Atomistry » Iron » PDB 8ttb-9nse » 8ucv
Atomistry »
  Iron »
    PDB 8ttb-9nse »
      8ucv »

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

Go back to Iron Binding Sites List in 8ucv
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: Thu Dec 28 06:31:05 2023

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy