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Manganese in PDB 6yvz: Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Bicyclic Jls- 367

Enzymatic activity of Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Bicyclic Jls- 367

All present enzymatic activity of Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Bicyclic Jls- 367:
1.14.11.29;

Protein crystallography data

The structure of Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Bicyclic Jls- 367, PDB code: 6yvz was solved by R.Chowdhury, J.L.Sorensen, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.15 / 1.91
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 109.88, 109.88, 39.08, 90, 90, 120
R / Rfree (%) 16.7 / 20.4

Other elements in 6yvz:

The structure of Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Bicyclic Jls- 367 also contains other interesting chemical elements:

Bromine (Br) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Bicyclic Jls- 367 (pdb code 6yvz). 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 Jls- 367, PDB code: 6yvz:

Manganese binding site 1 out of 1 in 6yvz

Go back to Manganese Binding Sites List in 6yvz
Manganese binding site 1 out of 1 in the Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Bicyclic Jls- 367


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 Jls- 367 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:27.9
occ:1.00
 N17 A:PW8502 2.0 50.1 1.0
NE2 A:HIS374 2.0 32.3 1.0
OD1 A:ASP315 2.1 36.2 1.0
O18 A:PW8502 2.1 29.4 1.0
NE2 A:HIS313 2.2 34.0 1.0
O A:HOH617 2.3 30.5 1.0
H161 A:PW8502 2.7 85.4 1.0
C16 A:PW8502 2.7 71.1 1.0
CE1 A:HIS374 3.0 30.1 1.0
CE1 A:HIS313 3.0 29.5 1.0
CD2 A:HIS374 3.0 29.1 1.0
C05 A:PW8502 3.0 34.1 1.0
CG A:ASP315 3.1 33.0 1.0
C07 A:PW8502 3.1 62.8 1.0
HE1 A:HIS313 3.1 35.5 1.0
HE1 A:HIS374 3.2 36.2 1.0
HD2 A:HIS374 3.2 35.0 1.0
CD2 A:HIS313 3.3 30.3 1.0
OD2 A:ASP315 3.4 32.2 1.0
N06 A:PW8502 3.5 45.8 1.0
HD2 A:HIS313 3.5 36.4 1.0
ND1 A:HIS374 4.1 29.0 1.0
C15 A:PW8502 4.1 94.0 1.0
HZ A:PHE366 4.1 35.9 1.0
CG A:HIS374 4.1 28.4 1.0
ND1 A:HIS313 4.2 29.5 1.0
O A:HOH643 4.3 33.6 1.0
HA A:ASP315 4.3 39.7 1.0
H061 A:PW8502 4.3 55.0 1.0
CG A:HIS313 4.3 31.2 1.0
C08 A:PW8502 4.4 81.9 1.0
HZ2 A:TRP389 4.4 39.2 1.0
C04 A:PW8502 4.4 34.2 1.0
CB A:ASP315 4.4 30.7 1.0
H032 A:PW8502 4.5 40.6 1.0
H031 A:PW8502 4.7 40.6 1.0
H041 A:PW8502 4.7 41.2 1.0
CA A:ASP315 4.8 33.0 1.0
C03 A:PW8502 4.8 33.8 1.0
C09 A:PW8502 4.8 102.9 1.0
HG21 A:THR325 4.8 34.2 1.0
HD1 A:HIS374 4.9 34.9 1.0
HB2 A:ASP315 4.9 37.0 1.0
HE1 A:TRP389 4.9 34.6 1.0
HD1 A:HIS313 4.9 35.5 1.0
HB3 A:ASP315 5.0 37.0 1.0
N A:ASP315 5.0 33.5 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 07:55:21 2024

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