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Iron in PDB 5lfa: Crystal Structure of Iron-Sulfur Cluster Containing Bacterial (6-4) Photolyase Phrb - Y424F Mutant with Impaired Dna Repair Activity

Enzymatic activity of Crystal Structure of Iron-Sulfur Cluster Containing Bacterial (6-4) Photolyase Phrb - Y424F Mutant with Impaired Dna Repair Activity

All present enzymatic activity of Crystal Structure of Iron-Sulfur Cluster Containing Bacterial (6-4) Photolyase Phrb - Y424F Mutant with Impaired Dna Repair Activity:
4.1.99.13;

Protein crystallography data

The structure of Crystal Structure of Iron-Sulfur Cluster Containing Bacterial (6-4) Photolyase Phrb - Y424F Mutant with Impaired Dna Repair Activity, PDB code: 5lfa was solved by D.Kwiatkowski, F.Zhang, N.Krauss, T.Lamparter, P.Scheerer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 69.79 / 2.50
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.183, 94.441, 103.579, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 24

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Iron-Sulfur Cluster Containing Bacterial (6-4) Photolyase Phrb - Y424F Mutant with Impaired Dna Repair Activity (pdb code 5lfa). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of Iron-Sulfur Cluster Containing Bacterial (6-4) Photolyase Phrb - Y424F Mutant with Impaired Dna Repair Activity, PDB code: 5lfa:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 5lfa

Go back to Iron Binding Sites List in 5lfa
Iron binding site 1 out of 4 in the Crystal Structure of Iron-Sulfur Cluster Containing Bacterial (6-4) Photolyase Phrb - Y424F Mutant with Impaired Dna Repair Activity


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Iron-Sulfur Cluster Containing Bacterial (6-4) Photolyase Phrb - Y424F Mutant with Impaired Dna Repair Activity within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe603

b:28.6
occ:1.00
 FE1 A:SF4603 0.0 28.6 1.0
S4 A:SF4603 2.1 26.2 1.0
S3 A:SF4603 2.1 25.5 1.0
S2 A:SF4603 2.1 26.0 1.0
SG A:CYS438 2.3 33.3 1.0
FE2 A:SF4603 2.9 26.7 1.0
FE3 A:SF4603 3.0 28.4 1.0
FE4 A:SF4603 3.0 31.4 1.0
CB A:CYS438 3.2 33.4 1.0
CA A:CYS438 3.4 31.6 1.0
S1 A:SF4603 3.6 27.3 1.0
N A:CYS438 3.7 32.2 1.0
CG2 A:ILE431 4.1 28.2 1.0
C A:TYR437 4.5 29.0 1.0
CB A:PRO445 4.6 32.8 1.0
CB A:CYS441 4.7 31.2 1.0
CG A:PRO445 4.7 33.2 1.0
CB A:ILE431 4.8 26.1 1.0
C A:CYS438 4.9 33.2 1.0
O A:TYR437 4.9 26.2 1.0
SG A:CYS454 5.0 31.1 1.0
SG A:CYS350 5.0 27.2 1.0
CB A:TYR437 5.0 26.6 1.0

Iron binding site 2 out of 4 in 5lfa

Go back to Iron Binding Sites List in 5lfa
Iron binding site 2 out of 4 in the Crystal Structure of Iron-Sulfur Cluster Containing Bacterial (6-4) Photolyase Phrb - Y424F Mutant with Impaired Dna Repair Activity


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Iron-Sulfur Cluster Containing Bacterial (6-4) Photolyase Phrb - Y424F Mutant with Impaired Dna Repair Activity within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe603

b:26.7
occ:1.00
 FE2 A:SF4603 0.0 26.7 1.0
S3 A:SF4603 2.1 25.5 1.0
S4 A:SF4603 2.1 26.2 1.0
S1 A:SF4603 2.1 27.3 1.0
SG A:CYS350 2.3 27.2 1.0
FE1 A:SF4603 2.9 28.6 1.0
FE4 A:SF4603 3.0 31.4 1.0
FE3 A:SF4603 3.1 28.4 1.0
CB A:CYS350 3.1 27.6 1.0
S2 A:SF4603 3.7 26.0 1.0
N A:CYS350 3.8 27.0 1.0
CE1 A:PHE456 4.0 31.6 1.0
CA A:CYS350 4.1 27.0 1.0
CG2 A:ILE431 4.2 28.2 1.0
CD1 A:PHE456 4.4 30.1 1.0
CD1 A:ILE431 4.6 26.8 1.0
N A:ASN349 4.6 29.2 1.0
CZ A:PHE456 4.8 30.9 1.0
CB A:MET348 4.8 27.6 1.0
C A:MET348 4.9 28.4 1.0
C A:ASN349 4.9 28.3 1.0
N A:MET351 4.9 25.9 1.0

