Iron in PDB 9f6l: Human Dna Polymerase Epsilon Bound to T-C Mismatched Dna (Mismatch Excision State)

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

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

Calcium

(Ca)

2 atoms

The binding sites of Iron atom in the Human Dna Polymerase Epsilon Bound to T-C Mismatched Dna (Mismatch Excision State) (pdb code 9f6l). 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 (Mismatch Excision State), PDB code: 9f6l:
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 (Mismatch Excision 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 (Mismatch Excision State) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1301 b:99.9 occ:1.00 FE1 A:SF41301 0.0 99.9 1.0 S3 A:SF41301 2.3 99.9 1.0 S2 A:SF41301 2.3 99.9 1.0 S4 A:SF41301 2.3 99.9 1.0 SG A:CYS651 2.3 99.1 1.0 FE3 A:SF41301 2.7 99.9 1.0 FE2 A:SF41301 2.7 99.9 1.0 FE4 A:SF41301 2.7 99.9 1.0 CB A:CYS651 3.5 99.1 1.0 S1 A:SF41301 3.9 99.9 1.0 CA A:CYS651 4.0 99.1 1.0 SG A:CYS663 4.3 97.5 1.0 N A:CYS651 4.7 99.1 1.0 CG2 A:VAL646 4.7 92.7 1.0 CG A:GLN664 4.7 93.0 1.0 SG A:CYS747 4.8 94.2 1.0 CB A:CYS654 4.8 98.9 1.0 NE2 A:GLN664 4.9 93.0 1.0 SG A:CYS654 4.9 98.9 1.0

Iron binding site 2 out of 4 in the Human Dna Polymerase Epsilon Bound to T-C Mismatched Dna (Mismatch Excision 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 (Mismatch Excision State) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1301 b:99.9 occ:1.00 FE2 A:SF41301 0.0 99.9 1.0 S1 A:SF41301 2.3 99.9 1.0 S4 A:SF41301 2.3 99.9 1.0 S3 A:SF41301 2.3 99.9 1.0 SG A:CYS654 2.3 98.9 1.0 FE3 A:SF41301 2.7 99.9 1.0 FE1 A:SF41301 2.7 99.9 1.0 FE4 A:SF41301 2.7 99.9 1.0 CB A:CYS654 2.7 98.9 1.0 S2 A:SF41301 3.9 99.9 1.0 CA A:CYS654 4.2 98.9 1.0 SG A:CYS651 4.6 99.1 1.0 CB A:PHE656 4.6 102.0 1.0 CA A:CYS651 4.8 99.1 1.0 C A:CYS654 4.8 98.9 1.0 O A:CYS654 4.9 98.9 1.0 SG A:CYS663 4.9 97.5 1.0 SG A:CYS747 5.0 94.2 1.0

Iron binding site 3 out of 4 in the Human Dna Polymerase Epsilon Bound to T-C Mismatched Dna (Mismatch Excision 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 (Mismatch Excision State) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1301 b:99.9 occ:1.00 FE3 A:SF41301 0.0 99.9 1.0 S2 A:SF41301 2.3 99.9 1.0 S4 A:SF41301 2.3 99.9 1.0 S1 A:SF41301 2.3 99.9 1.0 SG A:CYS663 2.3 97.5 1.0 FE1 A:SF41301 2.7 99.9 1.0 FE4 A:SF41301 2.7 99.9 1.0 FE2 A:SF41301 2.7 99.9 1.0 CB A:CYS663 3.1 97.5 1.0 S3 A:SF41301 3.9 99.9 1.0 SG A:CYS747 4.4 94.2 1.0 SG A:CYS654 4.4 98.9 1.0 CA A:CYS663 4.5 97.5 1.0 CB A:PHE656 4.6 102.0 1.0 C A:CYS663 4.7 97.5 1.0 SG A:CYS651 4.9 99.1 1.0

Iron binding site 4 out of 4 in the Human Dna Polymerase Epsilon Bound to T-C Mismatched Dna (Mismatch Excision 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 (Mismatch Excision State) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1301 b:99.9 occ:1.00 FE4 A:SF41301 0.0 99.9 1.0 S1 A:SF41301 2.3 99.9 1.0 S2 A:SF41301 2.3 99.9 1.0 S3 A:SF41301 2.3 99.9 1.0 SG A:CYS747 2.3 94.2 1.0 FE3 A:SF41301 2.7 99.9 1.0 FE1 A:SF41301 2.7 99.9 1.0 FE2 A:SF41301 2.7 99.9 1.0 CB A:CYS747 3.4 94.2 1.0 S4 A:SF41301 3.9 99.9 1.0 CA A:CYS747 4.3 94.2 1.0 CD1 A:LEU145 4.6 100.2 1.0 SG A:CYS651 4.8 99.1 1.0 SG A:CYS663 4.8 97.5 1.0 SG A:CYS654 4.8 98.9 1.0 CB A:CYS663 5.0 97.5 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