Atomistry » Iron » PDB 8e3u-8eqm » 8ebv
Atomistry »
  Iron »
    PDB 8e3u-8eqm »
      8ebv »

Iron in PDB 8ebv: Initial Dna-Lesion (Ap) Binding By Xpc and Tfiih Complex 1

Enzymatic activity of Initial Dna-Lesion (Ap) Binding By Xpc and Tfiih Complex 1

All present enzymatic activity of Initial Dna-Lesion (Ap) Binding By Xpc and Tfiih Complex 1:
3.6.4.12;

Other elements in 8ebv:

The structure of Initial Dna-Lesion (Ap) Binding By Xpc and Tfiih Complex 1 also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Zinc (Zn) 5 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Initial Dna-Lesion (Ap) Binding By Xpc and Tfiih Complex 1 (pdb code 8ebv). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Initial Dna-Lesion (Ap) Binding By Xpc and Tfiih Complex 1, PDB code: 8ebv:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 8ebv

Go back to Iron Binding Sites List in 8ebv
Iron binding site 1 out of 4 in the Initial Dna-Lesion (Ap) Binding By Xpc and Tfiih Complex 1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Initial Dna-Lesion (Ap) Binding By Xpc and Tfiih Complex 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1000

b:541.8
occ:1.00
FE1 B:SF41000 0.0 541.8 1.0
SG B:CYS116 2.3 528.0 1.0
S4 B:SF41000 2.3 541.8 1.0
S3 B:SF41000 2.3 541.8 1.0
S2 B:SF41000 2.3 541.8 1.0
FE2 B:SF41000 2.7 541.8 1.0
FE4 B:SF41000 2.7 541.8 1.0
FE3 B:SF41000 2.7 541.8 1.0
CB B:CYS116 2.9 528.0 1.0
CA B:CYS116 3.2 528.0 1.0
N B:ILE117 3.7 493.5 1.0
S1 B:SF41000 3.9 541.8 1.0
C B:CYS116 3.9 528.0 1.0
N B:HIS118 4.0 494.1 1.0
CB B:HIS118 4.1 494.1 1.0
N B:CYS116 4.4 528.0 1.0
CG2 B:VAL121 4.7 548.9 1.0
CA B:HIS118 4.7 494.1 1.0
CB B:VAL121 4.8 548.9 1.0
O B:LEU115 4.8 497.0 1.0
SG B:CYS155 4.8 411.1 1.0
SG B:CYS134 4.8 513.9 1.0
SG B:CYS190 4.8 448.9 1.0
CA B:ILE117 4.8 493.5 1.0
CB B:CYS134 4.9 513.9 1.0
C B:ILE117 4.9 493.5 1.0

Iron binding site 2 out of 4 in 8ebv

Go back to Iron Binding Sites List in 8ebv
Iron binding site 2 out of 4 in the Initial Dna-Lesion (Ap) Binding By Xpc and Tfiih Complex 1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Initial Dna-Lesion (Ap) Binding By Xpc and Tfiih Complex 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1000

b:541.8
occ:1.00
FE2 B:SF41000 0.0 541.8 1.0
SG B:CYS155 2.3 411.1 1.0
S1 B:SF41000 2.3 541.8 1.0
S4 B:SF41000 2.3 541.8 1.0
S3 B:SF41000 2.3 541.8 1.0
FE1 B:SF41000 2.7 541.8 1.0
FE3 B:SF41000 2.7 541.8 1.0
FE4 B:SF41000 2.7 541.8 1.0
CB B:CYS155 3.6 411.1 1.0
CB B:HIS118 3.8 494.1 1.0
S2 B:SF41000 3.9 541.8 1.0
CD1 B:PHE157 4.1 418.7 1.0
CB B:PHE157 4.5 418.7 1.0
CG B:HIS118 4.5 494.1 1.0
N B:HIS118 4.5 494.1 1.0
SG B:CYS116 4.6 528.0 1.0
CG B:PHE157 4.6 418.7 1.0
CA B:HIS118 4.7 494.1 1.0
SG B:CYS134 4.7 513.9 1.0
SG B:CYS190 4.8 448.9 1.0
CD2 B:HIS118 4.8 494.1 1.0
CE1 B:PHE157 4.9 418.7 1.0
CA B:CYS155 4.9 411.1 1.0
CG2 B:THR138 5.0 505.0 1.0