Iron binding site 3 out of 4 in 5lfa

Go back to Iron Binding Sites List in 5lfa
Iron binding site 3 out of 4 in the Crystal Structure of Iron-Sulfur Cluster Containing Bacterial (6-4) Photolyase Phrb - Y424F Mutant with Impaired Dna Repair Activity


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Iron-Sulfur Cluster Containing Bacterial (6-4) Photolyase Phrb - Y424F Mutant with Impaired Dna Repair Activity within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe603

b:28.4
occ:1.00
 FE3 A:SF4603 0.0 28.4 1.0
S2 A:SF4603 2.1 26.0 1.0
S4 A:SF4603 2.1 26.2 1.0
S1 A:SF4603 2.2 27.3 1.0
SG A:CYS441 2.3 34.8 1.0
CB A:CYS441 2.9 31.2 1.0
FE1 A:SF4603 3.0 28.6 1.0
FE4 A:SF4603 3.1 31.4 1.0
FE2 A:SF4603 3.1 26.7 1.0
S3 A:SF4603 3.8 25.5 1.0
CB A:TYR443 3.9 34.1 1.0
N A:ASN349 4.0 29.2 1.0
CD2 A:TYR443 4.1 32.8 1.0
CA A:CYS441 4.3 33.0 1.0
O A:TYR443 4.4 36.7 1.0
CG A:TYR443 4.5 32.8 1.0
CB A:ASN349 4.5 30.5 1.0
CA A:CYS438 4.6 31.6 1.0
N A:TYR443 4.6 39.0 1.0
CA A:MET348 4.6 27.8 1.0
CA A:TYR443 4.6 37.1 1.0
C A:MET348 4.7 28.4 1.0
C A:TYR443 4.8 35.9 1.0
CA A:ASN349 4.8 28.8 1.0
N A:CYS350 4.8 27.0 1.0
SG A:CYS438 5.0 33.3 1.0
C A:CYS441 5.0 34.0 1.0

Iron binding site 4 out of 4 in 5lfa

Go back to Iron Binding Sites List in 5lfa
Iron binding site 4 out of 4 in the Crystal Structure of Iron-Sulfur Cluster Containing Bacterial (6-4) Photolyase Phrb - Y424F Mutant with Impaired Dna Repair Activity


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Iron-Sulfur Cluster Containing Bacterial (6-4) Photolyase Phrb - Y424F Mutant with Impaired Dna Repair Activity within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe603

b:31.4
occ:1.00
 FE4 A:SF4603 0.0 31.4 1.0
S1 A:SF4603 2.1 27.3 1.0
S3 A:SF4603 2.1 25.5 1.0
S2 A:SF4603 2.1 26.0 1.0
SG A:CYS454 2.3 31.1 1.0
FE1 A:SF4603 3.0 28.6 1.0
FE2 A:SF4603 3.0 26.7 1.0
FE3 A:SF4603 3.1 28.4 1.0
CB A:CYS454 3.1 29.8 1.0
S4 A:SF4603 3.7 26.2 1.0
CA A:CYS454 3.9 30.2 1.0
CD1 A:PHE456 4.0 30.1 1.0
CD A:PRO455 4.4 29.7 1.0
CA A:GLY428 4.6 26.9 1.0
CE1 A:PHE456 4.6 31.6 1.0
C A:CYS454 4.6 29.3 1.0
CB A:TYR443 4.6 34.1 1.0
CB A:PRO445 4.6 32.8 1.0
N A:PRO455 4.7 28.5 1.0
CG A:PHE456 4.9 28.5 1.0
SG A:CYS438 4.9 33.3 1.0
CA A:PRO445 4.9 33.7 1.0
CB A:PHE456 5.0 27.2 1.0

Reference:

F.Zhang, H.Ma, K.Bowatte, D.Kwiatkowski, E.Mittmann, H.Qasem, N.Krau, X.Zeng, Z.Ren, P.Scheerer, X.Yang, T.Lamparter. Crystal Structures of Bacterial (6-4) Photolyase Mutants with Impaired Dna Repair Activity. Photochem. Photobiol. V. 93 304 2017.
ISSN: ISSN 1751-1097
PubMed: 27992645
DOI: 10.1111/PHP.12699
Page generated: Tue Aug 5 23:10:05 2025

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