Iron in PDB 9b8t: Human Polymerase Epsilon Bound to Pcna and Dna in the Nucleotide Bound State

Enzymatic activity of Human Polymerase Epsilon Bound to Pcna and Dna in the Nucleotide Bound State

All present enzymatic activity of Human Polymerase Epsilon Bound to Pcna and Dna in the Nucleotide Bound State:
2.7.7.7;

Other elements in 9b8t:

The structure of Human Polymerase Epsilon Bound to Pcna and Dna in the Nucleotide Bound State 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 in the Nucleotide Bound State (pdb code 9b8t). 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 in the Nucleotide Bound State, PDB code: 9b8t:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 9b8t

Go back to Iron Binding Sites List in 9b8t
Iron binding site 1 out of 4 in the Human Polymerase Epsilon Bound to Pcna and Dna in the Nucleotide Bound 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 in the Nucleotide Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3003

b:90.6
occ:1.00
 FE1 A:SF43003 0.0 90.6 1.0
SG A:CYS663 2.3 72.9 1.0
S2 A:SF43003 2.3 68.2 1.0
S3 A:SF43003 2.3 107.1 1.0
S4 A:SF43003 2.3 111.1 1.0
FE3 A:SF43003 2.7 86.7 1.0
FE4 A:SF43003 2.7 129.8 1.0
FE2 A:SF43003 2.7 100.1 1.0
CB A:CYS663 3.7 64.8 1.0
O A:PHE656 3.7 99.0 1.0
S1 A:SF43003 3.9 87.7 1.0
O A:CYS663 4.3 56.3 1.0
C A:PHE656 4.5 98.7 1.0
NE2 A:GLN664 4.5 68.0 1.0
CG A:GLN664 4.5 53.5 1.0
C A:CYS663 4.6 61.7 1.0
SG A:CYS651 4.7 73.0 1.0
SG A:CYS747 4.8 39.7 1.0
SG A:CYS654 4.8 88.2 1.0
CA A:CYS663 4.8 61.0 1.0
OD1 A:ASN657 4.9 94.2 1.0
CB A:PHE656 4.9 84.5 1.0
CD A:GLN664 5.0 61.1 1.0

Iron binding site 2 out of 4 in 9b8t

Go back to Iron Binding Sites List in 9b8t
Iron binding site 2 out of 4 in the Human Polymerase Epsilon Bound to Pcna and Dna in the Nucleotide Bound 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 in the Nucleotide Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3003

b:100.1
occ:1.00
 FE2 A:SF43003 0.0 100.1 1.0
SG A:CYS654 2.3 88.2 1.0
S1 A:SF43003 2.3 87.7 1.0
S4 A:SF43003 2.3 111.1 1.0
S3 A:SF43003 2.3 107.1 1.0
CB A:CYS654 2.6 84.9 1.0
FE3 A:SF43003 2.7 86.7 1.0
FE4 A:SF43003 2.7 129.8 1.0
FE1 A:SF43003 2.7 90.6 1.0
S2 A:SF43003 3.9 68.2 1.0
O A:CYS651 4.1 88.9 1.0
CA A:CYS654 4.1 86.3 1.0
O A:PHE656 4.2 99.0 1.0
C A:PHE656 4.3 98.7 1.0
CB A:PHE656 4.3 84.5 1.0
N A:PHE656 4.4 90.2 1.0
CA A:PHE656 4.6 91.7 1.0
C A:CYS654 4.6 95.6 1.0
CA A:CYS651 4.7 76.8 1.0
N A:ASN657 4.7 100.5 1.0
SG A:CYS747 4.8 39.7 1.0
C A:CYS651 4.9 80.9 1.0
N A:CYS654 4.9 82.8 1.0
SG A:CYS663 4.9 72.9 1.0
SG A:CYS651 4.9 73.0 1.0
N A:ASP655 5.0 98.9 1.0

Iron binding site 3 out of 4 in 9b8t

Go back to Iron Binding Sites List in 9b8t
Iron binding site 3 out of 4 in the Human Polymerase Epsilon Bound to Pcna and Dna in the Nucleotide Bound 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 in the Nucleotide Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3003

b:86.7
occ:1.00
 FE3 A:SF43003 0.0 86.7 1.0
SG A:CYS747 2.3 39.7 1.0
S1 A:SF43003 2.3 87.7 1.0
S2 A:SF43003 2.3 68.2 1.0
S4 A:SF43003 2.3 111.1 1.0
FE2 A:SF43003 2.7 100.1 1.0
FE4 A:SF43003 2.7 129.8 1.0
FE1 A:SF43003 2.7 90.6 1.0
CB A:CYS747 3.3 38.5 1.0
S3 A:SF43003 3.9 107.1 1.0
CA A:CYS747 4.0 28.6 1.0
CB A:ARG749 4.4 48.4 1.0
SG A:CYS663 4.5 72.9 1.0
SG A:CYS654 4.6 88.2 1.0
SG A:CYS651 4.6 73.0 1.0
C A:CYS747 4.7 30.9 1.0
CD1 A:LEU145 4.7 43.5 1.0
N A:ARG749 4.8 38.0 1.0
N A:GLN748 4.8 38.0 1.0
O A:CYS663 4.9 56.3 1.0
CB A:CYS654 4.9 84.9 1.0

Iron binding site 4 out of 4 in 9b8t

Go back to Iron Binding Sites List in 9b8t
Iron binding site 4 out of 4 in the Human Polymerase Epsilon Bound to Pcna and Dna in the Nucleotide Bound 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 in the Nucleotide Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3003

b:129.8
occ:1.00
 FE4 A:SF43003 0.0 129.8 1.0
S2 A:SF43003 2.3 68.2 1.0
S3 A:SF43003 2.3 107.1 1.0
SG A:CYS651 2.3 73.0 1.0
S1 A:SF43003 2.3 87.7 1.0
FE3 A:SF43003 2.7 86.7 1.0
FE1 A:SF43003 2.7 90.6 1.0
FE2 A:SF43003 2.7 100.1 1.0
CB A:CYS651 2.9 78.7 1.0
CA A:CYS651 3.2 76.8 1.0
S4 A:SF43003 3.9 111.1 1.0
NE2 A:GLN664 4.0 68.0 1.0
O A:CYS651 4.0 88.9 1.0
C A:CYS651 4.1 80.9 1.0
N A:CYS651 4.3 79.2 1.0
CB A:CYS654 4.5 84.9 1.0
CG A:GLN664 4.6 53.5 1.0
SG A:CYS747 4.6 39.7 1.0
CG2 A:VAL646 4.7 59.1 1.0
SG A:CYS663 4.7 72.9 1.0
CB A:CYS747 4.8 38.5 1.0
CD A:GLN664 4.8 61.1 1.0
O A:THR650 4.8 84.3 1.0
SG A:CYS654 4.9 88.2 1.0
OD1 A:ASN657 4.9 94.2 1.0

Reference:

F.Wang, Q.He, H.Li. The Processive State of Human Polymerase Epsilon Bound to Dna and Pcna To Be Published.
Page generated: Sat Sep 28 21:53:31 2024

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