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Iron in PDB 4rh1: Spore Photoproduct Lyase C140A/S76C Mutant with Bound Adomet and Dinucleoside Spore Photoproduct

Enzymatic activity of Spore Photoproduct Lyase C140A/S76C Mutant with Bound Adomet and Dinucleoside Spore Photoproduct

All present enzymatic activity of Spore Photoproduct Lyase C140A/S76C Mutant with Bound Adomet and Dinucleoside Spore Photoproduct:
4.1.99.14;

Protein crystallography data

The structure of Spore Photoproduct Lyase C140A/S76C Mutant with Bound Adomet and Dinucleoside Spore Photoproduct, PDB code: 4rh1 was solved by A.Benjdia, K.Heil, A.Winkler, T.Carell, I.Schlichting, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.53 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 53.440, 58.560, 130.960, 90.00, 90.00, 90.00
R / Rfree (%) 26.4 / 32.5

Iron Binding Sites:

The binding sites of Iron atom in the Spore Photoproduct Lyase C140A/S76C Mutant with Bound Adomet and Dinucleoside Spore Photoproduct (pdb code 4rh1). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Spore Photoproduct Lyase C140A/S76C Mutant with Bound Adomet and Dinucleoside Spore Photoproduct, PDB code: 4rh1:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 4rh1

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Iron binding site 1 out of 4 in the Spore Photoproduct Lyase C140A/S76C Mutant with Bound Adomet and Dinucleoside Spore Photoproduct


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Spore Photoproduct Lyase C140A/S76C Mutant with Bound Adomet and Dinucleoside Spore Photoproduct within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:41.9
occ:1.00
 FE1 A:SF4401 0.0 41.9 1.0
S2 A:SF4401 2.1 38.2 1.0
S4 A:SF4401 2.1 39.9 1.0
S3 A:SF4401 2.1 38.3 1.0
SG A:CYS97 2.2 34.7 1.0
FE3 A:SF4401 3.1 39.2 1.0
FE4 A:SF4401 3.1 41.1 1.0
FE2 A:SF4401 3.2 39.4 1.0
CB A:CYS97 3.2 37.0 1.0
S1 A:SF4401 3.7 38.5 1.0
CE A:EEM402 3.8 41.1 1.0
CA A:CYS97 4.1 38.6 1.0
CD1 A:LEU99 4.2 44.7 1.0
CG A:LEU99 4.3 45.0 1.0
SE A:EEM402 4.5 40.0 1.0
CB A:CYS94 4.6 35.4 1.0
CB A:LEU99 4.8 45.2 1.0
SG A:CYS94 4.8 34.5 1.0
C A:CYS97 4.9 41.5 1.0
N A:TYR98 4.9 42.2 1.0
C8 A:EEM402 4.9 33.1 1.0
N A:EEM402 5.0 36.6 1.0
O A:EEM402 5.0 36.4 1.0
CB A:CYS90 5.0 31.0 1.0

Iron binding site 2 out of 4 in 4rh1

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Iron binding site 2 out of 4 in the Spore Photoproduct Lyase C140A/S76C Mutant with Bound Adomet and Dinucleoside Spore Photoproduct


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Spore Photoproduct Lyase C140A/S76C Mutant with Bound Adomet and Dinucleoside Spore Photoproduct within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:39.4
occ:1.00
 FE2 A:SF4401 0.0 39.4 1.0
O A:EEM402 2.0 36.4 1.0
S3 A:SF4401 2.1 38.3 1.0
S4 A:SF4401 2.1 39.9 1.0
S1 A:SF4401 2.1 38.5 1.0
N A:EEM402 2.3 36.6 1.0
C A:EEM402 2.8 36.8 1.0
CA A:EEM402 3.0 36.8 1.0
FE4 A:SF4401 3.1 41.1 1.0
FE3 A:SF4401 3.1 39.2 1.0
FE1 A:SF4401 3.2 41.9 1.0
SE A:EEM402 3.2 40.0 1.0
NZ A:LYS174 3.5 39.0 1.0
CG A:EEM402 3.5 38.2 1.0
S2 A:SF4401 3.7 38.2 1.0
CB A:EEM402 3.8 37.8 1.0
OXT A:EEM402 3.9 36.6 1.0
CE A:EEM402 4.1 41.1 1.0
OD1 A:ASP143 4.5 26.9 1.0
CE A:LYS174 4.7 38.2 1.0
C3' A:EEM402 4.7 33.9 1.0
C2' A:EEM402 4.7 33.2 1.0
CD A:LYS174 4.7 37.9 1.0
SG A:CYS90 4.7 29.3 1.0
CG A:LYS174 4.8 37.4 1.0
C5' A:EEM402 4.9 37.0 1.0
SG A:CYS94 5.0 34.5 1.0

Iron binding site 3 out of 4 in 4rh1

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Iron binding site 3 out of 4 in the Spore Photoproduct Lyase C140A/S76C Mutant with Bound Adomet and Dinucleoside Spore Photoproduct


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Spore Photoproduct Lyase C140A/S76C Mutant with Bound Adomet and Dinucleoside Spore Photoproduct within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:39.2
occ:1.00
 FE3 A:SF4401 0.0 39.2 1.0
SG A:CYS90 2.1 29.3 1.0
S4 A:SF4401 2.1 39.9 1.0
S2 A:SF4401 2.1 38.2 1.0
S1 A:SF4401 2.1 38.5 1.0
CB A:CYS90 2.9 31.0 1.0
FE1 A:SF4401 3.1 41.9 1.0
FE2 A:SF4401 3.1 39.4 1.0
FE4 A:SF4401 3.1 41.1 1.0
S3 A:SF4401 3.7 38.3 1.0
N A:EEM402 3.9 36.6 1.0
CA A:GLY92 4.2 40.4 1.0
N A:GLY92 4.2 39.8 1.0
CA A:CYS90 4.4 32.6 1.0
CB A:ASP143 4.6 28.2 1.0
C A:GLY92 4.8 40.4 1.0
C A:CYS90 4.8 34.5 1.0
O A:EEM402 4.9 36.4 1.0
SG A:CYS97 4.9 34.7 1.0
O A:GLY92 4.9 42.7 1.0

Iron binding site 4 out of 4 in 4rh1

Go back to Iron Binding Sites List in 4rh1
Iron binding site 4 out of 4 in the Spore Photoproduct Lyase C140A/S76C Mutant with Bound Adomet and Dinucleoside Spore Photoproduct


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Spore Photoproduct Lyase C140A/S76C Mutant with Bound Adomet and Dinucleoside Spore Photoproduct within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:41.1
occ:1.00
 FE4 A:SF4401 0.0 41.1 1.0
SG A:CYS94 2.1 34.5 1.0
S2 A:SF4401 2.1 38.2 1.0
S1 A:SF4401 2.1 38.5 1.0
S3 A:SF4401 2.1 38.3 1.0
CB A:CYS94 2.9 35.4 1.0
FE2 A:SF4401 3.1 39.4 1.0
FE1 A:SF4401 3.1 41.9 1.0
FE3 A:SF4401 3.1 39.2 1.0
NZ A:LYS174 3.5 39.0 1.0
S4 A:SF4401 3.7 39.9 1.0
CA A:CYS94 4.1 36.1 1.0
N A:CYS94 4.1 36.2 1.0
CD A:LYS174 4.2 37.9 1.0
O A:EEM402 4.2 36.4 1.0
CE A:LYS174 4.3 38.2 1.0
CG2 A:THR209 4.4 40.1 1.0
OH A:TYR96 4.8 36.9 1.0
SG A:CYS97 4.9 34.7 1.0
CB A:CYS97 4.9 37.0 1.0

Reference:

A.Benjdia, K.Heil, A.Winkler, T.Carell, I.Schlichting. Rescuing Dna Repair Activity By Rewiring the H-Atom Transfer Pathway in the Radical Sam Enzyme, Spore Photoproduct Lyase. Chem.Commun.(Camb.) V. 50 14201 2014.
ISSN: ISSN 1359-7345
PubMed: 25285338
DOI: 10.1039/C4CC05158K
Page generated: Mon Aug 5 09:17:35 2024

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