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Manganese in PDB 6yw3: Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with N-Oxalyl Glycine (Nog), Hif-1ALPHA Codd (556-574) and A Rapid-Derived Cyclic Peptide 3C (14-Mer)

Enzymatic activity of Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with N-Oxalyl Glycine (Nog), Hif-1ALPHA Codd (556-574) and A Rapid-Derived Cyclic Peptide 3C (14-Mer)

All present enzymatic activity of Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with N-Oxalyl Glycine (Nog), Hif-1ALPHA Codd (556-574) and A 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 N-Oxalyl Glycine (Nog), Hif-1ALPHA Codd (556-574) and A Rapid-Derived Cyclic Peptide 3C (14-Mer), PDB code: 6yw3 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) 55.69 / 2.28
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 76.443, 81.285, 43.219, 90, 90, 90
R / Rfree (%) 18.8 / 20.8

Manganese Binding Sites:

The binding sites of Manganese atom in the Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with N-Oxalyl Glycine (Nog), Hif-1ALPHA Codd (556-574) and A Rapid-Derived Cyclic Peptide 3C (14-Mer) (pdb code 6yw3). 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 N-Oxalyl Glycine (Nog), Hif-1ALPHA Codd (556-574) and A Rapid-Derived Cyclic Peptide 3C (14-Mer), PDB code: 6yw3:

Manganese binding site 1 out of 1 in 6yw3

Go back to Manganese Binding Sites List in 6yw3
Manganese binding site 1 out of 1 in the Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with N-Oxalyl Glycine (Nog), Hif-1ALPHA Codd (556-574) and A 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 N-Oxalyl Glycine (Nog), Hif-1ALPHA Codd (556-574) and A Rapid-Derived Cyclic Peptide 3C (14-Mer) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:15.2
occ:1.00
 O A:HOH612 2.0 20.2 1.0
NE2 A:HIS374 2.1 22.9 1.0
O2' A:OGA502 2.1 19.9 1.0
NE2 A:HIS313 2.2 19.9 1.0
OD1 A:ASP315 2.2 22.8 1.0
O1 A:OGA502 2.2 23.4 1.0
C2 A:OGA502 2.8 24.3 1.0
C1 A:OGA502 2.9 25.3 1.0
CE1 A:HIS313 2.9 19.9 1.0
HE1 A:HIS313 2.9 23.8 1.0
CE1 A:HIS374 3.1 20.7 1.0
CD2 A:HIS374 3.1 19.8 1.0
CG A:ASP315 3.2 18.9 1.0
HE1 A:HIS374 3.2 24.8 1.0
HD2 A:HIS374 3.3 23.8 1.0
CD2 A:HIS313 3.3 19.9 1.0
OD2 A:ASP315 3.4 18.3 1.0
HG3 S:PRO564 3.5 31.7 1.0
HD2 A:HIS313 3.6 23.9 1.0
ND1 A:HIS313 4.1 20.4 1.0
HD3 S:PRO564 4.1 32.4 1.0
N1 A:OGA502 4.1 26.1 1.0
HZ A:PHE366 4.1 23.1 1.0
HZ2 A:TRP389 4.1 28.8 1.0
O2 A:OGA502 4.2 27.0 1.0
ND1 A:HIS374 4.2 20.2 1.0
CG A:HIS374 4.2 20.2 1.0
O A:HOH630 4.2 26.4 1.0
CG A:HIS313 4.3 20.4 1.0
HA A:ASP315 4.4 22.4 1.0
CG S:PRO564 4.4 26.4 1.0
H4C1 A:OGA502 4.5 32.0 1.0
H4C2 A:OGA502 4.5 32.0 1.0
CB A:ASP315 4.6 17.6 1.0
C4 A:OGA502 4.7 26.6 1.0
CD S:PRO564 4.7 27.0 1.0
HB3 S:PRO564 4.7 32.2 1.0
HD1 A:HIS313 4.8 24.5 1.0
H1 A:OGA502 4.9 31.4 1.0
CE2 A:TYR310 4.9 21.8 1.0
CA A:ASP315 4.9 18.7 1.0
HE2 A:TYR310 4.9 26.1 1.0
HD1 A:HIS374 4.9 24.3 1.0
HG21 A:THR325 5.0 24.2 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 07:55:29 2024

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