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Iron in PDB 7kc0: Structure of the Saccharomyces Cerevisiae Replicative Polymerase Delta in Complex with A Primer/Template and the Pcna Clamp

Enzymatic activity of Structure of the Saccharomyces Cerevisiae Replicative Polymerase Delta in Complex with A Primer/Template and the Pcna Clamp

All present enzymatic activity of Structure of the Saccharomyces Cerevisiae Replicative Polymerase Delta in Complex with A Primer/Template and the Pcna Clamp:
2.7.7.7;

Other elements in 7kc0:

The structure of Structure of the Saccharomyces Cerevisiae Replicative Polymerase Delta in Complex with A Primer/Template and the Pcna Clamp also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Zinc (Zn) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Structure of the Saccharomyces Cerevisiae Replicative Polymerase Delta in Complex with A Primer/Template and the Pcna Clamp (pdb code 7kc0). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Structure of the Saccharomyces Cerevisiae Replicative Polymerase Delta in Complex with A Primer/Template and the Pcna Clamp, PDB code: 7kc0:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 7kc0

Go back to Iron Binding Sites List in 7kc0
Iron binding site 1 out of 4 in the Structure of the Saccharomyces Cerevisiae Replicative Polymerase Delta in Complex with A Primer/Template and the Pcna Clamp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of the Saccharomyces Cerevisiae Replicative Polymerase Delta in Complex with A Primer/Template and the Pcna Clamp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1101

b:56.3
occ:1.00
 FE1 A:SF41101 0.0 56.3 1.0
S4 A:SF41101 2.3 56.3 1.0
S2 A:SF41101 2.3 56.3 1.0
S3 A:SF41101 2.3 56.3 1.0
SG A:CYS1069 2.3 55.4 1.0
FE3 A:SF41101 2.7 56.3 1.0
FE4 A:SF41101 2.7 56.3 1.0
FE2 A:SF41101 2.7 56.3 1.0
CB A:CYS1069 3.1 55.4 1.0
NH2 A:ARG1080 3.2 54.9 1.0
S1 A:SF41101 3.9 56.3 1.0
CZ A:ARG1080 4.1 54.9 1.0
SG A:CYS1056 4.1 54.4 1.0
NH1 A:ARG1080 4.4 54.9 1.0
CA A:CYS1069 4.5 55.4 1.0
CB A:ASN1071 4.7 56.5 1.0
O A:ASN1071 4.8 56.5 1.0
CG A:GLU492 4.9 57.6 1.0
O A:CYS1069 4.9 55.4 1.0
C A:CYS1069 4.9 55.4 1.0
CA A:GLU492 4.9 57.6 1.0
CD1 A:PHE1077 4.9 57.0 1.0

Iron binding site 2 out of 4 in 7kc0

Go back to Iron Binding Sites List in 7kc0
Iron binding site 2 out of 4 in the Structure of the Saccharomyces Cerevisiae Replicative Polymerase Delta in Complex with A Primer/Template and the Pcna Clamp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of the Saccharomyces Cerevisiae Replicative Polymerase Delta in Complex with A Primer/Template and the Pcna Clamp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1101

b:56.3
occ:1.00
 FE2 A:SF41101 0.0 56.3 1.0
S1 A:SF41101 2.3 56.3 1.0
S3 A:SF41101 2.3 56.3 1.0
S4 A:SF41101 2.3 56.3 1.0
SG A:CYS1074 2.4 57.0 1.0
FE3 A:SF41101 2.7 56.3 1.0
FE1 A:SF41101 2.7 56.3 1.0
FE4 A:SF41101 2.7 56.3 1.0
CB A:CYS1074 2.9 57.0 1.0
S2 A:SF41101 3.9 56.3 1.0
O A:GLN490 3.9 63.3 1.0
CA A:CYS1074 4.4 57.0 1.0
SG A:CYS1069 4.5 55.4 1.0
SG A:CYS1059 4.6 55.7 1.0
CD1 B:LEU119 4.7 60.8 1.0
ND2 A:ASN1071 4.8 56.5 1.0
CB A:GLN490 4.8 63.3 1.0
NH2 A:ARG1080 4.8 54.9 1.0
O A:ASN1071 4.9 56.5 1.0
C A:GLN490 5.0 63.3 1.0
CG A:ASN1071 5.0 56.5 1.0
N A:PHE1077 5.0 57.0 1.0
CB A:ILE1076 5.0 57.4 1.0

