Zinc in PDB 8ebt: Xpa Repositioning CORE7 of Tfiih Relative to Xpc-Dna Lesion (CY5)

Enzymatic activity of Xpa Repositioning CORE7 of Tfiih Relative to Xpc-Dna Lesion (CY5)

All present enzymatic activity of Xpa Repositioning CORE7 of Tfiih Relative to Xpc-Dna Lesion (CY5):
3.6.4.12;

Other elements in 8ebt:

The structure of Xpa Repositioning CORE7 of Tfiih Relative to Xpc-Dna Lesion (CY5) 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 Xpa Repositioning CORE7 of Tfiih Relative to Xpc-Dna Lesion (CY5) (pdb code 8ebt). 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 (CY5), PDB code: 8ebt:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 8ebt

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Zinc binding site 1 out of 6 in the Xpa Repositioning CORE7 of Tfiih Relative to Xpc-Dna Lesion (CY5)


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 (CY5) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn401

b:163.4
occ:1.00
 SG E:CYS371 2.3 133.8 1.0
SG E:CYS348 2.3 125.1 1.0
SG E:CYS345 2.3 129.1 1.0
SG E:CYS368 2.3 136.0 1.0
CB E:CYS371 3.1 133.8 1.0
CB E:CYS345 3.2 129.1 1.0
CB E:CYS348 3.3 125.1 1.0
N E:CYS348 3.6 125.1 1.0
CB E:CYS368 3.7 136.0 1.0
N E:CYS368 3.9 136.0 1.0
CA E:CYS348 4.0 125.1 1.0
N E:CYS371 4.3 133.8 1.0
CA E:CYS371 4.3 133.8 1.0
CA E:CYS368 4.4 136.0 1.0
C E:GLY347 4.6 124.0 1.0
CA E:CYS345 4.7 129.1 1.0
C E:CYS348 4.8 125.1 1.0
N E:GLY347 4.8 124.0 1.0
CA E:GLY347 4.8 124.0 1.0
C E:PHE367 5.0 138.1 1.0

Zinc binding site 2 out of 6 in 8ebt

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Zinc binding site 2 out of 6 in the Xpa Repositioning CORE7 of Tfiih Relative to Xpc-Dna Lesion (CY5)


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 (CY5) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn402

b:187.5
occ:1.00
 SG E:CYS382 2.3 131.4 1.0
SG E:CYS363 2.3 142.2 1.0
SG E:CYS360 2.3 139.1 1.0
SG E:CYS385 2.3 137.0 1.0
CB E:CYS360 3.1 139.1 1.0
CB E:CYS382 3.2 131.4 1.0
N E:CYS385 3.6 137.0 1.0
CB E:CYS363 3.7 142.2 1.0
CB E:CYS385 3.8 137.0 1.0
N E:CYS363 3.8 142.2 1.0
CA E:CYS385 4.2 137.0 1.0
CA E:CYS363 4.4 142.2 1.0
CB E:VAL362 4.4 142.4 1.0
C E:GLY384 4.4 130.4 1.0
CA E:GLY384 4.6 130.4 1.0
CA E:CYS360 4.6 139.1 1.0
CA E:CYS382 4.6 131.4 1.0
N E:GLY384 4.7 130.4 1.0
CE1 E:PHE331 4.7 132.8 1.0
N E:VAL362 4.8 142.4 1.0
CZ E:PHE331 4.8 132.8 1.0
C E:VAL362 4.8 142.4 1.0
C E:CYS382 4.9 131.4 1.0
CA E:VAL362 4.9 142.4 1.0
O E:CYS382 5.0 131.4 1.0

Zinc binding site 3 out of 6 in 8ebt

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Zinc binding site 3 out of 6 in the Xpa Repositioning CORE7 of Tfiih Relative to Xpc-Dna Lesion (CY5)


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 (CY5) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn403

b:195.8
occ:1.00
 SG E:CYS308 2.3 163.0 1.0
SG E:CYS294 2.3 160.5 1.0
SG E:CYS305 2.3 159.0 1.0
SG E:CYS291 2.3 151.4 1.0
CB E:CYS291 3.3 151.4 1.0
CB E:CYS305 3.4 159.0 1.0
CB E:CYS308 3.7 163.0 1.0
CB E:CYS294 3.8 160.5 1.0
N E:CYS294 3.9 160.5 1.0
N E:CYS308 4.0 163.0 1.0
CA E:CYS294 4.4 160.5 1.0
CA E:CYS308 4.4 163.0 1.0
CB E:ALA296 4.4 163.1 1.0
CB E:GLN293 4.5 150.7 1.0
CB E:ILE307 4.7 179.1 1.0
CB E:LEU310 4.7 135.1 1.0
CA E:CYS291 4.7 151.4 1.0
CA E:CYS305 4.8 159.0 1.0
C E:GLN293 4.9 150.7 1.0
C E:CYS294 4.9 160.5 1.0
N E:ALA296 4.9 163.1 1.0

Zinc binding site 4 out of 6 in 8ebt

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Zinc binding site 4 out of 6 in the Xpa Repositioning CORE7 of Tfiih Relative to Xpc-Dna Lesion (CY5)


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 (CY5) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn401

b:155.3
occ:1.00
 SG F:CYS282 2.3 128.3 1.0
SG F:CYS285 2.3 133.6 1.0
SG F:CYS271 2.3 115.6 1.0
SG F:CYS268 2.3 114.0 1.0
OG1 F:THR284 3.1 125.7 1.0
CB F:CYS268 3.2 114.0 1.0
CB F:CYS282 3.2 128.3 1.0
OG F:SER273 3.5 116.9 1.0
CB F:CYS285 3.6 133.6 1.0
CB F:CYS271 3.7 115.6 1.0
N F:CYS285 3.9 133.6 1.0
N F:CYS271 3.9 115.6 1.0
CA F:CYS285 4.3 133.6 1.0
CA F:CYS271 4.4 115.6 1.0
CB F:THR284 4.5 125.7 1.0
CB F:VAL270 4.6 119.5 1.0
CA F:CYS268 4.6 114.0 1.0
CA F:CYS282 4.7 128.3 1.0
CB F:SER273 4.8 116.9 1.0
C F:THR284 4.8 125.7 1.0
N F:VAL270 4.9 119.5 1.0
C F:VAL270 4.9 119.5 1.0
C F:CYS271 5.0 115.6 1.0

Zinc binding site 5 out of 6 in 8ebt

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Zinc binding site 5 out of 6 in the Xpa Repositioning CORE7 of Tfiih Relative to Xpc-Dna Lesion (CY5)


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 (CY5) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn402

b:180.4
occ:1.00
 NE2 F:HIS258 2.1 130.7 1.0
CD2 F:HIS258 2.2 130.7 1.0
SG F:CYS255 2.3 130.3 1.0
SG F:CYS257 2.3 131.8 1.0
SG F:CYS276 2.3 130.8 1.0
N F:CYS276 2.7 130.8 1.0
CB F:CYS276 3.0 130.8 1.0
CA F:CYS276 3.4 130.8 1.0
CE1 F:HIS258 3.4 130.7 1.0
CG F:HIS258 3.6 130.7 1.0
C F:PHE275 3.7 118.6 1.0
CB F:CYS257 3.8 131.8 1.0
CA F:PHE275 3.9 118.6 1.0
N F:ASN277 3.9 128.6 1.0
CB F:CYS255 4.0 130.3 1.0
ND1 F:HIS258 4.1 130.7 1.0
C F:CYS276 4.2 130.8 1.0
N F:CYS257 4.3 131.8 1.0
CB F:PHE275 4.3 118.6 1.0
CA F:CYS257 4.4 131.8 1.0
C F:CYS257 4.6 131.8 1.0
N F:HIS258 4.6 130.7 1.0
CD2 F:PHE275 4.7 118.6 1.0
CB F:HIS258 4.8 130.7 1.0
O F:PHE275 4.9 118.6 1.0

Zinc binding site 6 out of 6 in 8ebt

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Zinc binding site 6 out of 6 in the Xpa Repositioning CORE7 of Tfiih Relative to Xpc-Dna Lesion (CY5)


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 (CY5) within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn301

b:281.3
occ:1.00
 SG K:CYS108 2.3 257.1 1.0
SG K:CYS129 2.3 226.6 1.0
SG K:CYS126 2.3 230.6 1.0
SG K:CYS105 2.3 249.9 1.0
CB K:CYS105 3.1 249.9 1.0
CB K:CYS129 3.1 226.6 1.0
CB K:CYS108 3.2 257.1 1.0
N K:CYS108 3.5 257.1 1.0
CB K:CYS126 3.8 230.6 1.0
CA K:CYS108 3.9 257.1 1.0
N K:CYS129 4.1 226.6 1.0
N K:CYS126 4.1 230.6 1.0
CA K:CYS129 4.2 226.6 1.0
CB K:GLU107 4.4 246.0 1.0
CA K:CYS126 4.5 230.6 1.0
CA K:CYS105 4.6 249.9 1.0
C K:GLU107 4.6 246.0 1.0
N K:GLY109 4.7 250.9 1.0
C K:CYS108 4.7 257.1 1.0
N K:GLU107 4.8 246.0 1.0
CA K:GLU107 4.8 246.0 1.0
O K:CYS126 4.9 230.6 1.0
CG2 K:THR125 5.0 230.7 1.0
C K:CYS126 5.0 230.6 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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