Zinc 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
Iron (Fe) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 5 binding sites of Zinc where determined in the Initial Dna-Lesion (CY5) Binding By Xpc and Tfiih, PDB code: 8ebs:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 8ebs

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Zinc binding site 1 out of 5 in the Initial Dna-Lesion (CY5) Binding By Xpc and Tfiih


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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
E:Zn401

b:245.4
occ:1.00
 SG E:CYS345 2.3 190.6 1.0
SG E:CYS371 2.3 188.7 1.0
SG E:CYS348 2.3 180.4 1.0
SG E:CYS368 2.3 194.1 1.0
CB E:CYS345 3.2 190.6 1.0
CB E:CYS371 3.2 188.7 1.0
CB E:CYS348 3.6 180.4 1.0
CB E:CYS368 3.7 194.1 1.0
N E:CYS348 3.9 180.4 1.0
N E:CYS368 3.9 194.1 1.0
N E:CYS371 4.2 188.7 1.0
CA E:CYS348 4.3 180.4 1.0
CA E:CYS371 4.3 188.7 1.0
CA E:CYS368 4.4 194.1 1.0
C E:GLY347 4.5 180.7 1.0
CA E:CYS345 4.6 190.6 1.0
N E:GLY347 4.7 180.7 1.0
CA E:GLY347 4.8 180.7 1.0
C E:PHE367 5.0 193.9 1.0

Zinc binding site 2 out of 5 in 8ebs

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Zinc binding site 2 out of 5 in the Initial Dna-Lesion (CY5) Binding By Xpc and Tfiih


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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
E:Zn402

b:233.9
occ:1.00
 SG E:CYS360 2.3 195.4 1.0
SG E:CYS382 2.3 182.9 1.0
SG E:CYS363 2.3 198.0 1.0
SG E:CYS385 2.3 193.6 1.0
CB E:CYS382 2.9 182.9 1.0
CB E:CYS360 3.3 195.4 1.0
N E:CYS385 3.5 193.6 1.0
N E:CYS363 3.8 198.0 1.0
CB E:CYS385 3.8 193.6 1.0
CB E:CYS363 3.8 198.0 1.0
CA E:CYS385 4.1 193.6 1.0
C E:GLY384 4.2 188.8 1.0
CA E:CYS382 4.2 182.9 1.0
ND2 E:ASN365 4.3 191.0 1.0
CA E:CYS363 4.3 198.0 1.0
CB E:VAL362 4.4 197.7 1.0
CA E:GLY384 4.4 188.8 1.0
C E:CYS382 4.5 182.9 1.0
N E:GLY384 4.5 188.8 1.0
O E:CYS382 4.5 182.9 1.0
CZ E:PHE331 4.6 191.2 1.0
N E:VAL362 4.7 197.7 1.0
CA E:CYS360 4.7 195.4 1.0
C E:VAL362 4.8 197.7 1.0
CA E:VAL362 4.8 197.7 1.0
N E:GLN364 4.9 193.1 1.0
C E:CYS363 5.0 198.0 1.0
CE2 E:PHE367 5.0 193.9 1.0

Zinc binding site 3 out of 5 in 8ebs

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Zinc binding site 3 out of 5 in the Initial Dna-Lesion (CY5) Binding By Xpc and Tfiih


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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
E:Zn403

b:252.7
occ:1.00
 SG E:CYS305 2.3 188.7 1.0
SG E:CYS308 2.3 185.5 1.0
SG E:CYS291 2.3 199.7 1.0
SG E:CYS294 2.3 199.7 1.0
CB E:CYS291 3.3 199.7 1.0
CB E:CYS305 3.4 188.7 1.0
CB E:CYS308 3.5 185.5 1.0
CB E:CYS294 3.6 199.7 1.0
N E:CYS294 3.7 199.7 1.0
N E:CYS308 3.9 185.5 1.0
CA E:CYS294 4.2 199.7 1.0
CB E:GLN293 4.2 193.9 1.0
CA E:CYS308 4.3 185.5 1.0
CB E:ALA296 4.3 193.1 1.0
C E:GLN293 4.6 193.9 1.0
CB E:ILE307 4.7 192.2 1.0
C E:CYS294 4.7 199.7 1.0
CA E:CYS291 4.7 199.7 1.0
CB E:LEU310 4.7 180.6 1.0
CA E:CYS305 4.8 188.7 1.0
N E:ALA296 4.8 193.1 1.0
CA E:GLN293 4.8 193.9 1.0
N E:GLN293 4.9 193.9 1.0
CG E:GLN293 4.9 193.9 1.0
C E:ILE307 5.0 192.2 1.0
N E:ARG295 5.0 195.1 1.0
C E:CYS308 5.0 185.5 1.0

