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Iron in PDB 8tdp: Time-Resolved Sfx-Xfel Crystal Structure of CYP121 Bound with Cyy Reacted with Peracetic Acid For 200 Milliseconds

Enzymatic activity of Time-Resolved Sfx-Xfel Crystal Structure of CYP121 Bound with Cyy Reacted with Peracetic Acid For 200 Milliseconds

All present enzymatic activity of Time-Resolved Sfx-Xfel Crystal Structure of CYP121 Bound with Cyy Reacted with Peracetic Acid For 200 Milliseconds:
1.14.19.70;

Protein crystallography data

The structure of Time-Resolved Sfx-Xfel Crystal Structure of CYP121 Bound with Cyy Reacted with Peracetic Acid For 200 Milliseconds, PDB code: 8tdp was solved by R.C.Nguyen, M.Dasgupta, A.Bhowmick, J.F.Kern, A.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.18 / 1.85
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 78.728, 78.728, 265.884, 90, 90, 120
R / Rfree (%) 18.1 / 22.8

Iron Binding Sites:

The binding sites of Iron atom in the Time-Resolved Sfx-Xfel Crystal Structure of CYP121 Bound with Cyy Reacted with Peracetic Acid For 200 Milliseconds (pdb code 8tdp). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total only one binding site of Iron was determined in the Time-Resolved Sfx-Xfel Crystal Structure of CYP121 Bound with Cyy Reacted with Peracetic Acid For 200 Milliseconds, PDB code: 8tdp:

Iron binding site 1 out of 1 in 8tdp

Go back to Iron Binding Sites List in 8tdp
Iron binding site 1 out of 1 in the Time-Resolved Sfx-Xfel Crystal Structure of CYP121 Bound with Cyy Reacted with Peracetic Acid For 200 Milliseconds


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Time-Resolved Sfx-Xfel Crystal Structure of CYP121 Bound with Cyy Reacted with Peracetic Acid For 200 Milliseconds within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe404

b:25.1
occ:1.00
 FE A:HEM404 0.0 25.1 1.0
NB A:HEM404 2.1 23.6 1.0
NA A:HEM404 2.1 24.2 1.0
NC A:HEM404 2.1 23.9 1.0
ND A:HEM404 2.1 22.5 1.0
SG A:CYS345 2.3 23.4 1.0
O1 A:PEO406 2.5 20.6 0.5
C1A A:HEM404 3.0 23.1 1.0
C1C A:HEM404 3.0 23.3 1.0
C4B A:HEM404 3.0 19.2 1.0
C4D A:HEM404 3.1 23.6 1.0
C4C A:HEM404 3.1 23.3 1.0
C1B A:HEM404 3.1 23.6 1.0
C4A A:HEM404 3.1 21.7 1.0
C1D A:HEM404 3.2 24.9 1.0
O2 A:PEO406 3.2 29.0 0.5
CB A:CYS345 3.3 23.3 1.0
CHA A:HEM404 3.4 26.1 1.0
CHC A:HEM404 3.4 22.2 1.0
CHB A:HEM404 3.5 20.1 1.0
CHD A:HEM404 3.5 23.7 1.0
CA A:CYS345 4.2 21.0 1.0
C2C A:HEM404 4.3 24.3 1.0
C2A A:HEM404 4.3 23.0 1.0
C3C A:HEM404 4.3 25.7 1.0
C3B A:HEM404 4.3 20.0 1.0
C3D A:HEM404 4.3 25.6 1.0
C3A A:HEM404 4.3 20.9 1.0
C2B A:HEM404 4.3 23.1 1.0
C2D A:HEM404 4.3 23.6 1.0
OG A:SER237 4.6 23.9 1.0
CD A:PRO346 4.9 26.4 1.0
CB A:SER237 4.9 24.7 1.0
C A:CYS345 4.9 25.5 1.0

Reference:

R.C.Nguyen, I.Davis, M.Dasgupta, Y.Wang, P.S.Simon, A.Butryn, H.Makita, I.Bogacz, K.Dornevil, P.Aller, A.Bhowmick, R.Chatterjee, I.S.Kim, T.Zhou, D.Mendez, D.W.Paley, F.Fuller, R.Alonso Mori, A.Batyuk, N.K.Sauter, A.S.Brewster, A.M.Orville, V.K.Yachandra, J.Yano, J.F.Kern, A.Liu. In Situ Structural Observation of A Substrate- and Peroxide-Bound High-Spin Ferric-Hydroperoxo Intermediate in the P450 Enzyme CYP121. J.Am.Chem.Soc. 2023.
ISSN: ESSN 1520-5126
PubMed: 37939223
DOI: 10.1021/JACS.3C04991
Page generated: Thu Aug 7 23:42:44 2025

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