Iron in PDB 8d9d: Human Dna Polymerase-Alpha/Primase Elongation Complex II Bound to Primer/Template

Enzymatic activity of Human Dna Polymerase-Alpha/Primase Elongation Complex II Bound to Primer/Template

All present enzymatic activity of Human Dna Polymerase-Alpha/Primase Elongation Complex II Bound to Primer/Template:
2.7.7.102; 2.7.7.7;

Other elements in 8d9d:

The structure of Human Dna Polymerase-Alpha/Primase Elongation Complex II Bound to Primer/Template also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Zinc (Zn) 3 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Human Dna Polymerase-Alpha/Primase Elongation Complex II Bound to Primer/Template (pdb code 8d9d). 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 Dna Polymerase-Alpha/Primase Elongation Complex II Bound to Primer/Template, PDB code: 8d9d:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 8d9d

Go back to Iron Binding Sites List in 8d9d
Iron binding site 1 out of 4 in the Human Dna Polymerase-Alpha/Primase Elongation Complex II Bound to Primer/Template


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Human Dna Polymerase-Alpha/Primase Elongation Complex II Bound to Primer/Template within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe601

b:79.4
occ:1.00
FE1 B:SF4601 0.0 79.4 1.0
SG B:CYS367 2.3 98.2 1.0
S4 B:SF4601 2.3 79.4 1.0
S3 B:SF4601 2.3 79.4 1.0
S2 B:SF4601 2.3 79.4 1.0
FE2 B:SF4601 2.7 79.4 1.0
FE3 B:SF4601 2.7 79.4 1.0
FE4 B:SF4601 2.7 79.4 1.0
CB B:CYS367 3.6 98.2 1.0
S1 B:SF4601 3.9 79.4 1.0
CA B:CYS367 4.4 98.2 1.0
SG B:CYS384 4.5 92.4 1.0
CG B:PRO444 4.7 96.0 1.0
SG B:CYS424 4.7 116.9 1.0
SG B:CYS287 4.9 83.0 1.0
O B:CYS367 4.9 98.2 1.0

Iron binding site 2 out of 4 in 8d9d

Go back to Iron Binding Sites List in 8d9d
Iron binding site 2 out of 4 in the Human Dna Polymerase-Alpha/Primase Elongation Complex II Bound to Primer/Template


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Human Dna Polymerase-Alpha/Primase Elongation Complex II Bound to Primer/Template within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe601

b:79.4
occ:1.00
FE2 B:SF4601 0.0 79.4 1.0
SG B:CYS384 2.3 92.4 1.0
S3 B:SF4601 2.3 79.4 1.0
S1 B:SF4601 2.3 79.4 1.0
S4 B:SF4601 2.3 79.4 1.0
FE1 B:SF4601 2.7 79.4 1.0
FE4 B:SF4601 2.7 79.4 1.0
FE3 B:SF4601 2.7 79.4 1.0
CB B:CYS384 3.7 92.4 1.0
S2 B:SF4601 3.9 79.4 1.0
CA B:CYS384 4.3 92.4 1.0
SG B:CYS367 4.4 98.2 1.0
SG B:CYS287 4.5 83.0 1.0
CD2 B:PHE386 4.5 101.9 1.0
CD B:PRO385 4.6 97.7 1.0
SG B:CYS424 4.8 116.9 1.0
CB B:PHE386 4.9 101.9 1.0
CB B:CYS287 4.9 83.0 1.0
C B:CYS384 5.0 92.4 1.0
N B:PRO385 5.0 97.7 1.0

Iron binding site 3 out of 4 in 8d9d

Go back to Iron Binding Sites List in 8d9d
Iron binding site 3 out of 4 in the Human Dna Polymerase-Alpha/Primase Elongation Complex II Bound to Primer/Template


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Human Dna Polymerase-Alpha/Primase Elongation Complex II Bound to Primer/Template within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe601

b:79.4
occ:1.00
FE3 B:SF4601 0.0 79.4 1.0
S4 B:SF4601 2.3 79.4 1.0
S2 B:SF4601 2.3 79.4 1.0
S1 B:SF4601 2.3 79.4 1.0
SG B:CYS424 2.3 116.9 1.0
FE1 B:SF4601 2.7 79.4 1.0
FE4 B:SF4601 2.7 79.4 1.0
FE2 B:SF4601 2.7 79.4 1.0
CB B:CYS424 3.3 116.9 1.0
S3 B:SF4601 3.9 79.4 1.0
CB B:PRO285 4.5 72.1 1.0
CD2 B:LEU441 4.6 112.6 1.0
CA B:CYS424 4.6 116.9 1.0
SG B:CYS367 4.8 98.2 1.0
CD2 B:PHE386 4.8 101.9 1.0
CE2 B:PHE386 4.8 101.9 1.0
SG B:CYS287 4.8 83.0 1.0
CD B:PRO286 4.8 79.0 1.0
CG B:PRO286 4.9 79.0 1.0
SG B:CYS384 4.9 92.4 1.0

Iron binding site 4 out of 4 in 8d9d

Go back to Iron Binding Sites List in 8d9d
Iron binding site 4 out of 4 in the Human Dna Polymerase-Alpha/Primase Elongation Complex II Bound to Primer/Template


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Human Dna Polymerase-Alpha/Primase Elongation Complex II Bound to Primer/Template within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe601

b:79.4
occ:1.00
FE4 B:SF4601 0.0 79.4 1.0
S3 B:SF4601 2.3 79.4 1.0
S1 B:SF4601 2.3 79.4 1.0
SG B:CYS287 2.3 83.0 1.0
S2 B:SF4601 2.3 79.4 1.0
FE2 B:SF4601 2.7 79.4 1.0
FE1 B:SF4601 2.7 79.4 1.0
FE3 B:SF4601 2.7 79.4 1.0
CB B:CYS287 3.6 83.0 1.0
S4 B:SF4601 3.9 79.4 1.0
CB B:PRO285 4.0 72.1 1.0
N B:CYS287 4.4 83.0 1.0
CG B:PRO285 4.4 72.1 1.0
CG B:PRO444 4.6 96.0 1.0
CA B:CYS287 4.6 83.0 1.0
SG B:CYS384 4.6 92.4 1.0
SG B:CYS424 4.8 116.9 1.0
SG B:CYS367 4.9 98.2 1.0

Reference:

Q.He, A.G.Baranovskiy, L.M.Morstadt, A.E.Lisova, N.D.Babayeva, B.L.Lusk, C.Lim, T.H.Tahirov. Structures of Human Primosome Elongation Complexes Nat.Struct.Mol.Biol. 2023.
ISSN: ESSN 1545-9985
DOI: 10.1038/S41594-023-00971-3
Page generated: Tue Apr 25 20:46:18 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