Zinc binding site 4 out of 5 in 8ebs

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Zinc binding site 4 out of 5 in the Initial Dna-Lesion (CY5) Binding By Xpc and Tfiih


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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
F:Zn401

b:221.0
occ:1.00
 SG F:CYS282 2.3 185.5 1.0
SG F:CYS285 2.3 183.6 1.0
SG F:CYS271 2.3 180.5 1.0
SG F:CYS268 2.3 173.2 1.0
CB F:CYS282 2.8 185.5 1.0
CB F:CYS285 2.9 183.6 1.0
OG F:SER273 3.3 182.6 1.0
CB F:CYS268 3.4 173.2 1.0
N F:CYS285 3.5 183.6 1.0
N F:CYS271 3.7 180.5 1.0
CB F:CYS271 3.7 180.5 1.0
CA F:CYS285 3.8 183.6 1.0
CB F:VAL270 4.1 172.1 1.0
CA F:CYS271 4.2 180.5 1.0
CA F:CYS282 4.3 185.5 1.0
CB F:SER273 4.5 182.6 1.0
CZ F:PHE289 4.5 187.0 1.0
C F:VAL270 4.7 172.1 1.0
C F:CYS271 4.7 180.5 1.0
C F:CYS285 4.7 183.6 1.0
C F:THR284 4.7 183.5 1.0
CG1 F:VAL270 4.8 172.1 1.0
CA F:VAL270 4.8 172.1 1.0
N F:SER273 4.8 182.6 1.0
CA F:CYS268 4.8 173.2 1.0
N F:LEU272 4.9 175.4 1.0
N F:VAL270 4.9 172.1 1.0
CB F:THR284 4.9 183.5 1.0
C F:CYS282 4.9 185.5 1.0
CG2 F:VAL270 4.9 172.1 1.0
N F:GLU286 5.0 189.5 1.0

Zinc binding site 5 out of 5 in 8ebs

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Zinc binding site 5 out of 5 in the Initial Dna-Lesion (CY5) Binding By Xpc and Tfiih


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Initial Dna-Lesion (CY5) Binding By Xpc and Tfiih within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn402

b:233.8
occ:1.00
 CE1 F:HIS258 1.0 205.0 1.0
NE2 F:HIS258 1.9 205.0 1.0
ND1 F:HIS258 2.1 205.0 1.0
SG F:CYS255 2.3 192.2 1.0
SG F:CYS257 2.3 198.5 1.0
SG F:CYS276 2.3 203.0 1.0
CD2 F:HIS258 3.0 205.0 1.0
CB F:CYS276 3.0 203.0 1.0
CG F:HIS258 3.1 205.0 1.0
CB F:CYS255 3.3 192.2 1.0
N F:CYS276 3.5 203.0 1.0
CA F:CYS276 3.9 203.0 1.0
CB F:CYS257 4.1 198.5 1.0
O F:CYS255 4.1 192.2 1.0
N F:HIS258 4.2 205.0 1.0
CA F:CYS255 4.4 192.2 1.0
C F:CYS255 4.4 192.2 1.0
CB F:HIS258 4.5 205.0 1.0
N F:CYS257 4.6 198.5 1.0
C F:PHE275 4.6 187.1 1.0
CA F:CYS257 4.7 198.5 1.0
C F:CYS257 4.7 198.5 1.0
CA F:PHE275 4.9 187.1 1.0
N F:ASN277 4.9 192.0 1.0
C F:CYS276 4.9 203.0 1.0
CA F:HIS258 5.0 205.0 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: Wed Apr 26 00:38:09 2023

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