Zinc in PDB 8eby: Xpc Release From CORE7-Xpa-Dna (Ap)

Enzymatic activity of Xpc Release From CORE7-Xpa-Dna (Ap)

All present enzymatic activity of Xpc Release From CORE7-Xpa-Dna (Ap):
3.6.4.12;

Other elements in 8eby:

The structure of Xpc Release From CORE7-Xpa-Dna (Ap) also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Zinc Binding Sites:

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

Zinc binding site 1 out of 6 in 8eby

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Zinc binding site 1 out of 6 in the Xpc Release From CORE7-Xpa-Dna (Ap)


Mono view


Stereo pair view

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

b:153.0
occ:1.00
 SG E:CYS371 2.3 118.3 1.0
SG E:CYS348 2.3 116.7 1.0
SG E:CYS345 2.3 122.9 1.0
SG E:CYS368 2.3 122.8 1.0
CB E:CYS371 3.1 118.3 1.0
CB E:CYS348 3.2 116.7 1.0
CB E:CYS345 3.2 122.9 1.0
N E:CYS348 3.6 116.7 1.0
CB E:CYS368 3.7 122.8 1.0
N E:CYS368 3.8 122.8 1.0
CA E:CYS348 4.0 116.7 1.0
N E:CYS371 4.2 118.3 1.0
CA E:CYS371 4.3 118.3 1.0
CA E:CYS368 4.3 122.8 1.0
C E:GLY347 4.6 116.2 1.0
CA E:CYS345 4.7 122.9 1.0
C E:CYS348 4.7 116.7 1.0
N E:GLY347 4.8 116.2 1.0
CA E:GLY347 4.8 116.2 1.0
C E:PHE367 4.9 120.1 1.0
N E:GLN349 5.0 122.4 1.0

Zinc binding site 2 out of 6 in 8eby

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Zinc binding site 2 out of 6 in the Xpc Release From CORE7-Xpa-Dna (Ap)


Mono view


Stereo pair view

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

b:179.6
occ:1.00
 SG E:CYS382 2.3 115.6 1.0
SG E:CYS360 2.3 130.0 1.0
SG E:CYS385 2.3 119.5 1.0
SG E:CYS363 2.3 135.1 1.0
CB E:CYS360 3.1 130.0 1.0
CB E:CYS382 3.3 115.6 1.0
N E:CYS385 3.6 119.5 1.0
CB E:CYS363 3.7 135.1 1.0
CB E:CYS385 3.7 119.5 1.0
N E:CYS363 3.8 135.1 1.0
CA E:CYS385 4.2 119.5 1.0
CA E:CYS363 4.4 135.1 1.0
CB E:VAL362 4.4 126.7 1.0
C E:GLY384 4.4 113.2 1.0
CA E:GLY384 4.6 113.2 1.0
CA E:CYS360 4.6 130.0 1.0
CA E:CYS382 4.7 115.6 1.0
N E:GLY384 4.7 113.2 1.0
N E:VAL362 4.7 126.7 1.0
CE1 E:PHE331 4.8 124.0 1.0
C E:VAL362 4.8 126.7 1.0
CA E:VAL362 4.9 126.7 1.0
C E:CYS382 5.0 115.6 1.0
CZ E:PHE331 5.0 124.0 1.0

Zinc binding site 3 out of 6 in 8eby

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Zinc binding site 3 out of 6 in the Xpc Release From CORE7-Xpa-Dna (Ap)


Mono view


Stereo pair view

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

b:166.1
occ:1.00
 SG E:CYS308 2.3 141.0 1.0
SG E:CYS294 2.3 140.9 1.0
SG E:CYS305 2.3 128.5 1.0
SG E:CYS291 2.3 127.7 1.0
CB E:CYS291 3.3 127.7 1.0
CB E:CYS305 3.3 128.5 1.0
CB E:CYS308 3.6 141.0 1.0
CB E:CYS294 3.8 140.9 1.0
N E:CYS294 3.9 140.9 1.0
N E:CYS308 4.0 141.0 1.0
CA E:CYS308 4.4 141.0 1.0
CA E:CYS294 4.4 140.9 1.0
CB E:GLN293 4.5 129.8 1.0
CB E:ALA296 4.6 134.1 1.0
CA E:CYS291 4.7 127.7 1.0
CB E:ILE307 4.7 148.4 1.0
CA E:CYS305 4.7 128.5 1.0
CB E:LEU310 4.9 116.8 1.0
OH E:TYR298 4.9 135.2 1.0
C E:GLN293 4.9 129.8 1.0
C E:CYS294 4.9 140.9 1.0

