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Iron in PDB 5kcm: Crystal Structure of Iron-Sulfur Cluster Containing Photolyase Phrb Mutant I51W

Enzymatic activity of Crystal Structure of Iron-Sulfur Cluster Containing Photolyase Phrb Mutant I51W

All present enzymatic activity of Crystal Structure of Iron-Sulfur Cluster Containing Photolyase Phrb Mutant I51W:
4.1.99.13;

Protein crystallography data

The structure of Crystal Structure of Iron-Sulfur Cluster Containing Photolyase Phrb Mutant I51W, PDB code: 5kcm was solved by X.Yang, K.Bowatte, F.Zhang, T.Lamparter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.66 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 97.607, 107.243, 113.672, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 21.3

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Iron-Sulfur Cluster Containing Photolyase Phrb Mutant I51W (pdb code 5kcm). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure of Iron-Sulfur Cluster Containing Photolyase Phrb Mutant I51W, PDB code: 5kcm:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 5kcm

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Iron binding site 1 out of 8 in the Crystal Structure of Iron-Sulfur Cluster Containing Photolyase Phrb Mutant I51W


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 Photolyase Phrb Mutant I51W within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:31.8
occ:1.00
 FE1 A:SF4602 0.0 31.8 1.0
S4 A:SF4602 2.1 26.8 1.0
S2 A:SF4602 2.1 32.3 1.0
S3 A:SF4602 2.1 29.4 1.0
SG A:CYS438 2.2 30.7 1.0
FE2 A:SF4602 2.9 27.7 1.0
FE4 A:SF4602 2.9 29.8 1.0
FE3 A:SF4602 2.9 31.9 1.0
CB A:CYS438 3.2 30.8 1.0
CA A:CYS438 3.5 38.6 1.0
S1 A:SF4602 3.7 37.7 1.0
N A:CYS438 3.9 35.9 1.0
CG2 A:ILE431 4.3 30.0 1.0
CB A:PRO445 4.5 37.8 1.0
CG A:PRO445 4.6 32.7 1.0
C A:TYR437 4.6 34.6 1.0
CB A:CYS441 4.7 34.4 1.0
SG A:CYS454 4.8 29.4 1.0
CB A:ILE431 4.9 34.1 1.0
SG A:CYS441 4.9 33.8 1.0
C A:CYS438 4.9 41.1 1.0
CD A:PRO445 4.9 33.1 1.0
SG A:CYS350 5.0 27.5 1.0

Iron binding site 2 out of 8 in 5kcm

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Iron binding site 2 out of 8 in the Crystal Structure of Iron-Sulfur Cluster Containing Photolyase Phrb Mutant I51W


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 Photolyase Phrb Mutant I51W within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:27.7
occ:1.00
 FE2 A:SF4602 0.0 27.7 1.0
S3 A:SF4602 2.1 29.4 1.0
S1 A:SF4602 2.1 37.7 1.0
S4 A:SF4602 2.2 26.8 1.0
SG A:CYS454 2.3 29.4 1.0
FE1 A:SF4602 2.9 31.8 1.0
FE4 A:SF4602 2.9 29.8 1.0
FE3 A:SF4602 3.0 31.9 1.0
CB A:CYS454 3.0 31.8 1.0
S2 A:SF4602 3.7 32.3 1.0
CA A:CYS454 3.9 34.0 1.0
CD2 A:PHE456 4.0 24.2 1.0
CD A:PRO455 4.5 27.4 1.0
C A:CYS454 4.5 32.5 1.0
CE2 A:PHE456 4.6 24.5 1.0
N A:PRO455 4.7 31.1 1.0
CA A:GLY428 4.8 34.1 1.0
CB A:TYR443 4.8 34.0 1.0
SG A:CYS438 4.8 30.7 1.0
CA A:PRO445 5.0 36.8 1.0
CG A:PHE456 5.0 23.8 1.0

Iron binding site 3 out of 8 in 5kcm

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Iron binding site 3 out of 8 in the Crystal Structure of Iron-Sulfur Cluster Containing Photolyase Phrb Mutant I51W


