Zinc in PDB 8ebw: Initial Dna-Lesion (Ap) Binding By Xpc and Tfiih COMPLEX2

Enzymatic activity of Initial Dna-Lesion (Ap) Binding By Xpc and Tfiih COMPLEX2

All present enzymatic activity of Initial Dna-Lesion (Ap) Binding By Xpc and Tfiih COMPLEX2:
3.6.4.12;

Other elements in 8ebw:

The structure of Initial Dna-Lesion (Ap) Binding By Xpc and Tfiih COMPLEX2 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 (Ap) Binding By Xpc and Tfiih COMPLEX2 (pdb code 8ebw). 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 (Ap) Binding By Xpc and Tfiih COMPLEX2, PDB code: 8ebw:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 8ebw

Go back to Zinc Binding Sites List in 8ebw
Zinc binding site 1 out of 5 in the Initial Dna-Lesion (Ap) Binding By Xpc and Tfiih COMPLEX2


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 (Ap) Binding By Xpc and Tfiih COMPLEX2 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn401

b:408.1
occ:1.00
 SG E:CYS348 2.3 324.9 1.0
SG E:CYS371 2.3 331.9 1.0
SG E:CYS345 2.3 337.3 1.0
SG E:CYS368 2.3 321.6 1.0
CB E:CYS345 3.2 337.3 1.0
CB E:CYS371 3.2 331.9 1.0
CB E:CYS348 3.3 324.9 1.0
N E:CYS348 3.6 324.9 1.0
CB E:CYS368 3.8 321.6 1.0
N E:CYS368 3.9 321.6 1.0
CA E:CYS348 4.0 324.9 1.0
C E:GLY347 4.3 315.1 1.0
N E:CYS371 4.3 331.9 1.0
CA E:CYS368 4.4 321.6 1.0
CA E:CYS371 4.4 331.9 1.0
CA E:GLY347 4.5 315.1 1.0
N E:GLY347 4.6 315.1 1.0
CA E:CYS345 4.6 337.3 1.0
C E:CYS348 4.8 324.9 1.0
C E:PHE367 4.9 332.1 1.0
CA E:PHE367 5.0 332.1 1.0

Zinc binding site 2 out of 5 in 8ebw

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Zinc binding site 2 out of 5 in the Initial Dna-Lesion (Ap) Binding By Xpc and Tfiih COMPLEX2


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 (Ap) Binding By Xpc and Tfiih COMPLEX2 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn402

b:386.2
occ:1.00
 SG E:CYS360 2.3 333.0 1.0
SG E:CYS382 2.3 303.7 1.0
SG E:CYS363 2.3 355.6 1.0
SG E:CYS385 2.3 295.8 1.0
CB E:CYS382 2.8 303.7 1.0
CB E:CYS360 3.1 333.0 1.0
N E:CYS385 3.6 295.8 1.0
N E:CYS363 3.7 355.6 1.0
CB E:CYS385 3.8 295.8 1.0
CB E:CYS363 3.8 355.6 1.0
CA E:CYS385 4.2 295.8 1.0
CA E:CYS382 4.2 303.7 1.0
CB E:VAL362 4.3 344.7 1.0
CA E:CYS363 4.4 355.6 1.0
ND2 E:ASN365 4.4 345.1 1.0
C E:GLY384 4.4 300.1 1.0
C E:CYS382 4.5 303.7 1.0
CA E:CYS360 4.5 333.0 1.0
N E:VAL362 4.6 344.7 1.0
N E:GLY384 4.6 300.1 1.0
CZ E:PHE331 4.6 294.6 1.0
CA E:GLY384 4.6 300.1 1.0
O E:CYS382 4.7 303.7 1.0
C E:VAL362 4.7 344.7 1.0
CA E:VAL362 4.8 344.7 1.0
N E:GLN364 4.8 352.8 1.0
CE1 E:PHE331 4.9 294.6 1.0
C E:CYS363 5.0 355.6 1.0

Zinc binding site 3 out of 5 in 8ebw

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Zinc binding site 3 out of 5 in the Initial Dna-Lesion (Ap) Binding By Xpc and Tfiih COMPLEX2


