Zinc in PDB 8ebx: Xpa Repositioning CORE7 of Tfiih Relative to Xpc-Dna Lesion (Ap)

Enzymatic activity of Xpa Repositioning CORE7 of Tfiih Relative to Xpc-Dna Lesion (Ap)

All present enzymatic activity of Xpa Repositioning CORE7 of Tfiih Relative to Xpc-Dna Lesion (Ap):
3.6.4.12;

Other elements in 8ebx:

The structure of Xpa Repositioning CORE7 of Tfiih Relative to Xpc-Dna Lesion (Ap) also contains other interesting chemical elements:

Iron (Fe) 4 atoms
Calcium (Ca) 2 atoms

Zinc Binding Sites:

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

Zinc binding site 1 out of 6 in 8ebx

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Zinc binding site 1 out of 6 in the Xpa Repositioning CORE7 of Tfiih Relative to Xpc-Dna Lesion (Ap)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Xpa Repositioning CORE7 of Tfiih Relative to Xpc-Dna Lesion (Ap) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn401

b:170.7
occ:1.00
 SG E:CYS371 2.3 135.4 1.0
SG E:CYS345 2.3 136.6 1.0
SG E:CYS348 2.3 128.8 1.0
SG E:CYS368 2.3 139.2 1.0
CB E:CYS371 3.0 135.4 1.0
CB E:CYS348 3.1 128.8 1.0
CB E:CYS345 3.1 136.6 1.0
N E:CYS348 3.6 128.8 1.0
CB E:CYS368 3.7 139.2 1.0
N E:CYS368 3.9 139.2 1.0
CA E:CYS348 3.9 128.8 1.0
CA E:CYS371 4.2 135.4 1.0
N E:CYS371 4.2 135.4 1.0
CA E:CYS368 4.4 139.2 1.0
C E:GLY347 4.6 128.1 1.0
CA E:CYS345 4.6 136.6 1.0
C E:CYS348 4.7 128.8 1.0
N E:GLY347 4.8 128.1 1.0
CA E:GLY347 4.9 128.1 1.0
C E:PHE367 5.0 139.8 1.0

Zinc binding site 2 out of 6 in 8ebx

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Zinc binding site 2 out of 6 in the Xpa Repositioning CORE7 of Tfiih Relative to Xpc-Dna Lesion (Ap)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Xpa Repositioning CORE7 of Tfiih Relative to Xpc-Dna Lesion (Ap) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn402

b:199.4
occ:1.00
 SG E:CYS382 2.3 136.2 1.0
SG E:CYS360 2.3 149.7 1.0
SG E:CYS363 2.3 149.3 1.0
SG E:CYS385 2.3 134.7 1.0
CB E:CYS360 3.1 149.7 1.0
CB E:CYS382 3.2 136.2 1.0
N E:CYS385 3.6 134.7 1.0
CB E:CYS385 3.8 134.7 1.0
CB E:CYS363 3.8 149.3 1.0
N E:CYS363 3.8 149.3 1.0
CA E:CYS385 4.2 134.7 1.0
CB E:VAL362 4.2 145.5 1.0
C E:GLY384 4.4 133.2 1.0
CA E:CYS363 4.4 149.3 1.0
CA E:CYS382 4.5 136.2 1.0
CA E:GLY384 4.6 133.2 1.0
CA E:CYS360 4.6 149.7 1.0
N E:GLY384 4.7 133.2 1.0
N E:VAL362 4.7 145.5 1.0
CE1 E:PHE331 4.8 148.2 1.0
C E:VAL362 4.8 145.5 1.0
CA E:VAL362 4.8 145.5 1.0
C E:CYS382 4.9 136.2 1.0
CZ E:PHE331 4.9 148.2 1.0
CG2 E:VAL362 5.0 145.5 1.0
O E:CYS382 5.0 136.2 1.0
CG1 E:VAL362 5.0 145.5 1.0

Zinc binding site 3 out of 6 in 8ebx

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Zinc binding site 3 out of 6 in the Xpa Repositioning CORE7 of Tfiih Relative to Xpc-Dna Lesion (Ap)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Xpa Repositioning CORE7 of Tfiih Relative to Xpc-Dna Lesion (Ap) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn403

b:184.6
occ:1.00
 SG E:CYS305 2.3 141.6 1.0
SG E:CYS294 2.3 155.3 1.0
SG E:CYS308 2.3 154.0 1.0
SG E:CYS291 2.3 142.5 1.0
CB E:CYS291 3.3 142.5 1.0
CB E:CYS305 3.4 141.6 1.0
CB E:CYS308 3.6 154.0 1.0
CB E:CYS294 3.6 155.3 1.0
N E:CYS294 3.8 155.3 1.0
N E:CYS308 3.9 154.0 1.0
CA E:CYS294 4.2 155.3 1.0
CA E:CYS308 4.3 154.0 1.0
CB E:ALA296 4.3 149.8 1.0
CB E:GLN293 4.4 144.4 1.0
CB E:ILE307 4.6 157.6 1.0
CA E:CYS291 4.8 142.5 1.0
CB E:LEU310 4.8 135.6 1.0
C E:GLN293 4.8 144.4 1.0
C E:CYS294 4.8 155.3 1.0
CA E:CYS305 4.8 141.6 1.0
N E:ALA296 4.9 149.8 1.0
CA E:GLN293 5.0 144.4 1.0
N E:GLN293 5.0 144.4 1.0
C E:ILE307 5.0 157.6 1.0

