Zinc in PDB 8ebv: Initial Dna-Lesion (Ap) Binding By Xpc and Tfiih Complex 1

Enzymatic activity of Initial Dna-Lesion (Ap) Binding By Xpc and Tfiih Complex 1

All present enzymatic activity of Initial Dna-Lesion (Ap) Binding By Xpc and Tfiih Complex 1:
3.6.4.12;

Other elements in 8ebv:

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

Zinc binding site 1 out of 5 in 8ebv

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


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 Complex 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn401

b:492.2
occ:1.00
 SG E:CYS348 2.3 418.6 1.0
SG E:CYS371 2.3 535.4 1.0
SG E:CYS345 2.3 434.5 1.0
SG E:CYS368 2.3 543.7 1.0
CB E:CYS345 3.2 434.5 1.0
CB E:CYS371 3.2 535.4 1.0
CB E:CYS348 3.3 418.6 1.0
N E:CYS348 3.7 418.6 1.0
CB E:CYS368 3.7 543.7 1.0
N E:CYS368 3.9 543.7 1.0
CA E:CYS348 4.1 418.6 1.0
N E:CYS371 4.3 535.4 1.0
CA E:CYS371 4.3 535.4 1.0
CA E:CYS368 4.4 543.7 1.0
C E:GLY347 4.5 446.6 1.0
CA E:CYS345 4.7 434.5 1.0
N E:GLY347 4.7 446.6 1.0
CA E:GLY347 4.7 446.6 1.0
C E:CYS348 4.8 418.6 1.0
C E:PHE367 5.0 499.7 1.0

Zinc binding site 2 out of 5 in 8ebv

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Zinc binding site 2 out of 5 in the Initial Dna-Lesion (Ap) Binding By Xpc and Tfiih Complex 1


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 Complex 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn402

b:547.6
occ:1.00
 SG E:CYS382 2.3 434.8 1.0
SG E:CYS360 2.3 513.3 1.0
SG E:CYS363 2.3 478.1 1.0
SG E:CYS385 2.3 436.9 1.0
CB E:CYS382 2.9 434.8 1.0
CB E:CYS360 3.2 513.3 1.0
N E:CYS385 3.7 436.9 1.0
CB E:CYS385 3.8 436.9 1.0
N E:CYS363 3.9 478.1 1.0
CB E:CYS363 3.9 478.1 1.0
CA E:CYS385 4.2 436.9 1.0
ND2 E:ASN365 4.3 472.6 1.0
CB E:VAL362 4.3 546.2 1.0
CA E:CYS382 4.3 434.8 1.0
C E:GLY384 4.4 428.7 1.0
CA E:CYS363 4.5 478.1 1.0
CA E:GLY384 4.6 428.7 1.0
CA E:CYS360 4.7 513.3 1.0
C E:CYS382 4.7 434.8 1.0
N E:GLY384 4.7 428.7 1.0
CZ E:PHE331 4.7 457.5 1.0
N E:VAL362 4.7 546.2 1.0
O E:CYS382 4.8 434.8 1.0
CA E:VAL362 4.8 546.2 1.0
C E:VAL362 4.8 546.2 1.0
CE1 E:PHE331 4.9 457.5 1.0
CG2 E:VAL362 5.0 546.2 1.0

Zinc binding site 3 out of 5 in 8ebv

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Zinc binding site 3 out of 5 in the Initial Dna-Lesion (Ap) Binding By Xpc and Tfiih Complex 1


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 Complex 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn403

