Iron in PDB 8ucv: Complete Dna Termination Subcomplex 1 of Xenopus Laevis Dna Polymerase Alpha-Primase

Enzymatic activity of Complete Dna Termination Subcomplex 1 of Xenopus Laevis Dna Polymerase Alpha-Primase

All present enzymatic activity of Complete Dna Termination Subcomplex 1 of Xenopus Laevis Dna Polymerase Alpha-Primase:
2.7.7.7;

Other elements in 8ucv:

The structure of Complete Dna Termination Subcomplex 1 of Xenopus Laevis Dna Polymerase Alpha-Primase also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Complete Dna Termination Subcomplex 1 of Xenopus Laevis Dna Polymerase Alpha-Primase (pdb code 8ucv). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Complete Dna Termination Subcomplex 1 of Xenopus Laevis Dna Polymerase Alpha-Primase, PDB code: 8ucv:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 8ucv

Go back to Iron Binding Sites List in 8ucv
Iron binding site 1 out of 4 in the Complete Dna Termination Subcomplex 1 of Xenopus Laevis Dna Polymerase Alpha-Primase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Complete Dna Termination Subcomplex 1 of Xenopus Laevis Dna Polymerase Alpha-Primase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe601

b:218.2
occ:1.00
 FE1 B:SF4601 0.0 218.2 1.0
S2 B:SF4601 2.3 218.2 1.0
S4 B:SF4601 2.3 218.2 1.0
S3 B:SF4601 2.3 218.2 1.0
SG B:CYS373 2.3 204.6 1.0
FE3 B:SF4601 2.7 218.2 1.0
FE4 B:SF4601 2.7 218.2 1.0
FE2 B:SF4601 2.7 218.2 1.0
HB3 B:CYS373 2.9 204.6 1.0
CB B:CYS373 3.1 204.6 1.0
HA B:CYS373 3.4 204.6 1.0
HG3 B:PRO450 3.6 187.8 1.0
CA B:CYS373 3.8 204.6 1.0
S1 B:SF4601 3.9 218.2 1.0
HB2 B:CYS373 4.0 204.6 1.0
HD3 B:PRO450 4.1 187.8 1.0
HD11 B:LEU447 4.1 226.1 1.0
HG B:LEU447 4.1 226.1 1.0
HA B:PRO450 4.3 187.8 1.0
CG B:PRO450 4.4 187.8 1.0
HD21 B:LEU447 4.4 226.1 1.0
N B:PRO450 4.5 187.8 1.0
CD B:PRO450 4.5 187.8 1.0
HB B:VAL376 4.7 204.4 1.0
HB2 B:CYS430 4.7 231.5 1.0
SG B:CYS430 4.7 231.5 1.0
N B:CYS373 4.7 204.6 1.0
CD1 B:LEU447 4.8 226.1 1.0
H B:CYS373 4.8 204.6 1.0
CG B:LEU447 4.8 226.1 1.0
SG B:CYS293 4.8 194.2 1.0
HD12 B:LEU447 4.8 226.1 1.0
HB2 B:CYS390 4.8 193.4 1.0
CA B:PRO450 4.8 187.8 1.0
C B:HIS449 4.8 185.7 1.0
HB3 B:CYS430 4.9 231.5 1.0
SG B:CYS390 4.9 193.4 1.0
HG3 B:GLN427 4.9 220.8 1.0
C B:CYS373 4.9 204.6 1.0
H B:HIS449 4.9 185.7 1.0
HB3 B:PRO450 5.0 187.8 1.0

