Iron in PDB 8ebu: Xpc Release From CORE7-Xpa-Dna (CY5)

All present enzymatic activity of Xpc Release From CORE7-Xpa-Dna (CY5):
3.6.4.12;

The structure of Xpc Release From CORE7-Xpa-Dna (CY5) also contains other interesting chemical elements:

Zinc

(Zn)

6 atoms

The binding sites of Iron atom in the Xpc Release From CORE7-Xpa-Dna (CY5) (pdb code 8ebu). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Xpc Release From CORE7-Xpa-Dna (CY5), PDB code: 8ebu:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Xpc Release From CORE7-Xpa-Dna (CY5)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Xpc Release From CORE7-Xpa-Dna (CY5) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1000 b:220.0 occ:1.00 FE1 B:SF41000 0.0 220.0 1.0 SG B:CYS116 2.3 125.2 1.0 S2 B:SF41000 2.3 220.0 1.0 S4 B:SF41000 2.3 220.0 1.0 S3 B:SF41000 2.3 220.0 1.0 FE3 B:SF41000 2.7 220.0 1.0 FE4 B:SF41000 2.7 220.0 1.0 FE2 B:SF41000 2.7 220.0 1.0 CB B:CYS116 3.4 125.2 1.0 CA B:CYS116 3.9 125.2 1.0 S1 B:SF41000 3.9 220.0 1.0 N B:ILE117 4.2 123.3 1.0 C B:CYS116 4.6 125.2 1.0 N B:HIS118 4.6 129.9 1.0 O B:LEU115 4.7 104.9 1.0 CB B:HIS118 4.8 129.9 1.0 SG B:CYS134 4.8 120.0 1.0 SG B:CYS155 4.9 126.8 1.0 SG B:CYS190 4.9 118.8 1.0 CG B:HIS118 4.9 129.9 1.0 CD2 B:HIS118 5.0 129.9 1.0

Iron binding site 2 out of 4 in the Xpc Release From CORE7-Xpa-Dna (CY5)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Xpc Release From CORE7-Xpa-Dna (CY5) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1000 b:220.0 occ:1.00 FE2 B:SF41000 0.0 220.0 1.0 SG B:CYS155 2.3 126.8 1.0 S1 B:SF41000 2.3 220.0 1.0 S3 B:SF41000 2.3 220.0 1.0 S4 B:SF41000 2.3 220.0 1.0 FE4 B:SF41000 2.7 220.0 1.0 FE3 B:SF41000 2.7 220.0 1.0 FE1 B:SF41000 2.7 220.0 1.0 CB B:CYS155 3.5 126.8 1.0 S2 B:SF41000 3.9 220.0 1.0 CD2 B:HIS118 4.2 129.9 1.0 NE2 B:HIS118 4.3 129.9 1.0 CD2 B:PHE157 4.3 116.3 1.0 CG B:HIS118 4.7 129.9 1.0 SG B:CYS190 4.8 118.8 1.0 SG B:CYS116 4.8 125.2 1.0 SG B:CYS134 4.8 120.0 1.0 CG2 B:THR138 4.8 114.1 1.0 CA B:CYS155 4.9 126.8 1.0 CE1 B:HIS118 4.9 129.9 1.0 CB B:PHE157 4.9 116.3 1.0 CB B:CYS190 4.9 118.8 1.0 CG B:PHE157 5.0 116.3 1.0

Iron binding site 3 out of 4 in the Xpc Release From CORE7-Xpa-Dna (CY5)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Xpc Release From CORE7-Xpa-Dna (CY5) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1000 b:220.0 occ:1.00 FE3 B:SF41000 0.0 220.0 1.0 SG B:CYS134 2.3 120.0 1.0 S1 B:SF41000 2.3 220.0 1.0 S2 B:SF41000 2.3 220.0 1.0 S4 B:SF41000 2.3 220.0 1.0 FE4 B:SF41000 2.7 220.0 1.0 FE1 B:SF41000 2.7 220.0 1.0 FE2 B:SF41000 2.7 220.0 1.0 CB B:CYS134 3.2 120.0 1.0 S3 B:SF41000 3.9 220.0 1.0 CA B:CYS134 3.9 120.0 1.0 O B:CYS134 4.5 120.0 1.0 SG B:CYS190 4.6 118.8 1.0 C B:CYS134 4.6 120.0 1.0 CG2 B:THR138 4.6 114.1 1.0 SG B:CYS116 4.7 125.2 1.0 SG B:CYS155 4.7 126.8 1.0

Iron binding site 4 out of 4 in the Xpc Release From CORE7-Xpa-Dna (CY5)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Xpc Release From CORE7-Xpa-Dna (CY5) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1000 b:220.0 occ:1.00 FE4 B:SF41000 0.0 220.0 1.0 SG B:CYS190 2.3 118.8 1.0 S1 B:SF41000 2.3 220.0 1.0 S2 B:SF41000 2.3 220.0 1.0 S3 B:SF41000 2.3 220.0 1.0 FE3 B:SF41000 2.7 220.0 1.0 FE2 B:SF41000 2.7 220.0 1.0 FE1 B:SF41000 2.7 220.0 1.0 CB B:CYS190 3.2 118.8 1.0 S4 B:SF41000 3.9 220.0 1.0 CA B:CYS190 4.1 118.8 1.0 SG B:CYS134 4.6 120.0 1.0 SG B:CYS155 4.7 126.8 1.0 SG B:CYS116 4.8 125.2 1.0 CD B:PRO191 4.8 107.8 1.0 O B:LEU115 4.8 104.9 1.0 CE2 B:PHE193 4.8 109.9 1.0 C B:CYS190 4.9 118.8 1.0

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