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Iron in PDB 28jv: Cryo-Em Structure of the Human Holo-Tfiih-Xpc Complex Bound to Bulky Lesion-Mimic Dna (Consensus Map)

Enzymatic activity of Cryo-Em Structure of the Human Holo-Tfiih-Xpc Complex Bound to Bulky Lesion-Mimic Dna (Consensus Map)

All present enzymatic activity of Cryo-Em Structure of the Human Holo-Tfiih-Xpc Complex Bound to Bulky Lesion-Mimic Dna (Consensus Map):
3.6.4.12;

Other elements in 28jv:

The structure of Cryo-Em Structure of the Human Holo-Tfiih-Xpc Complex Bound to Bulky Lesion-Mimic Dna (Consensus Map) also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Zinc (Zn) 5 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Cryo-Em Structure of the Human Holo-Tfiih-Xpc Complex Bound to Bulky Lesion-Mimic Dna (Consensus Map) (pdb code 28jv). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Cryo-Em Structure of the Human Holo-Tfiih-Xpc Complex Bound to Bulky Lesion-Mimic Dna (Consensus Map), PDB code: 28jv:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 28jv

Go back to Iron Binding Sites List in 28jv
Iron binding site 1 out of 4 in the Cryo-Em Structure of the Human Holo-Tfiih-Xpc Complex Bound to Bulky Lesion-Mimic Dna (Consensus Map)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cryo-Em Structure of the Human Holo-Tfiih-Xpc Complex Bound to Bulky Lesion-Mimic Dna (Consensus Map) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1000

b:93.9
occ:1.00
 FE1 B:SF41000 0.0 93.9 1.0
S2 B:SF41000 2.3 93.9 1.0
S4 B:SF41000 2.3 93.9 1.0
S3 B:SF41000 2.3 93.9 1.0
SG B:CYS116 2.3 100.0 1.0
FE3 B:SF41000 2.7 93.9 1.0
FE4 B:SF41000 2.7 93.9 1.0
FE2 B:SF41000 2.7 93.9 1.0
CB B:CYS116 3.4 100.0 1.0
S1 B:SF41000 3.9 93.9 1.0
CA B:CYS116 3.9 100.0 1.0
O B:LEU115 4.1 93.0 1.0
CG1 B:VAL121 4.5 76.5 1.0
CB B:CYS134 4.5 92.9 1.0
SG B:CYS134 4.7 92.9 1.0
SG B:CYS190 4.7 84.5 1.0
N B:CYS116 4.8 100.0 1.0
C B:LEU115 4.8 93.0 1.0
CB B:VAL121 4.9 76.5 1.0
CG2 B:VAL121 4.9 76.5 1.0
SG B:CYS155 4.9 109.9 1.0

Iron binding site 2 out of 4 in 28jv

Go back to Iron Binding Sites List in 28jv
Iron binding site 2 out of 4 in the Cryo-Em Structure of the Human Holo-Tfiih-Xpc Complex Bound to Bulky Lesion-Mimic Dna (Consensus Map)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cryo-Em Structure of the Human Holo-Tfiih-Xpc Complex Bound to Bulky Lesion-Mimic Dna (Consensus Map) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1000

b:93.9
occ:1.00
 FE2 B:SF41000 0.0 93.9 1.0
S1 B:SF41000 2.3 93.9 1.0
S3 B:SF41000 2.3 93.9 1.0
S4 B:SF41000 2.3 93.9 1.0
SG B:CYS155 2.3 109.9 1.0
FE4 B:SF41000 2.7 93.9 1.0
FE3 B:SF41000 2.7 93.9 1.0
FE1 B:SF41000 2.7 93.9 1.0
S2 B:SF41000 3.9 93.9 1.0
CB B:CYS155 3.9 109.9 1.0
CB B:HIS118 4.7 99.7 1.0
SG B:CYS190 4.7 84.5 1.0
SG B:CYS134 4.8 92.9 1.0
CD2 B:HIS118 4.9 99.7 1.0
CG2 B:THR138 5.0 103.6 1.0
SG B:CYS116 5.0 100.0 1.0

Iron binding site 3 out of 4 in 28jv

Go back to Iron Binding Sites List in 28jv
Iron binding site 3 out of 4 in the Cryo-Em Structure of the Human Holo-Tfiih-Xpc Complex Bound to Bulky Lesion-Mimic Dna (Consensus Map)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cryo-Em Structure of the Human Holo-Tfiih-Xpc Complex Bound to Bulky Lesion-Mimic Dna (Consensus Map) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1000

b:93.9
occ:1.00
 FE3 B:SF41000 0.0 93.9 1.0
S2 B:SF41000 2.3 93.9 1.0
S4 B:SF41000 2.3 93.9 1.0
S1 B:SF41000 2.3 93.9 1.0
SG B:CYS134 2.3 92.9 1.0
FE1 B:SF41000 2.7 93.9 1.0
FE2 B:SF41000 2.7 93.9 1.0
FE4 B:SF41000 2.7 93.9 1.0
CB B:CYS134 2.9 92.9 1.0
CA B:CYS134 3.8 92.9 1.0
S3 B:SF41000 3.9 93.9 1.0
CZ B:PHE193 3.9 88.8 1.0
C B:CYS134 4.5 92.9 1.0
CE2 B:PHE193 4.5 88.8 1.0
O B:CYS134 4.6 92.9 1.0
SG B:CYS116 4.6 100.0 1.0
OG1 B:THR138 4.7 103.6 1.0
SG B:CYS155 4.7 109.9 1.0
CE1 B:PHE193 4.8 88.8 1.0
SG B:CYS190 4.9 84.5 1.0
N B:CYS134 5.0 92.9 1.0
CG2 B:THR138 5.0 103.6 1.0

Iron binding site 4 out of 4 in 28jv

Go back to Iron Binding Sites List in 28jv
Iron binding site 4 out of 4 in the Cryo-Em Structure of the Human Holo-Tfiih-Xpc Complex Bound to Bulky Lesion-Mimic Dna (Consensus Map)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cryo-Em Structure of the Human Holo-Tfiih-Xpc Complex Bound to Bulky Lesion-Mimic Dna (Consensus Map) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1000

b:93.9
occ:1.00
 FE4 B:SF41000 0.0 93.9 1.0
S3 B:SF41000 2.3 93.9 1.0
S1 B:SF41000 2.3 93.9 1.0
S2 B:SF41000 2.3 93.9 1.0
SG B:CYS190 2.3 84.5 1.0
FE2 B:SF41000 2.7 93.9 1.0
FE1 B:SF41000 2.7 93.9 1.0
FE3 B:SF41000 2.7 93.9 1.0
CB B:CYS190 3.4 84.5 1.0
CE2 B:PHE193 3.6 88.8 1.0
CZ B:PHE193 3.7 88.8 1.0
S4 B:SF41000 3.9 93.9 1.0
O B:LEU115 4.3 93.0 1.0
CD2 B:PHE193 4.6 88.8 1.0
SG B:CYS155 4.6 109.9 1.0
CA B:CYS190 4.6 84.5 1.0
SG B:CYS116 4.7 100.0 1.0
CE1 B:PHE193 4.8 88.8 1.0
SG B:CYS134 4.8 92.9 1.0
CB B:TYR192 4.8 85.4 1.0

Reference:

N.De Martin Garrido, C.A.F.Haste, J.Feng, N.B.Cronin, B.J.Greber. Visualisation of Stepwise De-Repression of Tfiih in Global-Genome Nucleotide Excision Repair To Be Published.
Page generated: Sun Oct 4 09:33:01 2026

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