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 Photolyase Phrb Mutant I51W within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:31.9
occ:1.00
 FE3 A:SF4602 0.0 31.9 1.0
S1 A:SF4602 2.1 37.7 1.0
S4 A:SF4602 2.1 26.8 1.0
S2 A:SF4602 2.1 32.3 1.0
SG A:CYS350 2.3 27.5 1.0
FE4 A:SF4602 2.9 29.8 1.0
FE1 A:SF4602 2.9 31.8 1.0
FE2 A:SF4602 3.0 27.7 1.0
CB A:CYS350 3.2 24.7 1.0
N A:CYS350 3.7 29.6 1.0
S3 A:SF4602 3.7 29.4 1.0
CE2 A:PHE456 4.0 24.5 1.0
CA A:CYS350 4.1 25.0 1.0
CG2 A:ILE431 4.4 30.0 1.0
CD2 A:PHE456 4.4 24.2 1.0
N A:ASN349 4.5 27.6 1.0
CB A:MET348 4.6 30.7 1.0
CD1 A:ILE431 4.6 35.3 1.0
C A:MET348 4.8 30.1 1.0
SG A:CYS441 4.9 33.8 1.0
N A:MET351 4.9 23.8 1.0
C A:ASN349 4.9 33.0 1.0
CA A:MET348 4.9 33.6 1.0
SG A:CYS438 5.0 30.7 1.0
SG A:CYS454 5.0 29.4 1.0
CZ A:PHE456 5.0 22.7 1.0

Iron binding site 4 out of 8 in 5kcm

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Iron binding site 4 out of 8 in the Crystal Structure of Iron-Sulfur Cluster Containing Photolyase Phrb Mutant I51W


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 Photolyase Phrb Mutant I51W within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:29.8
occ:1.00
 FE4 A:SF4602 0.0 29.8 1.0
S1 A:SF4602 2.1 37.7 1.0
S3 A:SF4602 2.1 29.4 1.0
S2 A:SF4602 2.2 32.3 1.0
SG A:CYS441 2.3 33.8 1.0
FE3 A:SF4602 2.9 31.9 1.0
FE2 A:SF4602 2.9 27.7 1.0
FE1 A:SF4602 2.9 31.8 1.0
CB A:CYS441 3.0 34.4 1.0
S4 A:SF4602 3.7 26.8 1.0
N A:ASN349 4.0 27.6 1.0
CB A:TYR443 4.1 34.0 1.0
CD1 A:TYR443 4.3 35.6 1.0
CA A:CYS441 4.5 36.1 1.0
CA A:MET348 4.6 33.6 1.0
CB A:ASN349 4.6 28.9 1.0
O A:TYR443 4.7 33.1 1.0
C A:MET348 4.7 30.1 1.0
CA A:CYS438 4.7 38.6 1.0
N A:TYR443 4.7 34.0 1.0
CG A:TYR443 4.7 43.3 1.0
CA A:TYR443 4.8 36.0 1.0
N A:CYS350 4.8 29.6 1.0
C A:TYR443 4.8 36.8 1.0
CA A:ASN349 4.9 27.7 1.0
SG A:CYS438 4.9 30.7 1.0
SG A:CYS350 5.0 27.5 1.0

Iron binding site 5 out of 8 in 5kcm

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Iron binding site 5 out of 8 in the Crystal Structure of Iron-Sulfur Cluster Containing Photolyase Phrb Mutant I51W


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Iron-Sulfur Cluster Containing Photolyase Phrb Mutant I51W within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe602

b:22.3
occ:1.00
 FE1 B:SF4602 0.0 22.3 1.0
S4 B:SF4602 2.1 22.9 1.0
S2 B:SF4602 2.1 24.8 1.0
S3 B:SF4602 2.2 25.3 1.0
SG B:CYS438 2.2 25.7 1.0
FE2 B:SF4602 2.8 22.9 1.0
FE4 B:SF4602 2.8 24.7 1.0
FE3 B:SF4602 2.9 24.7 1.0
CB B:CYS438 3.3 22.8 1.0
S1 B:SF4602 3.6 23.2 1.0
CA B:CYS438 3.7 22.6 1.0
N B:CYS438 4.1 26.2 1.0
CG2 B:ILE431 4.4 16.3 1.0
CB B:PRO445 4.6 26.9 1.0
CG B:PRO445 4.7 22.8 1.0
C B:TYR437 4.7 26.6 1.0
CB B:CYS441 4.7 27.1 1.0
SG B:CYS441 4.8 24.6 1.0
SG B:CYS454 4.8 23.6 1.0
SG B:CYS350 4.8 21.1 1.0
CB B:ILE431 4.9 22.3 1.0

Iron binding site 6 out of 8 in 5kcm

Go back to Iron Binding Sites List in 5kcm
Iron binding site 6 out of 8 in the Crystal Structure of Iron-Sulfur Cluster Containing Photolyase Phrb Mutant I51W


