Atomistry » Iron » PDB 5jsh-5kja » 5kcm
Atomistry »
  Iron »
    PDB 5jsh-5kja »
      5kcm »

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

Go back to Iron Binding Sites List in 5kcm
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

Go back to Iron Binding Sites List in 5kcm
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

Go back to Iron Binding Sites List in 5kcm
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

Go back to Iron Binding Sites List in 5kcm
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

Go back to Iron Binding Sites List in 5kcm
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

Go back to Iron Binding Sites List in 5kcm
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 5 22:33:04 2025

Last articles

Fe in 6U7T
Fe in 6U97
Fe in 6U87
Fe in 6TXL
Fe in 6U4V
Fe in 6U4S
Fe in 6U4L
Fe in 6U3K
Fe in 6U31
Fe in 6TXE
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy