Zinc 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:

Iron

(Fe)

4 atoms

The binding sites of Zinc atom in the Xpc Release From CORE7-Xpa-Dna (CY5) (pdb code 8ebu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Xpc Release From CORE7-Xpa-Dna (CY5), PDB code: 8ebu:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Xpc Release From CORE7-Xpa-Dna (CY5)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Xpc Release From CORE7-Xpa-Dna (CY5) within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn401 b:64.8 occ:1.00 SG E:CYS371 2.3 41.0 1.0 SG E:CYS345 2.3 53.9 1.0 SG E:CYS348 2.3 43.6 1.0 SG E:CYS368 2.3 45.5 1.0 CB E:CYS371 3.1 41.0 1.0 CB E:CYS345 3.2 53.9 1.0 CB E:CYS348 3.3 43.6 1.0 N E:CYS348 3.7 43.6 1.0 CB E:CYS368 3.7 45.5 1.0 N E:CYS368 3.9 45.5 1.0 CA E:CYS348 4.1 43.6 1.0 N E:CYS371 4.2 41.0 1.0 CA E:CYS371 4.2 41.0 1.0 CA E:CYS368 4.4 45.5 1.0 C E:GLY347 4.6 38.9 1.0 CA E:CYS345 4.7 53.9 1.0 N E:GLY347 4.7 38.9 1.0 CA E:GLY347 4.8 38.9 1.0 C E:CYS348 4.8 43.6 1.0

Zinc binding site 2 out of 6 in the Xpc Release From CORE7-Xpa-Dna (CY5)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Xpc Release From CORE7-Xpa-Dna (CY5) within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn402 b:95.0 occ:1.00 SG E:CYS382 2.3 43.9 1.0 SG E:CYS360 2.3 57.7 1.0 SG E:CYS385 2.3 42.7 1.0 SG E:CYS363 2.3 61.6 1.0 CB E:CYS360 3.1 57.7 1.0 CB E:CYS382 3.2 43.9 1.0 N E:CYS385 3.7 42.7 1.0 CB E:CYS385 3.8 42.7 1.0 CB E:CYS363 3.8 61.6 1.0 N E:CYS363 3.9 61.6 1.0 CA E:CYS385 4.2 42.7 1.0 CB E:VAL362 4.3 59.2 1.0 C E:GLY384 4.4 41.7 1.0 CA E:CYS363 4.5 61.6 1.0 CA E:CYS360 4.6 57.7 1.0 CA E:CYS382 4.6 43.9 1.0 CA E:GLY384 4.6 41.7 1.0 ND2 E:ASN365 4.7 52.6 1.0 N E:GLY384 4.7 41.7 1.0 N E:VAL362 4.8 59.2 1.0 C E:VAL362 4.9 59.2 1.0 CA E:VAL362 4.9 59.2 1.0 CE1 E:PHE331 4.9 52.6 1.0 C E:CYS382 4.9 43.9 1.0

Zinc binding site 3 out of 6 in the Xpc Release From CORE7-Xpa-Dna (CY5)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Xpc Release From CORE7-Xpa-Dna (CY5) within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn403 b:87.6 occ:1.00 SG E:CYS308 2.3 57.4 1.0 SG E:CYS294 2.3 63.5 1.0 SG E:CYS305 2.3 52.1 1.0 SG E:CYS291 2.3 50.8 1.0 CB E:CYS291 3.3 50.8 1.0 CB E:CYS305 3.4 52.1 1.0 CB E:CYS308 3.6 57.4 1.0 CB E:CYS294 3.7 63.5 1.0 N E:CYS294 4.0 63.5 1.0 N E:CYS308 4.0 57.4 1.0 CA E:CYS308 4.3 57.4 1.0 CA E:CYS294 4.4 63.5 1.0 CB E:ALA296 4.4 59.8 1.0 CB E:GLN293 4.6 57.1 1.0 CA E:CYS291 4.7 50.8 1.0 CB E:LEU310 4.7 45.3 1.0 CB E:ILE307 4.8 61.1 1.0 CA E:CYS305 4.8 52.1 1.0 OH E:TYR298 4.8 55.9 1.0 C E:CYS294 4.9 63.5 1.0 C E:GLN293 4.9 57.1 1.0 N E:ALA296 4.9 59.8 1.0 C E:CYS308 5.0 57.4 1.0

Zinc binding site 4 out of 6 in the Xpc Release From CORE7-Xpa-Dna (CY5)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Xpc Release From CORE7-Xpa-Dna (CY5) within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn401 b:70.5 occ:1.00 SG F:CYS268 2.3 32.8 1.0 SG F:CYS271 2.3 35.1 1.0 SG F:CYS282 2.3 69.3 1.0 SG F:CYS285 2.3 68.4 1.0 CB F:CYS268 3.1 32.8 1.0 CB F:CYS282 3.3 69.3 1.0 OG1 F:THR284 3.3 60.5 1.0 CB F:CYS285 3.7 68.4 1.0 OG F:SER273 3.7 31.1 1.0 CB F:CYS271 3.7 35.1 1.0 N F:CYS285 3.9 68.4 1.0 N F:CYS271 4.0 35.1 1.0 CA F:CYS285 4.3 68.4 1.0 CA F:CYS271 4.5 35.1 1.0 CA F:CYS268 4.6 32.8 1.0 CB F:THR284 4.6 60.5 1.0 CA F:CYS282 4.7 69.3 1.0 CB F:VAL270 4.7 35.2 1.0 C F:THR284 4.8 60.5 1.0 N F:VAL270 5.0 35.2 1.0

Zinc binding site 5 out of 6 in the Xpc Release From CORE7-Xpa-Dna (CY5)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Xpc Release From CORE7-Xpa-Dna (CY5) within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn402 b:140.9 occ:1.00 NE2 F:HIS258 2.1 56.5 1.0 CD2 F:HIS258 2.2 56.5 1.0 SG F:CYS255 2.3 47.3 1.0 SG F:CYS257 2.3 56.6 1.0 SG F:CYS276 2.3 49.5 1.0 N F:CYS276 2.6 49.5 1.0 CB F:CYS276 3.0 49.5 1.0 CA F:CYS276 3.3 49.5 1.0 CE1 F:HIS258 3.4 56.5 1.0 CG F:HIS258 3.5 56.5 1.0 C F:PHE275 3.6 38.4 1.0 CA F:PHE275 3.8 38.4 1.0 CB F:CYS257 3.8 56.6 1.0 N F:ASN277 3.9 48.1 1.0 CB F:CYS255 4.0 47.3 1.0 ND1 F:HIS258 4.0 56.5 1.0 C F:CYS276 4.1 49.5 1.0 CB F:PHE275 4.2 38.4 1.0 N F:CYS257 4.3 56.6 1.0 CA F:CYS257 4.4 56.6 1.0 N F:HIS258 4.5 56.5 1.0 C F:CYS257 4.6 56.6 1.0 CB F:HIS258 4.7 56.5 1.0 O F:PHE275 4.8 38.4 1.0 CD1 F:PHE275 4.8 38.4 1.0

Zinc binding site 6 out of 6 in the Xpc Release From CORE7-Xpa-Dna (CY5)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Xpc Release From CORE7-Xpa-Dna (CY5) within 5.0Å range: probe atom residue distance (Å) B Occ K:Zn301 b:149.7 occ:1.00 SG K:CYS129 2.3 103.4 1.0 SG K:CYS126 2.3 98.2 1.0 SG K:CYS108 2.3 98.8 1.0 SG K:CYS105 2.3 103.0 1.0 CB K:CYS105 3.1 103.0 1.0 CB K:CYS129 3.1 103.4 1.0 CB K:CYS108 3.3 98.8 1.0 N K:CYS108 3.6 98.8 1.0 CB K:CYS126 3.9 98.2 1.0 CA K:CYS108 4.0 98.8 1.0 N K:CYS129 4.1 103.4 1.0 CA K:CYS129 4.3 103.4 1.0 N K:CYS126 4.3 98.2 1.0 CB K:GLU107 4.3 105.5 1.0 CA K:CYS105 4.6 103.0 1.0 C K:GLU107 4.6 105.5 1.0 CA K:CYS126 4.6 98.2 1.0 N K:GLY109 4.7 93.4 1.0 C K:CYS108 4.8 98.8 1.0 N K:GLU107 4.8 105.5 1.0 CA K:GLU107 4.8 105.5 1.0 O K:CYS126 4.9 98.2 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