Iron in PDB 9ne8: Human Polymerase Epsilon Bound to Pcna and Dna with An in-Situ- Generated Mismatch in the Mismatch-Locking State

All present enzymatic activity of Human Polymerase Epsilon Bound to Pcna and Dna with An in-Situ- Generated Mismatch in the Mismatch-Locking State:
2.7.7.7;

The binding sites of Iron atom in the Human Polymerase Epsilon Bound to Pcna and Dna with An in-Situ- Generated Mismatch in the Mismatch-Locking State (pdb code 9ne8). 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 Polymerase Epsilon Bound to Pcna and Dna with An in-Situ- Generated Mismatch in the Mismatch-Locking State, PDB code: 9ne8:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Human Polymerase Epsilon Bound to Pcna and Dna with An in-Situ- Generated Mismatch in the Mismatch-Locking State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Human Polymerase Epsilon Bound to Pcna and Dna with An in-Situ- Generated Mismatch in the Mismatch-Locking State within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1301 b:113.2 occ:1.00 FE1 A:SF41301 0.0 113.2 1.0 SG A:CYS651 2.3 111.0 1.0 S2 A:SF41301 2.3 113.2 1.0 S3 A:SF41301 2.3 113.2 1.0 S4 A:SF41301 2.3 113.2 1.0 FE2 A:SF41301 2.7 113.2 1.0 FE3 A:SF41301 2.7 113.2 1.0 FE4 A:SF41301 2.7 113.2 1.0 CB A:CYS651 3.1 111.0 1.0 NE2 A:GLN664 3.4 81.0 1.0 CA A:CYS651 3.5 111.0 1.0 OE1 A:GLN664 3.7 81.0 1.0 S1 A:SF41301 3.9 113.2 1.0 CD A:GLN664 4.0 81.0 1.0 SG A:CYS654 4.3 119.3 1.0 SG A:CYS663 4.4 87.5 1.0 CB A:CYS747 4.5 68.4 1.0 N A:CYS651 4.5 111.0 1.0 C A:CYS651 4.5 111.0 1.0 O A:CYS651 4.5 111.0 1.0 SG A:CYS747 4.6 68.4 1.0 CG2 A:VAL646 4.7 82.0 1.0 CB A:CYS654 4.9 119.3 1.0

Iron binding site 2 out of 4 in the Human Polymerase Epsilon Bound to Pcna and Dna with An in-Situ- Generated Mismatch in the Mismatch-Locking State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Human Polymerase Epsilon Bound to Pcna and Dna with An in-Situ- Generated Mismatch in the Mismatch-Locking State within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1301 b:113.2 occ:1.00 FE2 A:SF41301 0.0 113.2 1.0 SG A:CYS654 2.3 119.3 1.0 S3 A:SF41301 2.3 113.2 1.0 S4 A:SF41301 2.3 113.2 1.0 S1 A:SF41301 2.3 113.2 1.0 CB A:CYS654 2.7 119.3 1.0 FE1 A:SF41301 2.7 113.2 1.0 FE4 A:SF41301 2.7 113.2 1.0 FE3 A:SF41301 2.7 113.2 1.0 S2 A:SF41301 3.9 113.2 1.0 CD2 A:PHE656 4.0 117.7 1.0 CA A:CYS654 4.2 119.3 1.0 O A:CYS651 4.2 111.0 1.0 CA A:CYS651 4.3 111.0 1.0 CB A:PHE656 4.5 117.7 1.0 SG A:CYS651 4.7 111.0 1.0 CG A:PHE656 4.7 117.7 1.0 C A:CYS651 4.8 111.0 1.0 CB A:CYS651 4.8 111.0 1.0 CE2 A:PHE656 4.8 117.7 1.0 O A:THR650 4.8 113.4 1.0 N A:CYS654 4.9 119.3 1.0 SG A:CYS747 5.0 68.4 1.0 SG A:CYS663 5.0 87.5 1.0

Iron binding site 3 out of 4 in the Human Polymerase Epsilon Bound to Pcna and Dna with An in-Situ- Generated Mismatch in the Mismatch-Locking State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Human Polymerase Epsilon Bound to Pcna and Dna with An in-Situ- Generated Mismatch in the Mismatch-Locking State within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1301 b:113.2 occ:1.00 FE3 A:SF41301 0.0 113.2 1.0 SG A:CYS663 2.3 87.5 1.0 S2 A:SF41301 2.3 113.2 1.0 S4 A:SF41301 2.3 113.2 1.0 S1 A:SF41301 2.3 113.2 1.0 FE4 A:SF41301 2.7 113.2 1.0 FE1 A:SF41301 2.7 113.2 1.0 FE2 A:SF41301 2.7 113.2 1.0 CB A:CYS663 3.3 87.5 1.0 NE2 A:GLN664 3.6 81.0 1.0 S3 A:SF41301 3.9 113.2 1.0 O A:PHE656 4.3 117.7 1.0 CB A:PHE656 4.3 117.7 1.0 SG A:CYS747 4.4 68.4 1.0 CA A:CYS663 4.6 87.5 1.0 CD A:GLN664 4.6 81.0 1.0 C A:CYS663 4.7 87.5 1.0 C A:PHE656 4.7 117.7 1.0 O A:CYS663 4.8 87.5 1.0 SG A:CYS651 4.9 111.0 1.0 CB A:CYS654 4.9 119.3 1.0 SG A:CYS654 5.0 119.3 1.0 OE1 A:GLN664 5.0 81.0 1.0

Iron binding site 4 out of 4 in the Human Polymerase Epsilon Bound to Pcna and Dna with An in-Situ- Generated Mismatch in the Mismatch-Locking State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Human Polymerase Epsilon Bound to Pcna and Dna with An in-Situ- Generated Mismatch in the Mismatch-Locking State within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1301 b:113.2 occ:1.00 FE4 A:SF41301 0.0 113.2 1.0 SG A:CYS747 2.3 68.4 1.0 S2 A:SF41301 2.3 113.2 1.0 S1 A:SF41301 2.3 113.2 1.0 S3 A:SF41301 2.3 113.2 1.0 FE3 A:SF41301 2.7 113.2 1.0 FE2 A:SF41301 2.7 113.2 1.0 FE1 A:SF41301 2.7 113.2 1.0 CB A:CYS747 3.1 68.4 1.0 S4 A:SF41301 3.9 113.2 1.0 CA A:CYS747 4.2 68.4 1.0 SG A:CYS663 4.5 87.5 1.0 SG A:CYS654 4.5 119.3 1.0 NE2 A:HIS144 4.6 110.4 1.0 CB A:CYS663 4.6 87.5 1.0 SG A:CYS651 4.7 111.0 1.0 O A:CYS663 5.0 87.5 1.0

F.Wang, Q.He, M.E.O'donnell, H.Li. The Proofreading Mechanism of the Human Leading-Strand Dna Polymerase Epsilon Holoenzyme. Proc.Natl.Acad.Sci.Usa V. 122 32122 2025.
ISSN: ESSN 1091-6490
PubMed: 40440070
DOI: 10.1073/PNAS.2507232122