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Iron in PDB 9ne9: Human Polymerase Epsilon Bound to Pcna and Dna with A Pre-Existing Mismatch in the Blocked Conformation I

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

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

Other elements in 9ne9:

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

Magnesium (Mg) 2 atoms

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 I (pdb code 9ne9). 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 I, PDB code: 9ne9:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 9ne9

Go back to Iron Binding Sites List in 9ne9
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 I


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 I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1203

b:143.4
occ:1.00
 FE1 A:SF41203 0.0 143.4 1.0
SG A:CYS663 2.3 109.2 1.0
S2 A:SF41203 2.3 143.4 1.0
S3 A:SF41203 2.3 143.4 1.0
S4 A:SF41203 2.3 143.4 1.0
FE2 A:SF41203 2.7 143.4 1.0
FE4 A:SF41203 2.7 143.4 1.0
FE3 A:SF41203 2.7 143.4 1.0
OE1 A:GLN748 3.6 94.3 1.0
NE2 A:GLN664 3.6 108.8 1.0
S1 A:SF41203 3.9 143.4 1.0
O A:CYS663 4.0 109.2 1.0
CB A:CYS663 4.0 109.2 1.0
CD A:GLN664 4.4 108.8 1.0
CD A:GLN748 4.5 94.3 1.0
SG A:CYS747 4.5 83.2 1.0
C A:CYS663 4.5 109.2 1.0
OE1 A:GLN664 4.5 108.8 1.0
NE2 A:GLN748 4.6 94.3 1.0
SG A:CYS651 4.6 123.8 1.0
O A:PHE656 4.6 137.3 1.0
SG A:CYS654 4.6 133.4 1.0
CA A:CYS663 4.7 109.2 1.0
CB A:CYS747 4.8 83.2 1.0
C A:PHE656 4.9 137.3 1.0
CA A:ASN657 4.9 133.3 1.0
N A:ASN657 5.0 133.3 1.0

Iron binding site 2 out of 4 in 9ne9

Go back to Iron Binding Sites List in 9ne9
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 I


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 I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1203

b:143.4
occ:1.00
 FE2 A:SF41203 0.0 143.4 1.0
SG A:CYS654 2.3 133.4 1.0
S3 A:SF41203 2.3 143.4 1.0
S1 A:SF41203 2.3 143.4 1.0
S4 A:SF41203 2.3 143.4 1.0
CB A:CYS654 2.7 133.4 1.0
FE1 A:SF41203 2.7 143.4 1.0
FE3 A:SF41203 2.7 143.4 1.0
FE4 A:SF41203 2.7 143.4 1.0
S2 A:SF41203 3.9 143.4 1.0
CA A:CYS654 4.1 133.4 1.0
O A:CYS651 4.4 123.8 1.0
C A:CYS654 4.6 133.4 1.0
SG A:CYS663 4.8 109.2 1.0
O A:CYS654 4.9 133.4 1.0
N A:CYS654 4.9 133.4 1.0
SG A:CYS747 5.0 83.2 1.0
SG A:CYS651 5.0 123.8 1.0

Iron binding site 3 out of 4 in 9ne9

Go back to Iron Binding Sites List in 9ne9
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 I


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 I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1203

b:143.4
occ:1.00
 FE3 A:SF41203 0.0 143.4 1.0
SG A:CYS747 2.3 83.2 1.0
S1 A:SF41203 2.3 143.4 1.0
S2 A:SF41203 2.3 143.4 1.0
S4 A:SF41203 2.3 143.4 1.0
FE4 A:SF41203 2.7 143.4 1.0
FE2 A:SF41203 2.7 143.4 1.0
FE1 A:SF41203 2.7 143.4 1.0
CB A:CYS747 3.1 83.2 1.0
S3 A:SF41203 3.9 143.4 1.0
CA A:CYS747 4.1 83.2 1.0
OE1 A:GLN748 4.4 94.3 1.0
SG A:CYS651 4.5 123.8 1.0
SG A:CYS663 4.8 109.2 1.0
SG A:CYS654 4.9 133.4 1.0

Iron binding site 4 out of 4 in 9ne9

Go back to Iron Binding Sites List in 9ne9
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 I


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 I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1203

b:143.4
occ:1.00
 FE4 A:SF41203 0.0 143.4 1.0
SG A:CYS651 2.3 123.8 1.0
S2 A:SF41203 2.3 143.4 1.0
S3 A:SF41203 2.3 143.4 1.0
S1 A:SF41203 2.3 143.4 1.0
FE3 A:SF41203 2.7 143.4 1.0
FE1 A:SF41203 2.7 143.4 1.0
FE2 A:SF41203 2.7 143.4 1.0
O A:CYS651 3.4 123.8 1.0
CB A:CYS651 3.4 123.8 1.0
CA A:CYS651 3.4 123.8 1.0
NE2 A:GLN664 3.5 108.8 1.0
C A:CYS651 3.8 123.8 1.0
S4 A:SF41203 3.9 143.4 1.0
SG A:CYS747 4.1 83.2 1.0
CB A:CYS654 4.2 133.4 1.0
CD A:GLN664 4.6 108.8 1.0
SG A:CYS663 4.7 109.2 1.0
N A:CYS651 4.7 123.8 1.0
SG A:CYS654 4.7 133.4 1.0
O A:THR650 5.0 117.7 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 07:51:29 2025

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