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Iron in PDB 9nea: Human Polymerase Epsilon Bound to Pcna and Dna with A Pre-Existing Mismatch in the Blocked Conformation II

Enzymatic activity of Human Polymerase Epsilon Bound to Pcna and Dna with A Pre-Existing Mismatch in the Blocked Conformation II

All present enzymatic activity of Human Polymerase Epsilon Bound to Pcna and Dna with A Pre-Existing Mismatch in the Blocked Conformation II:
2.7.7.7;

Other elements in 9nea:

The structure of Human Polymerase Epsilon Bound to Pcna and Dna with A Pre-Existing Mismatch in the Blocked Conformation II also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Human Polymerase Epsilon Bound to Pcna and Dna with A Pre-Existing Mismatch in the Blocked Conformation II (pdb code 9nea). 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 A Pre-Existing Mismatch in the Blocked Conformation II, PDB code: 9nea:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 9nea

Go back to Iron Binding Sites List in 9nea
Iron binding site 1 out of 4 in the Human Polymerase Epsilon Bound to Pcna and Dna with A Pre-Existing Mismatch in the Blocked Conformation II


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 A Pre-Existing Mismatch in the Blocked Conformation II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe2302

b:18.9
occ:1.00
 FE1 A:SF42302 0.0 18.9 1.0
SG A:CYS663 2.3 18.0 1.0
S4 A:SF42302 2.3 18.9 1.0
S3 A:SF42302 2.3 18.9 1.0
S2 A:SF42302 2.3 18.9 1.0
CB A:CYS663 2.6 18.0 1.0
FE4 A:SF42302 2.7 18.9 1.0
FE2 A:SF42302 2.7 18.9 1.0
FE3 A:SF42302 2.7 18.9 1.0
NE2 A:GLN664 3.3 14.3 1.0
C A:CYS663 3.8 18.0 1.0
O A:CYS663 3.8 18.0 1.0
CA A:CYS663 3.8 18.0 1.0
S1 A:SF42302 3.9 18.9 1.0
NH2 A:ARG749 4.0 20.8 1.0
CZ A:ARG749 4.0 20.8 1.0
NH1 A:ARG749 4.1 20.8 1.0
CD A:GLN664 4.2 14.3 1.0
N A:GLN664 4.4 14.3 1.0
NE A:ARG749 4.5 20.8 1.0
CA A:CYS747 4.6 8.2 1.0
SG A:CYS651 4.6 15.1 1.0
OE1 A:GLN664 4.6 14.3 1.0
N A:CYS663 4.7 18.0 1.0
N A:GLN748 4.7 9.4 1.0
CB A:CYS654 4.8 18.6 1.0
CB A:CYS747 4.9 8.2 1.0
SG A:CYS654 5.0 18.6 1.0

Iron binding site 2 out of 4 in 9nea

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Iron binding site 2 out of 4 in the Human Polymerase Epsilon Bound to Pcna and Dna with A Pre-Existing Mismatch in the Blocked Conformation II


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 A Pre-Existing Mismatch in the Blocked Conformation II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe2302

b:18.9
occ:1.00
 FE2 A:SF42302 0.0 18.9 1.0
SG A:CYS654 2.3 18.6 1.0
S1 A:SF42302 2.3 18.9 1.0
S4 A:SF42302 2.3 18.9 1.0
S3 A:SF42302 2.3 18.9 1.0
CB A:CYS654 2.3 18.6 1.0
FE3 A:SF42302 2.7 18.9 1.0
FE1 A:SF42302 2.7 18.9 1.0
FE4 A:SF42302 2.7 18.9 1.0
NH2 A:ARG749 3.3 20.8 1.0
CZ A:ARG749 3.8 20.8 1.0
CA A:CYS654 3.8 18.6 1.0
S2 A:SF42302 3.9 18.9 1.0
NE A:ARG749 3.9 20.8 1.0
SG A:CYS747 4.5 8.2 1.0
O A:CYS651 4.5 15.1 1.0
N A:CYS654 4.5 18.6 1.0
SG A:CYS663 4.5 18.0 1.0
CB A:CYS747 4.6 8.2 1.0
C A:CYS654 4.6 18.6 1.0
NH1 A:ARG749 4.7 20.8 1.0
SG A:CYS651 4.8 15.1 1.0
O A:CYS654 4.8 18.6 1.0
CD A:ARG749 5.0 20.8 1.0
CB A:CYS663 5.0 18.0 1.0
CG A:ARG749 5.0 20.8 1.0

Iron binding site 3 out of 4 in 9nea

Go back to Iron Binding Sites List in 9nea
Iron binding site 3 out of 4 in the Human Polymerase Epsilon Bound to Pcna and Dna with A Pre-Existing Mismatch in the Blocked Conformation II


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 A Pre-Existing Mismatch in the Blocked Conformation II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe2302

b:18.9
occ:1.00
 FE3 A:SF42302 0.0 18.9 1.0
S4 A:SF42302 2.3 18.9 1.0
S1 A:SF42302 2.3 18.9 1.0
S2 A:SF42302 2.3 18.9 1.0
CB A:CYS747 2.4 8.2 1.0
CA A:CYS747 2.5 8.2 1.0
FE2 A:SF42302 2.7 18.9 1.0
FE4 A:SF42302 2.7 18.9 1.0
FE1 A:SF42302 2.7 18.9 1.0
SG A:CYS747 3.2 8.2 1.0
N A:CYS747 3.5 8.2 1.0
C A:CYS747 3.7 8.2 1.0
S3 A:SF42302 3.9 18.9 1.0
N A:GLN748 3.9 9.4 1.0
SG A:CYS654 4.1 18.6 1.0
CG2 A:VAL646 4.4 10.9 1.0
C A:ILE746 4.4 7.6 1.0
O A:CYS663 4.6 18.0 1.0
CB A:CYS663 4.6 18.0 1.0
O A:ILE746 4.7 7.6 1.0
O A:CYS747 4.8 8.2 1.0
SG A:CYS651 4.8 15.1 1.0
CB A:CYS654 4.9 18.6 1.0
SG A:CYS663 5.0 18.0 1.0

Iron binding site 4 out of 4 in 9nea

Go back to Iron Binding Sites List in 9nea
Iron binding site 4 out of 4 in the Human Polymerase Epsilon Bound to Pcna and Dna with A Pre-Existing Mismatch in the Blocked Conformation II


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 A Pre-Existing Mismatch in the Blocked Conformation II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe2302

b:18.9
occ:1.00
 FE4 A:SF42302 0.0 18.9 1.0
SG A:CYS651 2.3 15.1 1.0
S2 A:SF42302 2.3 18.9 1.0
S3 A:SF42302 2.3 18.9 1.0
S1 A:SF42302 2.3 18.9 1.0
FE1 A:SF42302 2.7 18.9 1.0
FE3 A:SF42302 2.7 18.9 1.0
FE2 A:SF42302 2.7 18.9 1.0
NE2 A:GLN664 3.3 14.3 1.0
O A:CYS651 3.6 15.1 1.0
CB A:CYS651 3.7 15.1 1.0
S4 A:SF42302 3.9 18.9 1.0
OE1 A:GLN664 3.9 14.3 1.0
CG2 A:VAL646 4.0 10.9 1.0
CA A:CYS651 4.0 15.1 1.0
CD A:GLN664 4.1 14.3 1.0
SG A:CYS654 4.2 18.6 1.0
C A:CYS651 4.2 15.1 1.0
CB A:CYS654 4.2 18.6 1.0
SG A:CYS663 4.6 18.0 1.0
ND2 A:ASN657 4.7 36.0 1.0
CB A:CYS747 5.0 8.2 1.0

Reference:

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
Page generated: Fri Aug 8 07:51:57 2025

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