Iron binding site 2 out of 4 in 8ucv

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Iron binding site 2 out of 4 in the Complete Dna Termination Subcomplex 1 of Xenopus Laevis Dna Polymerase Alpha-Primase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Complete Dna Termination Subcomplex 1 of Xenopus Laevis Dna Polymerase Alpha-Primase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe601

b:218.2
occ:1.00
 FE2 B:SF4601 0.0 218.2 1.0
S1 B:SF4601 2.3 218.2 1.0
S4 B:SF4601 2.3 218.2 1.0
S3 B:SF4601 2.3 218.2 1.0
SG B:CYS390 2.3 193.4 1.0
FE4 B:SF4601 2.7 218.2 1.0
FE3 B:SF4601 2.7 218.2 1.0
FE1 B:SF4601 2.7 218.2 1.0
HB2 B:CYS390 3.0 193.4 1.0
CB B:CYS390 3.2 193.4 1.0
HD2 B:PHE392 3.4 235.1 1.0
HA B:CYS390 3.5 193.4 1.0
HD2 B:PRO391 3.8 211.5 1.0
S2 B:SF4601 3.9 218.2 1.0
CA B:CYS390 3.9 193.4 1.0
HD11 B:ILE377 4.0 202.8 1.0
HB3 B:CYS390 4.0 193.4 1.0
CD2 B:PHE392 4.2 235.1 1.0
HB3 B:CYS293 4.2 194.2 1.0
HB2 B:CYS430 4.3 231.5 1.0
HB2 B:PHE392 4.3 235.1 1.0
H B:PHE392 4.4 235.1 1.0
HB3 B:CYS373 4.4 204.6 1.0
HG12 B:VAL376 4.5 204.4 1.0
HG11 B:VAL376 4.6 204.4 1.0
CD B:PRO391 4.6 211.5 1.0
HG12 B:ILE377 4.6 202.8 1.0
C B:CYS390 4.6 193.4 1.0
HE2 B:PHE392 4.6 235.1 1.0
HB3 B:TYR426 4.7 235.1 1.0
SG B:CYS293 4.8 194.2 1.0
SG B:CYS430 4.8 231.5 1.0
HB B:VAL376 4.8 204.4 1.0
HD3 B:PRO391 4.8 211.5 1.0
N B:PRO391 4.8 211.5 1.0
CD1 B:ILE377 4.9 202.8 1.0
CE2 B:PHE392 4.9 235.1 1.0
HA B:CYS373 4.9 204.6 1.0
SG B:CYS373 4.9 204.6 1.0
CG1 B:VAL376 4.9 204.4 1.0
CB B:CYS430 5.0 231.5 1.0
CB B:CYS293 5.0 194.2 1.0

Iron binding site 3 out of 4 in 8ucv

Go back to Iron Binding Sites List in 8ucv
Iron binding site 3 out of 4 in the Complete Dna Termination Subcomplex 1 of Xenopus Laevis Dna Polymerase Alpha-Primase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Complete Dna Termination Subcomplex 1 of Xenopus Laevis Dna Polymerase Alpha-Primase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe601

b:218.2
occ:1.00
 FE3 B:SF4601 0.0 218.2 1.0
SG B:CYS430 2.3 231.5 1.0
S1 B:SF4601 2.3 218.2 1.0
S2 B:SF4601 2.3 218.2 1.0
S4 B:SF4601 2.3 218.2 1.0
FE1 B:SF4601 2.7 218.2 1.0
FE4 B:SF4601 2.7 218.2 1.0
FE2 B:SF4601 2.7 218.2 1.0
HB2 B:CYS430 2.8 231.5 1.0
CB B:CYS430 3.0 231.5 1.0
HB3 B:CYS430 3.3 231.5 1.0
HE2 B:PHE392 3.4 235.1 1.0
HD21 B:LEU447 3.4 226.1 1.0
HD2 B:PHE392 3.6 235.1 1.0
HB2 B:PRO291 3.8 203.3 1.0
S3 B:SF4601 3.9 218.2 1.0
HD2 B:TYR453 4.0 212.0 1.0
CE2 B:PHE392 4.1 235.1 1.0
HB3 B:PRO291 4.2 203.3 1.0
CD2 B:PHE392 4.2 235.1 1.0
CD2 B:LEU447 4.3 226.1 1.0
HG B:LEU447 4.4 226.1 1.0
CA B:CYS430 4.4 231.5 1.0
CB B:PRO291 4.4 203.3 1.0
HA B:CYS430 4.5 231.5 1.0
HD23 B:LEU447 4.6 226.1 1.0
HD11 B:LEU447 4.6 226.1 1.0
H B:LEU292 4.6 215.7 1.0
HE2 B:TYR453 4.6 212.0 1.0
H B:CYS293 4.6 194.2 1.0
CD2 B:TYR453 4.7 212.0 1.0
SG B:CYS373 4.7 204.6 1.0
SG B:CYS293 4.7 194.2 1.0
SG B:CYS390 4.8 193.4 1.0
CG B:LEU447 4.9 226.1 1.0
O B:TYR426 5.0 235.1 1.0
HD22 B:LEU447 5.0 226.1 1.0