Iron binding site 3 out of 4 in 8ebv

Go back to Iron Binding Sites List in 8ebv
Iron binding site 3 out of 4 in the Initial Dna-Lesion (Ap) Binding By Xpc and Tfiih Complex 1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Initial Dna-Lesion (Ap) Binding By Xpc and Tfiih Complex 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1000

b:541.8
occ:1.00
FE3 B:SF41000 0.0 541.8 1.0
SG B:CYS134 2.3 513.9 1.0
S4 B:SF41000 2.3 541.8 1.0
S2 B:SF41000 2.3 541.8 1.0
S1 B:SF41000 2.3 541.8 1.0
FE4 B:SF41000 2.7 541.8 1.0
FE2 B:SF41000 2.7 541.8 1.0
FE1 B:SF41000 2.7 541.8 1.0
CB B:CYS134 3.0 513.9 1.0
CA B:CYS134 3.9 513.9 1.0
S3 B:SF41000 3.9 541.8 1.0
CE1 B:PHE193 4.3 470.3 1.0
SG B:CYS190 4.6 448.9 1.0
CD B:ARG112 4.6 525.1 1.0
SG B:CYS155 4.6 411.1 1.0
C B:CYS134 4.7 513.9 1.0
CG2 B:THR138 4.7 505.0 1.0
O B:CYS134 4.8 513.9 1.0
SG B:CYS116 4.8 528.0 1.0
NH1 B:ARG112 4.9 525.1 1.0
CZ B:PHE193 5.0 470.3 1.0
N B:CYS134 5.0 513.9 1.0
OG1 B:THR138 5.0 505.0 1.0

Iron binding site 4 out of 4 in 8ebv

Go back to Iron Binding Sites List in 8ebv
Iron binding site 4 out of 4 in the Initial Dna-Lesion (Ap) Binding By Xpc and Tfiih Complex 1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Initial Dna-Lesion (Ap) Binding By Xpc and Tfiih Complex 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1000

b:541.8
occ:1.00
FE4 B:SF41000 0.0 541.8 1.0
SG B:CYS190 2.3 448.9 1.0
S1 B:SF41000 2.3 541.8 1.0
S2 B:SF41000 2.3 541.8 1.0
S3 B:SF41000 2.3 541.8 1.0
FE3 B:SF41000 2.7 541.8 1.0
FE2 B:SF41000 2.7 541.8 1.0
FE1 B:SF41000 2.7 541.8 1.0
CB B:CYS190 3.2 448.9 1.0
S4 B:SF41000 3.9 541.8 1.0
O B:LEU115 4.2 497.0 1.0
CE1 B:PHE193 4.3 470.3 1.0
CA B:CYS116 4.3 528.0 1.0
CA B:CYS190 4.3 448.9 1.0
CD1 B:PHE193 4.5 470.3 1.0
N B:ILE117 4.6 493.5 1.0
CB B:PHE157 4.7 418.7 1.0
SG B:CYS134 4.7 513.9 1.0
SG B:CYS155 4.8 411.1 1.0
CB B:CYS116 4.8 528.0 1.0
SG B:CYS116 4.8 528.0 1.0

Reference:

J.Kim, C.L.Li, X.Chen, Y.Cui, F.M.Golebiowski, H.Wang, F.Hanaoka, K.Sugasawa, W.Yang. Lesion Recognition By Xpc, Tfiih and Xpa in Dna Excision Repair Nature 2023.
ISSN: ESSN 1476-4687
Page generated: Sat Aug 10 01:07:00 2024

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy