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Iron in PDB 8foe: Cryo-Em Structure of S. Cerevisiae Dna Polymerase Alpha-Primase Complex Bound to A Template Dna

Iron Binding Sites:

The binding sites of Iron atom in the Cryo-Em Structure of S. Cerevisiae Dna Polymerase Alpha-Primase Complex Bound to A Template Dna (pdb code 8foe). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Cryo-Em Structure of S. Cerevisiae Dna Polymerase Alpha-Primase Complex Bound to A Template Dna, PDB code: 8foe:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 8foe

Go back to Iron Binding Sites List in 8foe
Iron binding site 1 out of 4 in the Cryo-Em Structure of S. Cerevisiae Dna Polymerase Alpha-Primase Complex Bound to A Template Dna


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cryo-Em Structure of S. Cerevisiae Dna Polymerase Alpha-Primase Complex Bound to A Template Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe601

b:15.8
occ:1.00
FE1 B:SF4601 0.0 15.8 1.0
SG B:CYS336 2.3 16.4 1.0
S2 B:SF4601 2.3 16.4 1.0
S3 B:SF4601 2.4 17.0 1.0
S4 B:SF4601 2.4 17.9 1.0
FE3 B:SF4601 2.7 16.1 1.0
FE4 B:SF4601 2.7 15.8 1.0
FE2 B:SF4601 2.7 16.8 1.0
CB B:CYS336 3.2 14.9 1.0
S1 B:SF4601 4.0 17.2 1.0
N B:CYS336 4.0 15.5 1.0
CA B:CYS336 4.2 14.7 1.0
CG B:PRO500 4.3 21.0 1.0
CB B:PRO334 4.3 14.5 1.0
CG B:PRO334 4.5 16.9 1.0
CB B:PRO500 4.7 15.2 1.0
SG B:CYS417 4.7 17.9 1.0
SG B:CYS434 4.8 18.7 1.0
CD1 B:ILE420 4.9 15.7 1.0
SG B:CYS474 4.9 16.5 1.0

Iron binding site 2 out of 4 in 8foe

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Iron binding site 2 out of 4 in the Cryo-Em Structure of S. Cerevisiae Dna Polymerase Alpha-Primase Complex Bound to A Template Dna


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cryo-Em Structure of S. Cerevisiae Dna Polymerase Alpha-Primase Complex Bound to A Template Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe601

b:16.8
occ:1.00
FE2 B:SF4601 0.0 16.8 1.0
S1 B:SF4601 2.3 17.2 1.0
SG B:CYS434 2.3 18.7 1.0
S4 B:SF4601 2.3 17.9 1.0
S3 B:SF4601 2.4 17.0 1.0
FE3 B:SF4601 2.7 16.1 1.0
FE4 B:SF4601 2.7 15.8 1.0
FE1 B:SF4601 2.7 15.8 1.0
CB B:CYS434 3.2 16.4 1.0
CA B:CYS434 3.9 16.5 1.0
S2 B:SF4601 4.0 16.4 1.0
CD2 B:PHE436 4.1 17.1 1.0
C B:CYS434 4.6 18.3 1.0
CD B:PRO435 4.6 18.2 1.0
CE2 B:PHE436 4.7 18.5 1.0
SG B:CYS336 4.7 16.4 1.0
SG B:CYS474 4.7 16.5 1.0
CB B:CYS336 4.8 14.9 1.0
N B:PRO435 4.8 17.2 1.0
CB B:CYS474 4.8 15.0 1.0
SG B:CYS417 4.8 17.9 1.0

Iron binding site 3 out of 4 in 8foe

Go back to Iron Binding Sites List in 8foe
Iron binding site 3 out of 4 in the Cryo-Em Structure of S. Cerevisiae Dna Polymerase Alpha-Primase Complex Bound to A Template Dna


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cryo-Em Structure of S. Cerevisiae Dna Polymerase Alpha-Primase Complex Bound to A Template Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe601

b:16.1
occ:1.00
FE3 B:SF4601 0.0 16.1 1.0
SG B:CYS417 2.2 17.9 1.0
S4 B:SF4601 2.3 17.9 1.0
S1 B:SF4601 2.3 17.2 1.0
S2 B:SF4601 2.3 16.4 1.0
FE4 B:SF4601 2.7 15.8 1.0
FE2 B:SF4601 2.7 16.8 1.0
FE1 B:SF4601 2.7 15.8 1.0
CB B:CYS417 3.2 16.2 1.0
S3 B:SF4601 3.9 17.0 1.0
CA B:CYS417 4.1 16.1 1.0
CD B:PRO500 4.5 16.6 1.0
CG2 B:THR471 4.6 17.7 1.0
CG B:PRO500 4.6 21.0 1.0
SG B:CYS474 4.7 16.5 1.0
SG B:CYS434 4.8 18.7 1.0
N B:CYS417 4.8 16.8 1.0
SG B:CYS336 4.8 16.4 1.0
N B:PRO500 4.8 14.7 1.0

Iron binding site 4 out of 4 in 8foe

Go back to Iron Binding Sites List in 8foe
Iron binding site 4 out of 4 in the Cryo-Em Structure of S. Cerevisiae Dna Polymerase Alpha-Primase Complex Bound to A Template Dna


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cryo-Em Structure of S. Cerevisiae Dna Polymerase Alpha-Primase Complex Bound to A Template Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe601

b:15.8
occ:1.00
FE4 B:SF4601 0.0 15.8 1.0
SG B:CYS474 2.3 16.5 1.0
S2 B:SF4601 2.3 16.4 1.0
S3 B:SF4601 2.3 17.0 1.0
S1 B:SF4601 2.3 17.2 1.0
FE3 B:SF4601 2.7 16.1 1.0
FE2 B:SF4601 2.7 16.8 1.0
FE1 B:SF4601 2.7 15.8 1.0
CB B:CYS474 3.1 15.0 1.0
S4 B:SF4601 3.9 17.9 1.0
CE2 B:PHE436 4.2 18.5 1.0
CB B:PRO334 4.2 14.5 1.0
CD2 B:PHE436 4.4 17.1 1.0
CA B:CYS474 4.5 14.9 1.0
SG B:CYS417 4.6 17.9 1.0
SG B:CYS434 4.8 18.7 1.0
SG B:CYS336 4.8 16.4 1.0

Reference:

Z.Yuan, R.Georgescu, H.Li, M.E.O'donnell. Molecular Choreography of Primer Synthesis By the Eukaryotic Pol Alpha-Primase. Biorxiv 2023.
ISSN: ISSN 2692-8205
PubMed: 37205351
DOI: 10.1101/2023.05.03.539257
Page generated: Sat Aug 10 04:27:06 2024

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