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Manganese in PDB 6i9m: Jmjc Domain-Containing Protein 5 (JMJD5) in Complex with Mn and R-2- Hydroxyglutarate

Enzymatic activity of Jmjc Domain-Containing Protein 5 (JMJD5) in Complex with Mn and R-2- Hydroxyglutarate

All present enzymatic activity of Jmjc Domain-Containing Protein 5 (JMJD5) in Complex with Mn and R-2- Hydroxyglutarate:
1.14.11.27;

Protein crystallography data

The structure of Jmjc Domain-Containing Protein 5 (JMJD5) in Complex with Mn and R-2- Hydroxyglutarate, PDB code: 6i9m was solved by R.Chowdhury, M.S.Islam, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.75 / 1.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.571, 64.674, 77.437, 90.00, 90.00, 90.00
R / Rfree (%) 15.1 / 18.1

Manganese Binding Sites:

The binding sites of Manganese atom in the Jmjc Domain-Containing Protein 5 (JMJD5) in Complex with Mn and R-2- Hydroxyglutarate (pdb code 6i9m). 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 Jmjc Domain-Containing Protein 5 (JMJD5) in Complex with Mn and R-2- Hydroxyglutarate, PDB code: 6i9m:

Manganese binding site 1 out of 1 in 6i9m

Go back to Manganese Binding Sites List in 6i9m
Manganese binding site 1 out of 1 in the Jmjc Domain-Containing Protein 5 (JMJD5) in Complex with Mn and R-2- Hydroxyglutarate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Jmjc Domain-Containing Protein 5 (JMJD5) in Complex with Mn and R-2- Hydroxyglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:12.4
occ:1.00
OD2 A:ASP323 2.2 11.5 1.0
O1 A:2HG502 2.2 17.1 1.0
O3 A:2HG502 2.2 13.4 1.0
O A:HOH666 2.2 13.7 1.0
NE2 A:HIS321 2.2 13.0 1.0
NE2 A:HIS400 2.3 12.7 1.0
HO3 A:2HG502 2.7 16.1 1.0
C1 A:2HG502 2.9 17.2 1.0
C2 A:2HG502 3.0 14.5 1.0
CG A:ASP323 3.1 16.1 1.0
H2 A:2HG502 3.2 17.4 1.0
CD2 A:HIS321 3.2 13.6 1.0
CE1 A:HIS321 3.2 15.7 1.0
CE1 A:HIS400 3.2 11.9 1.0
HE1 A:HIS400 3.3 14.2 1.0
HD2 A:HIS321 3.3 16.3 1.0
CD2 A:HIS400 3.4 11.2 1.0
HE1 A:HIS321 3.4 18.9 1.0
OD1 A:ASP323 3.5 20.3 1.0
HD2 A:HIS400 3.6 13.5 1.0
HZ2 A:TRP414 3.7 25.9 1.0
O A:HOH646 3.9 20.4 1.0
O2 A:2HG502 4.1 17.3 1.0
HE1 A:TRP414 4.1 21.3 1.0
H2 A:GOL505 4.2 45.9 1.0
HD22 A:ASN327 4.3 19.5 1.0
ND1 A:HIS321 4.3 13.0 1.0
CG A:HIS321 4.3 11.4 1.0
ND1 A:HIS400 4.4 11.6 1.0
O2 A:GOL505 4.4 30.6 1.0
C3 A:2HG502 4.4 13.1 1.0
HH2 A:TRP310 4.4 18.8 1.0
CZ2 A:TRP414 4.5 21.6 1.0
CG A:HIS400 4.5 10.3 1.0
CB A:ASP323 4.5 12.4 1.0
HB2 A:ASP323 4.6 14.9 1.0
HZ2 A:TRP310 4.7 21.2 1.0
HD21 A:ASN327 4.7 19.5 1.0
NE1 A:TRP414 4.7 17.7 1.0
H3A A:2HG502 4.8 15.7 1.0
H4A A:2HG502 4.8 16.8 1.0
ND2 A:ASN327 4.8 16.3 1.0
H4 A:2HG502 4.8 16.8 1.0
C2 A:GOL505 4.9 38.2 1.0
CH2 A:TRP310 4.9 15.6 1.0
CE2 A:TRP414 5.0 15.5 1.0
C4 A:2HG502 5.0 14.0 1.0
H3 A:2HG502 5.0 15.7 1.0

Reference:

S.Islam, C.J.Schofield, R.Chowdhury. Jmjc Domain-Containing Protein 5 (JMJD5) in Complex with Mn and R-2-Hydroxyglutarate To Be Published.
Page generated: Tue Dec 15 04:54:31 2020

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