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Manganese in PDB 6yw2: Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Bicyclic FG2216 and Rapid-Derived Cyclic Peptide 3C (14-Mer)

Enzymatic activity of Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Bicyclic FG2216 and Rapid-Derived Cyclic Peptide 3C (14-Mer)

All present enzymatic activity of Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Bicyclic FG2216 and Rapid-Derived Cyclic Peptide 3C (14-Mer):
1.14.11.29;

Protein crystallography data

The structure of Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Bicyclic FG2216 and Rapid-Derived Cyclic Peptide 3C (14-Mer), PDB code: 6yw2 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) 37.19 / 2.14
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 46.181, 46.181, 202.262, 90, 90, 120
R / Rfree (%) 17 / 19.6

Other elements in 6yw2:

The structure of Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Bicyclic FG2216 and Rapid-Derived Cyclic Peptide 3C (14-Mer) also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Bicyclic FG2216 and Rapid-Derived Cyclic Peptide 3C (14-Mer) (pdb code 6yw2). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total only one binding site of Manganese was determined in the Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Bicyclic FG2216 and Rapid-Derived Cyclic Peptide 3C (14-Mer), PDB code: 6yw2:

Manganese binding site 1 out of 1 in 6yw2

Go back to Manganese Binding Sites List in 6yw2
Manganese binding site 1 out of 1 in the Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Bicyclic FG2216 and Rapid-Derived Cyclic Peptide 3C (14-Mer)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Bicyclic FG2216 and Rapid-Derived Cyclic Peptide 3C (14-Mer) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:27.9
occ:1.00
 NE2 A:HIS374 2.0 36.5 1.0
O13 A:UN9502 2.0 26.6 1.0
O A:HOH604 2.2 27.5 1.0
NE2 A:HIS313 2.2 35.3 1.0
OD1 A:ASP315 2.2 28.8 1.0
N8 A:UN9502 2.3 36.0 1.0
C12 A:UN9502 2.8 30.5 1.0
C9 A:UN9502 2.9 33.7 1.0
CE1 A:HIS374 3.0 34.6 1.0
CD2 A:HIS374 3.0 35.6 1.0
CE1 A:HIS313 3.1 31.6 1.0
CG A:ASP315 3.1 29.6 1.0
HE1 A:HIS313 3.2 38.0 1.0
HE1 A:HIS374 3.2 41.6 1.0
HD2 A:HIS374 3.2 42.7 1.0
CD2 A:HIS313 3.3 32.9 1.0
C7 A:UN9502 3.3 37.0 1.0
OD2 A:ASP315 3.4 29.5 1.0
HD2 A:HIS313 3.5 39.5 1.0
CL1 A:UN9502 3.6 38.9 1.0
HZ A:PHE366 3.9 35.4 1.0
N14 A:UN9502 4.1 30.9 1.0
ND1 A:HIS374 4.1 34.8 1.0
CG A:HIS374 4.1 34.1 1.0
O A:HOH657 4.2 27.0 1.0
ND1 A:HIS313 4.2 31.8 1.0
HZ2 A:TRP389 4.3 32.0 1.0
C10 A:UN9502 4.3 35.2 1.0
HA A:ASP315 4.3 35.4 1.0
CG A:HIS313 4.3 31.4 1.0
H152 A:UN9502 4.4 37.4 1.0
CB A:ASP315 4.5 29.5 1.0
C2 A:UN9502 4.6 36.6 1.0
C15 A:UN9502 4.6 31.2 1.0
H151 A:UN9502 4.7 37.4 1.0
HN14 A:UN9502 4.8 37.1 1.0
HG21 A:THR325 4.8 31.1 1.0
CA A:ASP315 4.8 29.5 1.0
CZ A:PHE366 4.8 29.5 1.0
HD1 A:HIS374 4.9 41.8 1.0
H A:ASP315 4.9 33.8 1.0
HE1 A:PHE366 4.9 36.7 1.0
HB2 A:ASP315 4.9 35.5 1.0
HD1 A:HIS313 5.0 38.2 1.0
C3 A:UN9502 5.0 36.3 1.0
N A:ASP315 5.0 28.1 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: Sun Oct 6 07:55:30 2024

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