Iron binding site 4 out of 4 in 8ucv

Go back to Iron Binding Sites List in 8ucv
Iron binding site 4 out of 4 in the Complete Dna Termination Subcomplex 1 of Xenopus Laevis Dna Polymerase Alpha-Primase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Complete Dna Termination Subcomplex 1 of Xenopus Laevis Dna Polymerase Alpha-Primase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe601

b:218.2
occ:1.00
 FE4 B:SF4601 0.0 218.2 1.0
SG B:CYS293 2.3 194.2 1.0
S2 B:SF4601 2.3 218.2 1.0
S1 B:SF4601 2.3 218.2 1.0
S3 B:SF4601 2.3 218.2 1.0
FE3 B:SF4601 2.7 218.2 1.0
FE2 B:SF4601 2.7 218.2 1.0
FE1 B:SF4601 2.7 218.2 1.0
HB3 B:CYS293 3.0 194.2 1.0
HB2 B:PRO291 3.1 203.3 1.0
CB B:CYS293 3.2 194.2 1.0
H B:CYS293 3.3 194.2 1.0
HG3 B:PRO450 3.4 187.8 1.0
S4 B:SF4601 3.9 218.2 1.0
HB2 B:CYS293 3.9 194.2 1.0
HB3 B:PRO450 3.9 187.8 1.0
CB B:PRO291 4.0 203.3 1.0
HD2 B:PRO391 4.0 211.5 1.0
N B:CYS293 4.1 194.2 1.0
HG2 B:PRO291 4.1 203.3 1.0
HB3 B:PRO291 4.2 203.3 1.0
HA B:CYS390 4.2 193.4 1.0
CG B:PRO450 4.3 187.8 1.0
HG11 B:VAL376 4.3 204.4 1.0
CA B:CYS293 4.3 194.2 1.0
HA B:PRO450 4.3 187.8 1.0
HG3 B:PRO291 4.4 203.3 1.0
CG B:PRO291 4.4 203.3 1.0
CB B:PRO450 4.5 187.8 1.0
HD3 B:PRO391 4.7 211.5 1.0
HB2 B:CYS390 4.7 193.4 1.0
HE2 B:MET294 4.7 181.0 1.0
H B:MET294 4.7 181.0 1.0
SG B:CYS430 4.7 231.5 1.0
SG B:CYS390 4.8 193.4 1.0
HG2 B:PRO450 4.8 187.8 1.0
CD B:PRO391 4.8 211.5 1.0
SG B:CYS373 4.8 204.6 1.0
HA B:CYS293 4.8 194.2 1.0
H B:LEU292 4.8 215.7 1.0
HG21 B:VAL376 4.9 204.4 1.0
CA B:PRO450 4.9 187.8 1.0

Reference:

E.A.Mullins, L.E.Salay, C.L.Durie, N.P.Bradley, J.E.Jackman, M.D.Ohi, W.J.Chazin, B.F.Eichman. A Mechanistic Model of Primer Synthesis From Catalytic Structures of Dna Polymerase Alpha-Primase. Biorxiv 2023.
ISSN: ISSN 2692-8205
PubMed: 36993335
DOI: 10.1101/2023.03.16.533013
Page generated: Sat Aug 10 18:27:52 2024

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