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Iron in PDB 6yvw: Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Monocyclic Bb- 328

Enzymatic activity of Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Monocyclic Bb- 328

All present enzymatic activity of Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Monocyclic Bb- 328:
1.14.11.29;

Protein crystallography data

The structure of Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Monocyclic Bb- 328, PDB code: 6yvw was solved by R.Chowdhury, B.Banerji, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.45 / 1.97
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 110.175, 110.175, 39.791, 90, 90, 120
R / Rfree (%) 18.7 / 20.8

Other elements in 6yvw:

The structure of Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Monocyclic Bb- 328 also contains other interesting chemical elements:

Bromine (Br) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Monocyclic Bb- 328 (pdb code 6yvw). 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 Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Monocyclic Bb- 328, PDB code: 6yvw:

Iron binding site 1 out of 1 in 6yvw

Go back to Iron Binding Sites List in 6yvw
Iron binding site 1 out of 1 in the Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Monocyclic Bb- 328


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Monocyclic Bb- 328 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:28.5
occ:1.00
 OAD A:PW5502 2.0 32.0 1.0
O A:HOH636 2.1 31.9 1.0
NE2 A:HIS374 2.2 31.3 1.0
NE2 A:HIS313 2.2 34.9 1.0
OD1 A:ASP315 2.2 35.1 1.0
NAJ A:PW5502 2.3 78.6 1.0
HAB1 A:PW5502 2.9 107.1 1.0
CE1 A:HIS313 3.0 32.0 1.0
CAM A:PW5502 3.0 45.7 1.0
HE1 A:HIS313 3.1 38.5 1.0
CD2 A:HIS374 3.1 28.6 1.0
CG A:ASP315 3.2 31.2 1.0
CE1 A:HIS374 3.2 28.5 1.0
CAP A:PW5502 3.2 77.5 1.0
HD2 A:HIS374 3.3 34.4 1.0
CD2 A:HIS313 3.3 31.3 1.0
CAO A:PW5502 3.3 97.0 1.0
HE1 A:HIS374 3.4 34.2 1.0
NAK A:PW5502 3.4 65.8 1.0
OD2 A:ASP315 3.5 29.8 1.0
HD2 A:HIS313 3.5 37.6 1.0
CAB A:PW5502 3.5 89.2 1.0
HAB2 A:PW5502 4.0 107.1 1.0
HZ A:PHE366 4.1 33.1 1.0
ND1 A:HIS313 4.2 31.8 1.0
HAA A:PW5502 4.2 79.0 1.0
HA A:ASP315 4.2 36.9 1.0
O A:HOH653 4.3 33.1 1.0
ND1 A:HIS374 4.3 27.9 1.0
HAB3 A:PW5502 4.3 107.1 1.0
CG A:HIS374 4.3 30.8 1.0
CAI A:PW5502 4.3 49.7 1.0
CG A:HIS313 4.3 31.5 1.0
HZ2 A:TRP389 4.4 42.6 1.0
CB A:ASP315 4.5 28.2 1.0
CAG A:PW5502 4.5 89.4 1.0
HAH2 A:PW5502 4.6 50.7 1.0
HAI1 A:PW5502 4.6 59.7 1.0
CAQ A:PW5502 4.6 122.7 1.0
HAH1 A:PW5502 4.7 50.7 1.0
CA A:ASP315 4.8 30.7 1.0
CAH A:PW5502 4.8 42.2 1.0
H A:ASP315 4.9 33.6 1.0
N A:ASP315 4.9 28.3 1.0
HD1 A:HIS313 4.9 38.2 1.0
HB3 A:ASP315 5.0 33.9 1.0
HG21 A:THR325 5.0 33.9 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 16:51:21 2024

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