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: Tue Apr 25 20:50:48 2023

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