Zinc binding site 4 out of 6 in 8eby

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Zinc binding site 4 out of 6 in the Xpc Release From CORE7-Xpa-Dna (Ap)


Mono view


Stereo pair view

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

b:144.8
occ:1.00
 SG F:CYS271 2.3 102.7 1.0
SG F:CYS282 2.3 125.8 1.0
SG F:CYS285 2.3 134.4 1.0
SG F:CYS268 2.3 96.7 1.0
OG1 F:THR284 3.1 126.4 1.0
CB F:CYS268 3.1 96.7 1.0
CB F:CYS282 3.3 125.8 1.0
CB F:CYS285 3.6 134.4 1.0
CB F:CYS271 3.6 102.7 1.0
OG F:SER273 3.7 99.5 1.0
N F:CYS285 3.8 134.4 1.0
N F:CYS271 3.8 102.7 1.0
CA F:CYS285 4.2 134.4 1.0
CA F:CYS271 4.3 102.7 1.0
CB F:THR284 4.5 126.4 1.0
CB F:VAL270 4.6 103.5 1.0
CA F:CYS268 4.6 96.7 1.0
CA F:CYS282 4.7 125.8 1.0
C F:THR284 4.8 126.4 1.0
N F:VAL270 4.9 103.5 1.0
C F:VAL270 4.9 103.5 1.0
CB F:SER273 4.9 99.5 1.0
C F:CYS271 5.0 102.7 1.0

Zinc binding site 5 out of 6 in 8eby

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Zinc binding site 5 out of 6 in the Xpc Release From CORE7-Xpa-Dna (Ap)


Mono view


Stereo pair view

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

b:176.8
occ:1.00
 NE2 F:HIS258 2.1 127.3 1.0
CD2 F:HIS258 2.2 127.3 1.0
SG F:CYS255 2.3 120.3 1.0
SG F:CYS257 2.3 127.4 1.0
SG F:CYS276 2.3 121.5 1.0
N F:CYS276 2.7 121.5 1.0
CB F:CYS276 3.1 121.5 1.0
CE1 F:HIS258 3.4 127.3 1.0
CA F:CYS276 3.4 121.5 1.0
CG F:HIS258 3.6 127.3 1.0
C F:PHE275 3.8 101.7 1.0
CB F:CYS257 3.8 127.4 1.0
CA F:PHE275 3.9 101.7 1.0
CB F:CYS255 4.0 120.3 1.0
N F:ASN277 4.0 115.9 1.0
ND1 F:HIS258 4.1 127.3 1.0
N F:CYS257 4.2 127.4 1.0
C F:CYS276 4.2 121.5 1.0
CB F:PHE275 4.3 101.7 1.0
CA F:CYS257 4.4 127.4 1.0
CD1 F:PHE275 4.6 101.7 1.0
N F:HIS258 4.6 127.3 1.0
C F:CYS257 4.6 127.4 1.0
CB F:HIS258 4.8 127.3 1.0
O F:PHE275 4.9 101.7 1.0
CG F:PHE275 4.9 101.7 1.0

Zinc binding site 6 out of 6 in 8eby

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Zinc binding site 6 out of 6 in the Xpc Release From CORE7-Xpa-Dna (Ap)


Mono view


Stereo pair view

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

b:285.3
occ:1.00
 SG K:CYS126 2.3 238.3 1.0
SG K:CYS129 2.3 238.8 1.0
SG K:CYS105 2.3 248.2 1.0
SG K:CYS108 2.3 258.0 1.0
CB K:CYS105 3.0 248.2 1.0
CB K:CYS129 3.1 238.8 1.0
CB K:CYS108 3.2 258.0 1.0
N K:CYS108 3.5 258.0 1.0
CB K:CYS126 3.8 238.3 1.0
CA K:CYS108 4.0 258.0 1.0
N K:CYS129 4.0 238.8 1.0
CA K:CYS129 4.2 238.8 1.0
N K:CYS126 4.3 238.3 1.0
CB K:GLU107 4.5 249.6 1.0
CA K:CYS105 4.5 248.2 1.0
CA K:CYS126 4.5 238.3 1.0
C K:GLU107 4.6 249.6 1.0
N K:GLY109 4.7 251.4 1.0
C K:CYS108 4.7 258.0 1.0
N K:GLU107 4.8 249.6 1.0
O K:CYS126 4.8 238.3 1.0
CA K:GLU107 4.9 249.6 1.0
C K:CYS126 5.0 238.3 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 00:38:10 2023

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