.5 1.0 SG A:CYS747 5.0 31.7 1.0 N A:CYS654 5.0 28.2 1.0 N A:PHE656 5.0 34.9 1.0

Iron binding site 3 out of 4 in the Human Dna Polymerase Epsilon Bound to Dna and Pcna (Open Conformation)


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 Dna and Pcna (Open Conformation) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1301 b:32.1 occ:1.00 FE3 A:SF41301 0.0 32.1 1.0 S4 A:SF41301 2.3 32.1 1.0 S2 A:SF41301 2.3 32.1 1.0 S1 A:SF41301 2.3 32.1 1.0 SG A:CYS663 2.3 22.8 1.0 FE2 A:SF41301 2.7 32.1 1.0 FE4 A:SF41301 2.7 32.1 1.0 FE1 A:SF41301 2.7 32.1 1.0 CB A:CYS663 3.7 22.8 1.0 S3 A:SF41301 3.9 32.1 1.0 SG A:CYS747 4.1 31.7 1.0 CG A:GLN664 4.5 19.8 1.0 C A:CYS663 4.7 22.8 1.0 SG A:CYS654 4.7 28.2 1.0 N A:GLN664 4.8 19.8 1.0 SG A:CYS651 4.8 36.5 1.0 CA A:CYS663 4.8 22.8 1.0 O A:CYS663 5.0 22.8 1.0

Iron binding site 4 out of 4 in the Human Dna Polymerase Epsilon Bound to Dna and Pcna (Open Conformation)


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 Dna and Pcna (Open Conformation) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1301 b:32.1 occ:1.00 FE4 A:SF41301 0.0 32.1 1.0 S3 A:SF41301 2.3 32.1 1.0 S2 A:SF41301 2.3 32.1 1.0 S1 A:SF41301 2.3 32.1 1.0 SG A:CYS747 2.3 31.7 1.0 FE3 A:SF41301 2.7 32.1 1.0 FE2 A:SF41301 2.7 32.1 1.0 FE1 A:SF41301 2.7 32.1 1.0 CB A:CYS747 3.4 31.7 1.0 S4 A:SF41301 3.9 32.1 1.0 CA A:CYS747 4.4 31.7 1.0 SG A:CYS654 4.5 28.2 1.0 CD2 A:LEU145 4.6 23.1 1.0 SG A:CYS663 4.7 22.8 1.0 SG A:CYS651 4.9 36.5 1.0 CG A:LEU145 5.0 23.1 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