Atomistry » Iron » PDB 5h2f-5i0r » 5h8w
Atomistry »
  Iron »
    PDB 5h2f-5i0r »
      5h8w »

Iron in PDB 5h8w: Xpd Mechanism

Enzymatic activity of Xpd Mechanism

All present enzymatic activity of Xpd Mechanism:
3.6.4.12;

Protein crystallography data

The structure of Xpd Mechanism, PDB code: 5h8w was solved by J.H.Naismith, D.Constantinescu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.22 / 2.20
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 78.569, 78.569, 177.832, 90.00, 90.00, 120.00
R / Rfree (%) 20.8 / 24.3

Other elements in 5h8w:

The structure of Xpd Mechanism also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Xpd Mechanism (pdb code 5h8w). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Xpd Mechanism, PDB code: 5h8w:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 5h8w

Go back to Iron Binding Sites List in 5h8w
Iron binding site 1 out of 4 in the Xpd Mechanism


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Xpd Mechanism within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe801

b:25.7
occ:1.00
FE1 A:SF4801 0.0 25.7 1.0
S3 A:SF4801 2.1 27.1 1.0
S2 A:SF4801 2.1 27.7 1.0
S4 A:SF4801 2.1 27.5 1.0
SG A:CYS164 2.3 28.1 1.0
FE2 A:SF4801 2.5 25.8 1.0
FE3 A:SF4801 2.5 24.2 1.0
FE4 A:SF4801 2.6 24.2 1.0
CB A:CYS164 3.3 28.4 1.0
S1 A:SF4801 3.5 25.7 1.0
CG A:GLU167 4.2 32.6 1.0
CA A:CYS164 4.4 28.0 1.0
SG A:CYS92 4.5 28.5 1.0
SG A:CYS128 4.5 31.8 1.0
SG A:CYS113 4.6 32.6 1.0
CA A:CYS92 4.6 27.9 1.0
CB A:CYS92 4.9 27.8 1.0
CB A:TYR166 4.9 28.6 1.0
N A:ILE93 5.0 28.5 1.0
N A:GLU167 5.0 31.6 1.0

Iron binding site 2 out of 4 in 5h8w

Go back to Iron Binding Sites List in 5h8w
Iron binding site 2 out of 4 in the Xpd Mechanism


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Xpd Mechanism within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe801

b:25.8
occ:1.00
FE2 A:SF4801 0.0 25.8 1.0
S3 A:SF4801 2.1 27.1 1.0
S1 A:SF4801 2.1 25.7 1.0
S4 A:SF4801 2.1 27.5 1.0
SG A:CYS113 2.3 32.6 1.0
FE1 A:SF4801 2.5 25.7 1.0
FE4 A:SF4801 2.6 24.2 1.0
FE3 A:SF4801 2.6 24.2 1.0
CB A:CYS113 3.3 32.1 1.0
S2 A:SF4801 3.6 27.7 1.0
CA A:CYS113 4.0 33.0 1.0
NE A:ARG88 4.3 28.7 1.0
SG A:CYS164 4.5 28.1 1.0
CG A:GLU167 4.5 32.6 1.0
O A:CYS113 4.6 35.7 1.0
SG A:CYS92 4.6 28.5 1.0
C A:CYS113 4.7 34.9 1.0
OE2 A:GLU167 4.7 33.1 1.0
CG A:LYS117 4.7 39.5 1.0
SG A:CYS128 4.8 31.8 1.0
CD A:LYS117 4.8 39.2 1.0
CD A:ARG88 4.8 28.1 1.0

Iron binding site 3 out of 4 in 5h8w

Go back to Iron Binding Sites List in 5h8w
Iron binding site 3 out of 4 in the Xpd Mechanism


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Xpd Mechanism within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe801

b:24.2
occ:1.00
FE3 A:SF4801 0.0 24.2 1.0
S2 A:SF4801 2.1 27.7 1.0
S1 A:SF4801 2.1 25.7 1.0
S4 A:SF4801 2.1 27.5 1.0
SG A:CYS92 2.3 28.5 1.0
FE1 A:SF4801 2.5 25.7 1.0
FE4 A:SF4801 2.6 24.2 1.0
FE2 A:SF4801 2.6 25.8 1.0
CB A:CYS92 3.4 27.8 1.0
S3 A:SF4801 3.6 27.1 1.0
CA A:CYS92 3.8 27.9 1.0
CB A:LEU94 4.0 31.5 1.0
N A:LEU94 4.2 30.4 1.0
N A:ILE93 4.3 28.5 1.0
C A:CYS92 4.3 28.1 1.0
SG A:CYS164 4.5 28.1 1.0
SG A:CYS113 4.6 32.6 1.0
SG A:CYS128 4.6 31.8 1.0
CA A:LEU94 4.7 31.3 1.0
CB A:CYS113 4.8 32.1 1.0
CE2 A:PHE112 4.9 28.9 1.0

Iron binding site 4 out of 4 in 5h8w

Go back to Iron Binding Sites List in 5h8w
Iron binding site 4 out of 4 in the Xpd Mechanism


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Xpd Mechanism within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe801

b:24.2
occ:1.00
FE4 A:SF4801 0.0 24.2 1.0
S1 A:SF4801 2.1 25.7 1.0
S2 A:SF4801 2.1 27.7 1.0
S3 A:SF4801 2.1 27.1 1.0
SG A:CYS128 2.3 31.8 1.0
FE3 A:SF4801 2.6 24.2 1.0
FE1 A:SF4801 2.6 25.7 1.0
FE2 A:SF4801 2.6 25.8 1.0
CB A:CYS128 3.5 32.3 1.0
S4 A:SF4801 3.6 27.5 1.0
CB A:LEU94 4.2 31.5 1.0
CD2 A:LEU94 4.4 33.2 1.0
SG A:CYS164 4.6 28.1 1.0
SG A:CYS92 4.7 28.5 1.0
CB A:TYR130 4.7 27.7 1.0
SG A:CYS113 4.7 32.6 1.0
CB A:PHE131 4.8 32.2 1.0
CA A:CYS128 4.8 32.4 1.0
N A:PHE131 4.9 30.7 1.0
CG A:LEU94 4.9 32.7 1.0
CB A:CYS164 4.9 28.4 1.0

Reference:

D.Constantinescu-Aruxandei, B.Petrovic-Stojanovska, J.C.Penedo, M.F.White, J.H.Naismith. Mechanism of Dna Loading By the Dna Repair Helicase Xpd. Nucleic Acids Res. V. 44 2806 2016.
ISSN: ESSN 1362-4962
PubMed: 26896802
DOI: 10.1093/NAR/GKW102
Page generated: Sun Dec 13 16:02:57 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy