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Zinc in PDB 6ro4: Structure of the Core Tfiih-Xpa-Dna Complex

Enzymatic activity of Structure of the Core Tfiih-Xpa-Dna Complex

All present enzymatic activity of Structure of the Core Tfiih-Xpa-Dna Complex:
3.6.4.12;

Other elements in 6ro4:

The structure of Structure of the Core Tfiih-Xpa-Dna Complex also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of the Core Tfiih-Xpa-Dna Complex (pdb code 6ro4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Structure of the Core Tfiih-Xpa-Dna Complex, PDB code: 6ro4:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 6ro4

Go back to Zinc Binding Sites List in 6ro4
Zinc binding site 1 out of 6 in the Structure of the Core Tfiih-Xpa-Dna Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Core Tfiih-Xpa-Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn401

b:0.2
occ:1.00
 SG E:CYS268 2.2 68.3 1.0
SG E:CYS282 2.2 96.2 1.0
SG E:CYS285 2.3 0.3 1.0
SG E:CYS271 2.3 80.2 1.0
CB E:CYS271 2.7 80.2 1.0
N E:CYS271 3.2 80.2 1.0
CB E:CYS268 3.3 68.3 1.0
CA E:CYS271 3.5 80.2 1.0
CG1 E:VAL270 3.5 79.1 1.0
OG1 E:THR284 3.6 94.2 1.0
CB E:CYS282 3.9 96.2 1.0
CB E:CYS285 3.9 0.3 1.0
N E:CYS285 4.0 0.3 1.0
C E:CYS271 4.2 80.2 1.0
C E:VAL270 4.3 79.1 1.0
N E:LEU272 4.4 66.1 1.0
CA E:CYS285 4.4 0.3 1.0
N E:VAL270 4.5 79.1 1.0
CB E:VAL270 4.7 79.1 1.0
CA E:CYS268 4.7 68.3 1.0
CA E:VAL270 4.7 79.1 1.0
C E:CYS285 4.8 0.3 1.0
CB E:THR284 4.8 94.2 1.0
CA E:CYS282 5.0 96.2 1.0
C E:THR284 5.0 94.2 1.0

Zinc binding site 2 out of 6 in 6ro4

Go back to Zinc Binding Sites List in 6ro4
Zinc binding site 2 out of 6 in the Structure of the Core Tfiih-Xpa-Dna Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Core Tfiih-Xpa-Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn402

b:0.7
occ:1.00
 SG E:CYS255 2.2 92.6 1.0
SG E:CYS257 2.2 0.5 1.0
ND1 E:HIS258 2.3 0.3 1.0
SG E:CYS276 2.4 95.6 1.0
CG E:HIS258 3.1 0.3 1.0
N E:HIS258 3.2 0.3 1.0
CB E:HIS258 3.2 0.3 1.0
CE1 E:HIS258 3.3 0.3 1.0
CB E:CYS255 3.5 92.6 1.0
CB E:CYS276 3.6 95.6 1.0
CB E:CYS257 3.8 0.5 1.0
CA E:HIS258 3.8 0.3 1.0
N E:CYS257 3.9 0.5 1.0
C E:CYS257 4.0 0.5 1.0
N E:CYS276 4.1 95.6 1.0
CA E:CYS257 4.1 0.5 1.0
CD2 E:HIS258 4.3 0.3 1.0
NE2 E:HIS258 4.4 0.3 1.0
CA E:CYS276 4.5 95.6 1.0
N E:PHE256 4.7 87.8 1.0
CA E:CYS255 4.8 92.6 1.0
C E:CYS255 4.9 92.6 1.0

Zinc binding site 3 out of 6 in 6ro4

Go back to Zinc Binding Sites List in 6ro4
Zinc binding site 3 out of 6 in the Structure of the Core Tfiih-Xpa-Dna Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the Core Tfiih-Xpa-Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:0.9
occ:1.00
 SG D:CYS294 2.2 0.8 1.0
SG D:CYS308 2.3 1.0 1.0
SG D:CYS291 2.3 0.7 1.0
SG D:CYS305 2.4 0.5 1.0
CB D:CYS305 3.0 0.5 1.0
CB D:CYS291 3.4 0.7 1.0
CB D:CYS308 3.5 1.0 1.0
CB D:CYS294 3.7 0.8 1.0
N D:CYS308 3.9 1.0 1.0
N D:CYS294 3.9 0.8 1.0
CA D:CYS308 4.2 1.0 1.0
CA D:CYS294 4.4 0.8 1.0
CA D:CYS305 4.4 0.5 1.0
CB D:GLN293 4.5 0.9 1.0
CB D:LEU310 4.5 98.7 1.0
C D:CYS308 4.6 1.0 1.0
O D:CYS305 4.7 0.5 1.0
N D:LEU310 4.7 98.7 1.0
C D:CYS305 4.7 0.5 1.0
CA D:CYS291 4.8 0.7 1.0
C D:GLN293 4.8 0.9 1.0
N D:GLY309 4.8 0.1 1.0
C D:ILE307 4.9 0.6 1.0
CB D:ILE307 5.0 0.6 1.0

Zinc binding site 4 out of 6 in 6ro4

Go back to Zinc Binding Sites List in 6ro4
Zinc binding site 4 out of 6 in the Structure of the Core Tfiih-Xpa-Dna Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of the Core Tfiih-Xpa-Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn402

b:0.7
occ:1.00
 SG D:CYS345 2.3 86.4 1.0
SG D:CYS368 2.3 96.6 1.0
SG D:CYS348 2.4 85.4 1.0
SG D:CYS371 2.4 95.3 1.0
CB D:CYS345 3.0 86.4 1.0
CB D:CYS371 3.3 95.3 1.0
CB D:CYS368 3.4 96.6 1.0
N D:CYS368 3.5 96.6 1.0
CB D:CYS348 3.7 85.4 1.0
N D:CYS348 3.7 85.4 1.0
CA D:CYS368 4.0 96.6 1.0
CA D:CYS348 4.3 85.4 1.0
C D:PHE367 4.3 87.6 1.0
CA D:CYS345 4.4 86.4 1.0
CA D:PHE367 4.5 87.6 1.0
CA D:CYS371 4.6 95.3 1.0
N D:GLY347 4.6 82.4 1.0
N D:CYS371 4.7 95.3 1.0
C D:GLY347 4.7 82.4 1.0
CA D:GLY347 4.8 82.4 1.0
N D:GLN349 4.8 79.2 1.0
C D:CYS368 4.9 96.6 1.0
C D:CYS348 4.9 85.4 1.0
CB D:PHE367 5.0 87.6 1.0

Zinc binding site 5 out of 6 in 6ro4

Go back to Zinc Binding Sites List in 6ro4
Zinc binding site 5 out of 6 in the Structure of the Core Tfiih-Xpa-Dna Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of the Core Tfiih-Xpa-Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn403

b:0.2
occ:1.00
 SG D:CYS385 2.3 95.0 1.0
SG D:CYS360 2.3 0.8 1.0
SG D:CYS382 2.3 92.1 1.0
SG D:CYS363 2.4 0.4 1.0
CB D:CYS382 3.2 92.1 1.0
CB D:CYS363 3.5 0.4 1.0
CB D:CYS360 3.5 0.8 1.0
N D:CYS363 3.7 0.4 1.0
CB D:CYS385 3.8 95.0 1.0
N D:CYS385 3.9 95.0 1.0
CB D:VAL362 4.1 0.4 1.0
CA D:CYS363 4.2 0.4 1.0
CA D:CYS385 4.3 95.0 1.0
C D:GLY384 4.6 90.2 1.0
CG2 D:VAL362 4.6 0.4 1.0
CA D:CYS382 4.6 92.1 1.0
C D:VAL362 4.6 0.4 1.0
CA D:VAL362 4.7 0.4 1.0
CA D:GLY384 4.8 90.2 1.0
N D:VAL362 4.8 0.4 1.0
CE1 D:PHE331 4.8 0.8 1.0
N D:GLY384 4.8 90.2 1.0
CA D:CYS360 4.8 0.8 1.0
C D:CYS382 5.0 92.1 1.0

Zinc binding site 6 out of 6 in 6ro4

Go back to Zinc Binding Sites List in 6ro4
Zinc binding site 6 out of 6 in the Structure of the Core Tfiih-Xpa-Dna Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of the Core Tfiih-Xpa-Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn301

b:0.7
occ:1.00
 SG G:CYS105 2.5 0.0 1.0
SG G:CYS108 2.5 0.3 1.0
SG G:CYS129 2.5 0.3 1.0
SG G:CYS126 2.5 0.4 1.0
CB G:CYS126 3.3 0.4 1.0
N G:CYS108 3.3 0.3 1.0
CB G:CYS108 3.4 0.3 1.0
N G:CYS126 3.5 0.4 1.0
OG1 G:THR125 3.7 0.6 1.0
CB G:CYS105 3.7 0.0 1.0
CA G:CYS126 3.9 0.4 1.0
CA G:CYS108 3.9 0.3 1.0
CB G:GLU107 4.0 0.1 1.0
C G:GLU107 4.2 0.1 1.0
CB G:CYS129 4.3 0.3 1.0
O G:CYS126 4.3 0.4 1.0
C G:CYS126 4.4 0.4 1.0
CA G:GLU107 4.5 0.1 1.0
N G:CYS129 4.5 0.3 1.0
N G:GLU107 4.6 0.1 1.0
C G:THR125 4.6 0.6 1.0
CA G:THR125 4.8 0.6 1.0
CB G:THR125 4.9 0.6 1.0
C G:CYS108 4.9 0.3 1.0
CA G:CYS129 5.0 0.3 1.0

Reference:

G.Kokic, A.Chernev, D.Tegunov, C.Dienemann, H.Urlaub, P.Cramer. Structural Basis of Tfiih Activation For Nucleotide Excision Repair. Nat Commun V. 10 2885 2019.
ISSN: ESSN 2041-1723
PubMed: 31253769
DOI: 10.1038/S41467-019-10745-5
Page generated: Tue Oct 29 06:39:58 2024

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