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Manganese in PDB 7uq3: Jmjc Domain-Containing Protein 5 (JMJD5) in Complex with Mn and (S)-2- (1-Hydroxy-2,5-Dioxopyrrolidin-3-Yl)Acetic Acid

Enzymatic activity of Jmjc Domain-Containing Protein 5 (JMJD5) in Complex with Mn and (S)-2- (1-Hydroxy-2,5-Dioxopyrrolidin-3-Yl)Acetic Acid

All present enzymatic activity of Jmjc Domain-Containing Protein 5 (JMJD5) in Complex with Mn and (S)-2- (1-Hydroxy-2,5-Dioxopyrrolidin-3-Yl)Acetic Acid:
1.14.11.73;

Protein crystallography data

The structure of Jmjc Domain-Containing Protein 5 (JMJD5) in Complex with Mn and (S)-2- (1-Hydroxy-2,5-Dioxopyrrolidin-3-Yl)Acetic Acid, PDB code: 7uq3 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) 49.85 / 1.49
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.479, 64.69, 78.23, 90, 90, 90
R / Rfree (%) 13.4 / 13.5

Manganese Binding Sites:

The binding sites of Manganese atom in the Jmjc Domain-Containing Protein 5 (JMJD5) in Complex with Mn and (S)-2- (1-Hydroxy-2,5-Dioxopyrrolidin-3-Yl)Acetic Acid (pdb code 7uq3). 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 (S)-2- (1-Hydroxy-2,5-Dioxopyrrolidin-3-Yl)Acetic Acid, PDB code: 7uq3:

Manganese binding site 1 out of 1 in 7uq3

Go back to Manganese Binding Sites List in 7uq3
Manganese binding site 1 out of 1 in the Jmjc Domain-Containing Protein 5 (JMJD5) in Complex with Mn and (S)-2- (1-Hydroxy-2,5-Dioxopyrrolidin-3-Yl)Acetic Acid


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 (S)-2- (1-Hydroxy-2,5-Dioxopyrrolidin-3-Yl)Acetic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:9.7
occ:1.00
 OD2 A:ASP323 2.1 10.4 1.0
OAA A:O2U502 2.1 11.3 1.0
NE2 A:HIS321 2.2 10.4 1.0
O A:HOH757 2.3 15.6 1.0
OAL A:O2U502 2.3 15.0 1.0
NE2 A:HIS400 2.3 10.8 1.0
NAB A:O2U502 2.9 9.8 1.0
CAC A:O2U502 2.9 16.4 1.0
CG A:ASP323 3.1 12.0 1.0
CE1 A:HIS321 3.1 11.2 1.0
CE1 A:HIS400 3.2 7.8 1.0
CD2 A:HIS321 3.3 9.3 1.0
HE1 A:HIS321 3.3 13.5 1.0
CD2 A:HIS400 3.3 7.8 1.0
HE1 A:HIS400 3.3 9.4 1.0
OD1 A:ASP323 3.4 15.1 1.0
HD2 A:HIS321 3.5 11.1 1.0
HD2 A:HIS400 3.5 9.4 1.0
HZ2 A:TRP414 3.7 23.3 1.0
O A:HOH676 3.9 16.2 1.0
CAJ A:O2U502 4.2 9.5 1.0
ND1 A:HIS321 4.3 9.8 1.0
ND1 A:HIS400 4.3 7.5 1.0
CG A:HIS321 4.4 8.4 1.0
CAD A:O2U502 4.4 14.4 1.0
HD22 A:ASN327 4.4 13.4 1.0
CG A:HIS400 4.4 7.3 1.0
O A:HOH817 4.5 32.6 1.0
CZ2 A:TRP414 4.5 19.4 1.0
CB A:ASP323 4.5 11.6 1.0
HB2 A:ASP323 4.5 13.9 1.0
O A:HOH833 4.6 40.7 1.0
HE1 A:TRP414 4.6 20.7 1.0
HAD A:O2U502 4.8 17.3 1.0
HH2 A:TRP310 4.8 16.5 1.0
HD21 A:ASN327 4.9 13.4 1.0
OAK A:O2U502 4.9 13.9 1.0
ND2 A:ASN327 5.0 11.1 1.0
HB3 A:ASP323 5.0 13.9 1.0
HAE A:O2U502 5.0 14.6 1.0

Reference:

M.S.Islam, M.Markoulides, R.Chowdhury, C.J.Schofield. Structural Analysis of the 2-Oxoglutarate Binding Site of the Circadian Rhythm Linked Oxygenase JMJD5. Sci Rep V. 12 20680 2022.
ISSN: ESSN 2045-2322
PubMed: 36450832
DOI: 10.1038/S41598-022-24154-0
Page generated: Sun Oct 6 10:56:40 2024

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