Iron binding site 3 out of 4 in 7kc0

Go back to Iron Binding Sites List in 7kc0
Iron binding site 3 out of 4 in the Structure of the Saccharomyces Cerevisiae Replicative Polymerase Delta in Complex with A Primer/Template and the Pcna Clamp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of the Saccharomyces Cerevisiae Replicative Polymerase Delta in Complex with A Primer/Template and the Pcna Clamp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1101

b:56.3
occ:1.00
 FE3 A:SF41101 0.0 56.3 1.0
S1 A:SF41101 2.3 56.3 1.0
S2 A:SF41101 2.3 56.3 1.0
S4 A:SF41101 2.3 56.3 1.0
SG A:CYS1056 2.5 54.4 1.0
FE1 A:SF41101 2.7 56.3 1.0
FE2 A:SF41101 2.7 56.3 1.0
FE4 A:SF41101 2.7 56.3 1.0
NH2 A:ARG1080 3.3 54.9 1.0
CA A:CYS1056 3.5 54.4 1.0
CB A:CYS1056 3.6 54.4 1.0
S3 A:SF41101 3.9 56.3 1.0
N A:CYS1056 4.4 54.4 1.0
O A:CYS1056 4.5 54.4 1.0
C A:CYS1056 4.5 54.4 1.0
SG A:CYS1074 4.5 57.0 1.0
CB A:CYS1059 4.6 55.7 1.0
CZ A:ARG1080 4.6 54.9 1.0
SG A:CYS1059 4.7 55.7 1.0
CG2 A:ILE1076 4.8 57.4 1.0
CB A:ILE1076 4.9 57.4 1.0
NE2 A:GLN1055 5.0 53.3 1.0
CD A:ARG1080 5.0 54.9 1.0

Iron binding site 4 out of 4 in 7kc0

Go back to Iron Binding Sites List in 7kc0
Iron binding site 4 out of 4 in the Structure of the Saccharomyces Cerevisiae Replicative Polymerase Delta in Complex with A Primer/Template and the Pcna Clamp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of the Saccharomyces Cerevisiae Replicative Polymerase Delta in Complex with A Primer/Template and the Pcna Clamp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1101

b:56.3
occ:1.00
 FE4 A:SF41101 0.0 56.3 1.0
S1 A:SF41101 2.3 56.3 1.0
S3 A:SF41101 2.3 56.3 1.0
S2 A:SF41101 2.3 56.3 1.0
SG A:CYS1059 2.5 55.7 1.0
FE3 A:SF41101 2.7 56.3 1.0
FE1 A:SF41101 2.7 56.3 1.0
FE2 A:SF41101 2.7 56.3 1.0
CB A:CYS1059 3.2 55.7 1.0
O A:GLN490 3.7 63.3 1.0
S4 A:SF41101 3.9 56.3 1.0
N A:GLU492 4.3 57.6 1.0
CA A:GLU492 4.3 57.6 1.0
CB A:GLU492 4.4 57.6 1.0
SG A:CYS1069 4.5 55.4 1.0
C A:LYS491 4.5 57.3 1.0
O A:CYS1056 4.5 54.4 1.0
CA A:CYS1059 4.5 55.7 1.0
C A:CYS1059 4.6 55.7 1.0
SG A:CYS1074 4.7 57.0 1.0
N A:ALA1060 4.7 56.8 1.0
O A:LYS491 4.8 57.3 1.0
SG A:CYS1056 4.8 54.4 1.0
CA A:CYS1056 4.9 54.4 1.0
C A:GLN490 4.9 63.3 1.0
CG A:GLU492 5.0 57.6 1.0

Reference:

F.Zheng, R.E.Georgescu, H.Li, M.E.O'donnell. Structure of Eukaryotic Dna Polymerase Delta Bound to the Pcna Clamp While Encircling Dna. Proc.Natl.Acad.Sci.Usa 2020.
ISSN: ESSN 1091-6490
PubMed: 33203675
DOI: 10.1073/PNAS.2017637117
Page generated: Thu Aug 8 06:23:58 2024

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