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Iron in PDB 6yw0: Lysine-N,N-Dimethylated Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Bb-287

Enzymatic activity of Lysine-N,N-Dimethylated Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Bb-287

All present enzymatic activity of Lysine-N,N-Dimethylated Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Bb-287:
1.14.11.29;

Protein crystallography data

The structure of Lysine-N,N-Dimethylated Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Bb-287, PDB code: 6yw0 was solved by R.Chowdhury, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.02 / 2.20
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 110.927, 110.927, 39.66, 90, 90, 120
R / Rfree (%) 19.2 / 22.1

Iron Binding Sites:

The binding sites of Iron atom in the Lysine-N,N-Dimethylated Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Bb-287 (pdb code 6yw0). 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 Lysine-N,N-Dimethylated Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Bb-287, PDB code: 6yw0:

Iron binding site 1 out of 1 in 6yw0

Go back to Iron Binding Sites List in 6yw0
Iron binding site 1 out of 1 in the Lysine-N,N-Dimethylated Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Bb-287


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Lysine-N,N-Dimethylated Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Bb-287 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:32.9
occ:1.00
O2 A:2JP502 2.0 29.9 1.0
N1 A:2JP502 2.1 33.6 1.0
NE2 A:HIS374 2.1 40.8 1.0
OD1 A:ASP315 2.1 39.0 1.0
NE2 A:HIS313 2.1 46.8 1.0
O A:HOH623 2.4 28.3 1.0
H6 A:2JP502 2.5 46.1 1.0
C4 A:2JP502 2.7 38.4 1.0
CE1 A:HIS313 2.9 38.2 1.0
HE1 A:HIS313 3.0 46.0 1.0
CE1 A:HIS374 3.0 29.3 1.0
C12 A:2JP502 3.0 34.7 1.0
CD2 A:HIS374 3.1 30.4 1.0
CG A:ASP315 3.1 33.8 1.0
C10 A:2JP502 3.1 38.0 1.0
HE1 A:HIS374 3.2 34.8 1.0
CD2 A:HIS313 3.3 41.2 1.0
HD2 A:HIS374 3.3 36.5 1.0
OD2 A:ASP315 3.5 32.4 1.0
N2 A:2JP502 3.5 34.2 1.0
HD2 A:HIS313 3.6 49.5 1.0
C1 A:2JP502 4.1 42.9 1.0
ND1 A:HIS313 4.1 39.9 1.0
ND1 A:HIS374 4.2 32.8 1.0
O A:HOH633 4.2 39.6 1.0
CG A:HIS374 4.2 33.8 1.0
HZ2 A:TRP389 4.3 38.7 1.0
HZ A:PHE366 4.3 40.2 1.0
HA A:ASP315 4.3 37.0 1.0
CG A:HIS313 4.3 40.8 1.0
C13 A:2JP502 4.4 33.5 1.0
C6 A:2JP502 4.4 40.1 1.0
H7 A:2JP502 4.4 41.1 1.0
H8 A:2JP502 4.5 40.2 1.0
CB A:ASP315 4.5 30.5 1.0
H10 A:2JP502 4.7 39.9 1.0
C2 A:2JP502 4.8 44.2 1.0
CA A:ASP315 4.8 31.1 1.0
H11 A:2JP502 4.8 39.9 1.0
HG21 A:THR325 4.8 43.4 1.0
HD1 A:HIS313 4.9 48.0 1.0
C11 A:2JP502 4.9 33.2 1.0
HD1 A:HIS374 4.9 39.4 1.0
H A:ASP315 4.9 40.5 1.0
N A:ASP315 5.0 33.7 1.0
HB2 A:ASP315 5.0 36.6 1.0

Reference:

R.Chowdhury, M.I.Abboud, T.E.Mcallister, B.Banerji, B.Bhushan, J.L.Sorensen, A.Kawamura, C.J.Schofield. Use of Cyclic Peptides to Induce Crystallization: Case Study with Prolyl Hydroxylase Domain 2. Sci Rep V. 10 21964 2020.
ISSN: ESSN 2045-2322
PubMed: 33319810
DOI: 10.1038/S41598-020-76307-8
Page generated: Wed Aug 7 16:51:25 2024

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