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:
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 Sites List in 8ebt
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 Sites List in 8ebt
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 Sites List in 8ebt
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 Sites List in 8ebt
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 Sites List in 8ebt
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 Sites List in 8ebt
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 Oct 30 19:36:34 2024
|