Zinc binding site 4 out of 6 in 8ebx

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Zinc binding site 4 out of 6 in the Xpa Repositioning CORE7 of Tfiih Relative to Xpc-Dna Lesion (Ap)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Xpa Repositioning CORE7 of Tfiih Relative to Xpc-Dna Lesion (Ap) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn401

b:180.3
occ:1.00
 SG F:CYS268 2.3 122.0 1.0
SG F:CYS282 2.3 145.9 1.0
SG F:CYS285 2.3 153.2 1.0
SG F:CYS271 2.3 128.0 1.0
OG1 F:THR284 3.1 149.5 1.0
CB F:CYS268 3.1 122.0 1.0
CB F:CYS282 3.3 145.9 1.0
CB F:CYS285 3.5 153.2 1.0
CB F:CYS271 3.6 128.0 1.0
OG F:SER273 3.7 123.1 1.0
N F:CYS285 3.8 153.2 1.0
N F:CYS271 3.8 128.0 1.0
CA F:CYS285 4.2 153.2 1.0
CA F:CYS271 4.3 128.0 1.0
CB F:VAL270 4.5 128.4 1.0
CB F:THR284 4.5 149.5 1.0
CA F:CYS268 4.6 122.0 1.0
CA F:CYS282 4.7 145.9 1.0
C F:THR284 4.8 149.5 1.0
N F:VAL270 4.8 128.4 1.0
C F:VAL270 4.9 128.4 1.0
CB F:SER273 4.9 123.1 1.0
C F:CYS271 4.9 128.0 1.0
CA F:VAL270 5.0 128.4 1.0

Zinc binding site 5 out of 6 in 8ebx

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Zinc binding site 5 out of 6 in the Xpa Repositioning CORE7 of Tfiih Relative to Xpc-Dna Lesion (Ap)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Xpa Repositioning CORE7 of Tfiih Relative to Xpc-Dna Lesion (Ap) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn402

b:197.1
occ:1.00
 NE2 F:HIS258 2.1 139.7 1.0
CD2 F:HIS258 2.2 139.7 1.0
SG F:CYS255 2.3 134.0 1.0
SG F:CYS257 2.3 138.3 1.0
SG F:CYS276 2.3 140.8 1.0
N F:CYS276 2.8 140.8 1.0
CB F:CYS276 3.1 140.8 1.0
CE1 F:HIS258 3.4 139.7 1.0
CA F:CYS276 3.5 140.8 1.0
CG F:HIS258 3.6 139.7 1.0
C F:PHE275 3.8 123.5 1.0
CB F:CYS257 3.8 138.3 1.0
CA F:PHE275 3.9 123.5 1.0
CB F:CYS255 4.0 134.0 1.0
N F:ASN277 4.1 137.7 1.0
ND1 F:HIS258 4.1 139.7 1.0
N F:CYS257 4.2 138.3 1.0
C F:CYS276 4.3 140.8 1.0
CB F:PHE275 4.3 123.5 1.0
CA F:CYS257 4.4 138.3 1.0
C F:CYS257 4.6 138.3 1.0
N F:HIS258 4.6 139.7 1.0
CD1 F:PHE275 4.7 123.5 1.0
CB F:HIS258 4.7 139.7 1.0
O F:PHE275 4.9 123.5 1.0

Zinc binding site 6 out of 6 in 8ebx

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Zinc binding site 6 out of 6 in the Xpa Repositioning CORE7 of Tfiih Relative to Xpc-Dna Lesion (Ap)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Xpa Repositioning CORE7 of Tfiih Relative to Xpc-Dna Lesion (Ap) within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn301

b:258.3
occ:1.00
 SG K:CYS126 2.3 202.3 1.0
SG K:CYS129 2.3 209.0 1.0
SG K:CYS108 2.3 222.7 1.0
SG K:CYS105 2.3 212.6 1.0
CB K:CYS105 3.1 212.6 1.0
CB K:CYS129 3.1 209.0 1.0
CB K:CYS108 3.3 222.7 1.0
N K:CYS108 3.6 222.7 1.0
CB K:CYS126 3.8 202.3 1.0
CA K:CYS108 4.0 222.7 1.0
N K:CYS129 4.1 209.0 1.0
N K:CYS126 4.2 202.3 1.0
CA K:CYS129 4.2 209.0 1.0
CB K:GLU107 4.3 212.8 1.0
CA K:CYS126 4.5 202.3 1.0
CA K:CYS105 4.6 212.6 1.0
C K:GLU107 4.6 212.8 1.0
N K:GLY109 4.7 211.1 1.0
N K:GLU107 4.8 212.8 1.0
C K:CYS108 4.8 222.7 1.0
CA K:GLU107 4.8 212.8 1.0
O K:CYS126 4.9 202.3 1.0
C K:CYS126 5.0 202.3 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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