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Iron-Sulfur Cluster Containing Photolyase Phrb Mutant I51W within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe602

b:22.9
occ:1.00
 FE2 B:SF4602 0.0 22.9 1.0
S3 B:SF4602 2.1 25.3 1.0
S1 B:SF4602 2.1 23.2 1.0
S4 B:SF4602 2.2 22.9 1.0
SG B:CYS454 2.3 23.6 1.0
FE1 B:SF4602 2.8 22.3 1.0
FE4 B:SF4602 2.9 24.7 1.0
FE3 B:SF4602 3.0 24.7 1.0
CB B:CYS454 3.0 18.9 1.0
S2 B:SF4602 3.7 24.8 1.0
CA B:CYS454 3.9 19.4 1.0
CD2 B:PHE456 4.0 16.4 1.0
C B:CYS454 4.6 20.9 1.0
CE2 B:PHE456 4.6 27.8 1.0
CA B:GLY428 4.7 19.9 1.0
CD B:PRO455 4.7 22.1 1.0
N B:PRO455 4.8 24.6 1.0
CB B:TYR443 4.8 32.9 1.0
SG B:CYS438 4.8 25.7 1.0
CG B:PHE456 4.9 16.1 1.0
CB B:PHE456 4.9 20.4 1.0
SG B:CYS441 5.0 24.6 1.0

Iron binding site 7 out of 8 in 5kcm

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Iron binding site 7 out of 8 in the Crystal Structure of Iron-Sulfur Cluster Containing Photolyase Phrb Mutant I51W


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of Iron-Sulfur Cluster Containing Photolyase Phrb Mutant I51W within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe602

b:24.7
occ:1.00
 FE3 B:SF4602 0.0 24.7 1.0
S2 B:SF4602 2.1 24.8 1.0
S4 B:SF4602 2.2 22.9 1.0
S1 B:SF4602 2.2 23.2 1.0
SG B:CYS350 2.2 21.1 1.0
FE1 B:SF4602 2.9 22.3 1.0
FE4 B:SF4602 2.9 24.7 1.0
FE2 B:SF4602 3.0 22.9 1.0
CB B:CYS350 3.3 25.6 1.0
S3 B:SF4602 3.8 25.3 1.0
N B:CYS350 3.8 21.4 1.0
CE2 B:PHE456 3.9 27.8 1.0
CA B:CYS350 4.2 22.3 1.0
CD2 B:PHE456 4.3 16.4 1.0
CG2 B:ILE431 4.4 16.3 1.0
CD1 B:ILE431 4.5 25.0 1.0
N B:ASN349 4.6 20.1 1.0
CB B:MET348 4.6 18.2 1.0
SG B:CYS441 4.8 24.6 1.0
C B:MET348 4.8 25.2 1.0
SG B:CYS438 4.9 25.7 1.0
CZ B:PHE456 4.9 18.6 1.0
N B:MET351 4.9 16.8 1.0
CA B:MET348 4.9 26.4 1.0
SG B:CYS454 4.9 23.6 1.0
C B:ASN349 5.0 21.4 1.0

Iron binding site 8 out of 8 in 5kcm

Go back to Iron Binding Sites List in 5kcm
Iron binding site 8 out of 8 in the Crystal Structure of Iron-Sulfur Cluster Containing Photolyase Phrb Mutant I51W


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of Iron-Sulfur Cluster Containing Photolyase Phrb Mutant I51W within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe602

b:24.7
occ:1.00
 FE4 B:SF4602 0.0 24.7 1.0
S3 B:SF4602 2.1 25.3 1.0
S1 B:SF4602 2.1 23.2 1.0
S2 B:SF4602 2.2 24.8 1.0
SG B:CYS441 2.2 24.6 1.0
FE1 B:SF4602 2.8 22.3 1.0
FE2 B:SF4602 2.9 22.9 1.0
FE3 B:SF4602 2.9 24.7 1.0
CB B:CYS441 3.1 27.1 1.0
S4 B:SF4602 3.7 22.9 1.0
N B:ASN349 4.0 20.1 1.0
CB B:TYR443 4.1 32.9 1.0
CD2 B:TYR443 4.2 28.9 1.0
CA B:MET348 4.5 26.4 1.0
CA B:CYS441 4.6 27.7 1.0
O B:TYR443 4.6 33.7 1.0
CG B:TYR443 4.7 35.0 1.0
C B:MET348 4.7 25.2 1.0
CB B:ASN349 4.7 20.9 1.0
SG B:CYS438 4.8 25.7 1.0
N B:TYR443 4.8 25.1 1.0
CA B:CYS438 4.8 22.6 1.0
CA B:TYR443 4.8 29.1 1.0
N B:CYS350 4.8 21.4 1.0
C B:TYR443 4.9 27.8 1.0
SG B:CYS350 4.9 21.1 1.0
CA B:ASN349 4.9 19.1 1.0
CB B:MET348 4.9 18.2 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 6 03:10:59 2024

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