b:517.1
occ:1.00
 SG E:CYS308 2.3 450.9 1.0
SG E:CYS305 2.3 448.0 1.0
SG E:CYS291 2.3 432.1 1.0
SG E:CYS294 2.3 396.0 1.0
CB E:CYS291 3.3 432.1 1.0
CB E:CYS305 3.3 448.0 1.0
CB E:CYS308 3.6 450.9 1.0
CB E:CYS294 3.8 396.0 1.0
N E:CYS308 3.9 450.9 1.0
N E:CYS294 3.9 396.0 1.0
CB E:ALA296 4.2 456.7 1.0
CB E:GLN293 4.2 386.1 1.0
CA E:CYS308 4.3 450.9 1.0
CA E:CYS294 4.4 396.0 1.0
CB E:ILE307 4.5 461.3 1.0
C E:GLN293 4.7 386.1 1.0
CA E:CYS291 4.7 432.1 1.0
CA E:CYS305 4.8 448.0 1.0
CB E:LEU310 4.8 429.5 1.0
CA E:GLN293 4.8 386.1 1.0
N E:ALA296 4.9 456.7 1.0
C E:ILE307 4.9 461.3 1.0
CG E:GLN293 4.9 386.1 1.0
N E:GLN293 4.9 386.1 1.0
C E:CYS294 4.9 396.0 1.0
N E:ILE307 5.0 461.3 1.0
CG2 E:ILE307 5.0 461.3 1.0
OE1 E:GLN293 5.0 386.1 1.0

Zinc binding site 4 out of 5 in 8ebv

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Zinc binding site 4 out of 5 in the Initial Dna-Lesion (Ap) Binding By Xpc and Tfiih Complex 1


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 Complex 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn401

b:491.4
occ:1.00
 SG F:CYS282 2.3 433.7 1.0
SG F:CYS285 2.3 475.4 1.0
SG F:CYS271 2.3 387.0 1.0
SG F:CYS268 2.3 401.4 1.0
CB F:CYS282 3.1 433.7 1.0
OG F:SER273 3.2 492.5 1.0
CB F:CYS285 3.3 475.4 1.0
CB F:CYS268 3.3 401.4 1.0
CB F:CYS271 3.6 387.0 1.0
N F:CYS271 3.6 387.0 1.0
N F:CYS285 3.7 475.4 1.0
CA F:CYS271 4.1 387.0 1.0
CA F:CYS285 4.1 475.4 1.0
CB F:VAL270 4.3 332.6 1.0
CB F:SER273 4.3 492.5 1.0
CA F:CYS282 4.5 433.7 1.0
C F:CYS271 4.6 387.0 1.0
C F:VAL270 4.7 332.6 1.0
N F:SER273 4.7 492.5 1.0
CB F:THR284 4.7 462.5 1.0
CZ F:PHE289 4.7 425.4 1.0
CA F:CYS268 4.8 401.4 1.0
N F:LEU272 4.8 463.2 1.0
CA F:VAL270 4.8 332.6 1.0
N F:VAL270 4.8 332.6 1.0
C F:THR284 4.9 462.5 1.0
N F:THR284 5.0 462.5 1.0
C F:CYS285 5.0 475.4 1.0
CG1 F:VAL270 5.0 332.6 1.0

Zinc binding site 5 out of 5 in 8ebv

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


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 Complex 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn402

b:633.5
occ:1.00
 NE2 F:HIS258 2.1 517.3 1.0
CE1 F:HIS258 2.2 517.3 1.0
SG F:CYS255 2.3 451.1 1.0
SG F:CYS257 2.3 461.9 1.0
SG F:CYS276 2.3 577.9 1.0
CB F:CYS276 3.0 577.9 1.0
CD2 F:HIS258 3.0 517.3 1.0
ND1 F:HIS258 3.1 517.3 1.0
CB F:CYS255 3.2 451.1 1.0
CG F:HIS258 3.5 517.3 1.0
N F:CYS276 3.5 577.9 1.0
CA F:CYS276 3.9 577.9 1.0
CB F:CYS257 3.9 461.9 1.0
O F:CYS255 4.4 451.1 1.0
N F:HIS258 4.4 517.3 1.0
CA F:CYS255 4.4 451.1 1.0
C F:CYS255 4.5 451.1 1.0
N F:CYS257 4.6 461.9 1.0
CA F:CYS257 4.7 461.9 1.0
C F:PHE275 4.7 504.1 1.0
C F:CYS257 4.9 461.9 1.0
C F:CYS276 4.9 577.9 1.0
CB F:HIS258 4.9 517.3 1.0
N F:ASN277 4.9 541.4 1.0
CA F:PHE275 5.0 504.1 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 19:36:51 2024

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