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 (Ap) Binding By Xpc and Tfiih COMPLEX2 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn403

b:391.5
occ:1.00
 SG E:CYS308 2.3 317.4 1.0
SG E:CYS294 2.3 330.5 1.0
SG E:CYS291 2.3 311.5 1.0
SG E:CYS305 2.3 331.9 1.0
CB E:CYS291 3.3 311.5 1.0
CB E:CYS305 3.3 331.9 1.0
CB E:CYS308 3.7 317.4 1.0
CB E:CYS294 3.7 330.5 1.0
N E:CYS294 3.8 330.5 1.0
N E:CYS308 3.9 317.4 1.0
CB E:ALA296 4.2 335.5 1.0
CB E:GLN293 4.2 311.4 1.0
CA E:CYS294 4.3 330.5 1.0
CA E:CYS308 4.4 317.4 1.0
CB E:ILE307 4.4 338.4 1.0
C E:GLN293 4.6 311.4 1.0
CA E:CYS291 4.7 311.5 1.0
CA E:CYS305 4.7 331.9 1.0
C E:CYS294 4.8 330.5 1.0
CA E:GLN293 4.8 311.4 1.0
N E:ALA296 4.8 335.5 1.0
CB E:LEU310 4.9 309.7 1.0
CG E:GLN293 4.9 311.4 1.0
N E:GLN293 4.9 311.4 1.0
C E:ILE307 4.9 338.4 1.0
N E:ILE307 4.9 338.4 1.0
CA E:ILE307 5.0 338.4 1.0

Zinc binding site 4 out of 5 in 8ebw

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Zinc binding site 4 out of 5 in the Initial Dna-Lesion (Ap) Binding By Xpc and Tfiih COMPLEX2


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 (Ap) Binding By Xpc and Tfiih COMPLEX2 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn401

b:331.7
occ:1.00
 SG F:CYS282 2.3 326.8 1.0
SG F:CYS285 2.3 290.4 1.0
SG F:CYS271 2.3 282.4 1.0
SG F:CYS268 2.3 285.3 1.0
OG F:SER273 3.2 305.1 1.0
CB F:CYS282 3.3 326.8 1.0
CB F:CYS268 3.3 285.3 1.0
CB F:CYS285 3.4 290.4 1.0
CB F:CYS271 3.4 282.4 1.0
N F:CYS271 3.5 282.4 1.0
N F:CYS285 3.7 290.4 1.0
CA F:CYS271 4.0 282.4 1.0
CA F:CYS285 4.1 290.4 1.0
CB F:VAL270 4.2 246.9 1.0
CB F:SER273 4.5 305.1 1.0
C F:CYS271 4.5 282.4 1.0
C F:VAL270 4.6 246.9 1.0
CB F:THR284 4.7 297.4 1.0
CA F:CYS282 4.7 326.8 1.0
N F:LEU272 4.8 289.7 1.0
CA F:VAL270 4.8 246.9 1.0
CA F:CYS268 4.8 285.3 1.0
N F:VAL270 4.8 246.9 1.0
N F:SER273 4.8 305.1 1.0
C F:THR284 4.9 297.4 1.0
CG1 F:VAL270 4.9 246.9 1.0
C F:CYS285 4.9 290.4 1.0
N F:THR284 5.0 297.4 1.0
CE2 F:PHE275 5.0 314.3 1.0
CZ F:PHE289 5.0 322.8 1.0

Zinc binding site 5 out of 5 in 8ebw

Go back to Zinc Binding Sites List in 8ebw
Zinc binding site 5 out of 5 in the Initial Dna-Lesion (Ap) Binding By Xpc and Tfiih COMPLEX2


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 (Ap) Binding By Xpc and Tfiih COMPLEX2 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn402

b:396.2
occ:1.00
 CE1 F:HIS258 1.3 339.9 1.0
NE2 F:HIS258 2.1 339.9 1.0
ND1 F:HIS258 2.2 339.9 1.0
SG F:CYS255 2.3 315.9 1.0
SG F:CYS257 2.3 331.6 1.0
SG F:CYS276 2.3 348.1 1.0
CB F:CYS276 3.1 348.1 1.0
CD2 F:HIS258 3.1 339.9 1.0
CB F:CYS255 3.2 315.9 1.0
CG F:HIS258 3.2 339.9 1.0
N F:CYS276 3.5 348.1 1.0
CB F:CYS257 3.9 331.6 1.0
CA F:CYS276 3.9 348.1 1.0
N F:HIS258 4.1 339.9 1.0
N F:CYS257 4.3 331.6 1.0
CA F:CYS255 4.4 315.9 1.0
O F:CYS255 4.4 315.9 1.0
C F:CYS255 4.4 315.9 1.0
CA F:CYS257 4.5 331.6 1.0
C F:CYS257 4.5 331.6 1.0
CB F:HIS258 4.6 339.9 1.0
C F:PHE275 4.7 314.3 1.0
N F:ASN277 4.7 306.1 1.0
C F:CYS276 4.8 348.1 1.0
CA F:PHE275 5.0 314.3 1.0
CA F:HIS258 5.0 339.9 1.0
N F:PHE256 5.0 282.8 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 Oct 30 19:37:35 2024

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