Iron in PDB 8ebs: Initial Dna-Lesion (CY5) Binding By Xpc and Tfiih

Enzymatic activity of Initial Dna-Lesion (CY5) Binding By Xpc and Tfiih

All present enzymatic activity of Initial Dna-Lesion (CY5) Binding By Xpc and Tfiih:
3.6.4.12;

Other elements in 8ebs:

The structure of Initial Dna-Lesion (CY5) Binding By Xpc and Tfiih 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 (CY5) Binding By Xpc and Tfiih (pdb code 8ebs). 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 (CY5) Binding By Xpc and Tfiih, PDB code: 8ebs:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 8ebs

Go back to Iron Binding Sites List in 8ebs
Iron binding site 1 out of 4 in the Initial Dna-Lesion (CY5) Binding By Xpc and Tfiih


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 (CY5) Binding By Xpc and Tfiih within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1000

b:241.1
occ:1.00
 FE1 B:SF41000 0.0 241.1 1.0
SG B:CYS116 2.3 227.8 1.0
S4 B:SF41000 2.3 241.1 1.0
S3 B:SF41000 2.3 241.1 1.0
S2 B:SF41000 2.3 241.1 1.0
CB B:CYS116 2.6 227.8 1.0
FE2 B:SF41000 2.7 241.1 1.0
FE4 B:SF41000 2.7 241.1 1.0
FE3 B:SF41000 2.7 241.1 1.0
CA B:CYS116 3.3 227.8 1.0
N B:ILE117 3.7 204.0 1.0
N B:HIS118 3.8 199.0 1.0
S1 B:SF41000 3.9 241.1 1.0
C B:CYS116 3.9 227.8 1.0
CB B:HIS118 4.0 199.0 1.0
N B:CYS116 4.5 227.8 1.0
CA B:HIS118 4.5 199.0 1.0
CG2 B:VAL121 4.6 203.8 1.0
SG B:CYS190 4.7 212.4 1.0
SG B:CYS134 4.7 233.8 1.0
CB B:VAL121 4.8 203.8 1.0
CB B:CYS134 4.8 233.8 1.0
C B:ILE117 4.8 204.0 1.0
CA B:ILE117 4.8 204.0 1.0
SG B:CYS155 4.9 215.5 1.0
O B:CYS116 4.9 227.8 1.0
O B:LEU115 5.0 222.9 1.0

Iron binding site 2 out of 4 in 8ebs

Go back to Iron Binding Sites List in 8ebs
Iron binding site 2 out of 4 in the Initial Dna-Lesion (CY5) Binding By Xpc and Tfiih


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 (CY5) Binding By Xpc and Tfiih within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1000

b:241.1
occ:1.00
 FE2 B:SF41000 0.0 241.1 1.0
SG B:CYS155 2.3 215.5 1.0
S1 B:SF41000 2.3 241.1 1.0
S4 B:SF41000 2.3 241.1 1.0
S3 B:SF41000 2.3 241.1 1.0
FE1 B:SF41000 2.7 241.1 1.0
FE3 B:SF41000 2.7 241.1 1.0
FE4 B:SF41000 2.7 241.1 1.0
CB B:HIS118 3.6 199.0 1.0
CB B:PHE157 3.7 199.4 1.0
CB B:CYS155 3.8 215.5 1.0
S2 B:SF41000 3.9 241.1 1.0
CG B:PHE157 4.0 199.4 1.0
CD1 B:PHE157 4.1 199.4 1.0
CG B:HIS118 4.2 199.0 1.0
CD2 B:HIS118 4.3 199.0 1.0
N B:HIS118 4.4 199.0 1.0
CA B:HIS118 4.5 199.0 1.0
SG B:CYS116 4.6 227.8 1.0
SG B:CYS134 4.8 233.8 1.0
CG2 B:THR138 4.8 238.0 1.0
CD2 B:PHE157 4.9 199.4 1.0
SG B:CYS190 4.9 212.4 1.0
CA B:PHE157 4.9 199.4 1.0
N B:TYR158 4.9 211.6 1.0
CB B:CYS190 5.0 212.4 1.0
CE1 B:PHE157 5.0 199.4 1.0
CA B:CYS155 5.0 215.5 1.0

Iron binding site 3 out of 4 in 8ebs

Go back to Iron Binding Sites List in 8ebs
Iron binding site 3 out of 4 in the Initial Dna-Lesion (CY5) Binding By Xpc and Tfiih


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 (CY5) Binding By Xpc and Tfiih within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1000

b:241.1
occ:1.00
 FE3 B:SF41000 0.0 241.1 1.0
SG B:CYS134 2.3 233.8 1.0
S2 B:SF41000 2.3 241.1 1.0
S4 B:SF41000 2.3 241.1 1.0
S1 B:SF41000 2.3 241.1 1.0
FE4 B:SF41000 2.7 241.1 1.0
FE2 B:SF41000 2.7 241.1 1.0
FE1 B:SF41000 2.7 241.1 1.0
CB B:CYS134 3.2 233.8 1.0
S3 B:SF41000 3.9 241.1 1.0
CA B:CYS134 4.0 233.8 1.0
CE1 B:PHE193 4.2 210.5 1.0
CG2 B:THR138 4.2 238.0 1.0
SG B:CYS155 4.4 215.5 1.0
CZ B:PHE193 4.6 210.5 1.0
SG B:CYS190 4.6 212.4 1.0
C B:CYS134 4.7 233.8 1.0
NH1 B:ARG112 4.7 224.9 1.0
O B:CYS134 4.8 233.8 1.0
OG1 B:THR138 4.8 238.0 1.0
CB B:CYS116 4.8 227.8 1.0
SG B:CYS116 4.9 227.8 1.0
CD B:ARG112 4.9 224.9 1.0

Iron binding site 4 out of 4 in 8ebs

Go back to Iron Binding Sites List in 8ebs
Iron binding site 4 out of 4 in the Initial Dna-Lesion (CY5) Binding By Xpc and Tfiih


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 (CY5) Binding By Xpc and Tfiih within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1000

b:241.1
occ:1.00
 FE4 B:SF41000 0.0 241.1 1.0
SG B:CYS190 2.3 212.4 1.0
S1 B:SF41000 2.3 241.1 1.0
S2 B:SF41000 2.3 241.1 1.0
S3 B:SF41000 2.3 241.1 1.0
FE1 B:SF41000 2.7 241.1 1.0
FE3 B:SF41000 2.7 241.1 1.0
FE2 B:SF41000 2.7 241.1 1.0
CB B:CYS190 3.0 212.4 1.0
S4 B:SF41000 3.9 241.1 1.0
CE1 B:PHE193 4.0 210.5 1.0
CA B:CYS190 4.1 212.4 1.0
CA B:CYS116 4.2 227.8 1.0
O B:LEU115 4.3 222.9 1.0
CB B:PHE157 4.3 199.4 1.0
CB B:CYS116 4.4 227.8 1.0
CD1 B:PHE193 4.4 210.5 1.0
N B:ILE117 4.5 204.0 1.0
SG B:CYS155 4.6 215.5 1.0
SG B:CYS116 4.7 227.8 1.0
SG B:CYS134 4.8 233.8 1.0
C B:CYS116 5.0 227.8 1.0
C B:CYS190 5.0 212.4 1.0
CG B:PHE157 5.0 199.4 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 20:50:49 2023

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