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Nickel in PDB 7eqv: Crystal Structure of JMJD2A Complexed with 3,4-Dihydroxybenzoic Acid

Enzymatic activity of Crystal Structure of JMJD2A Complexed with 3,4-Dihydroxybenzoic Acid

All present enzymatic activity of Crystal Structure of JMJD2A Complexed with 3,4-Dihydroxybenzoic Acid:
1.14.11.66; 1.14.11.69;

Protein crystallography data

The structure of Crystal Structure of JMJD2A Complexed with 3,4-Dihydroxybenzoic Acid, PDB code: 7eqv was solved by W.-K.Fang, S.-M.Yang, W.-C.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.60
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 149.396, 149.396, 62.175, 90, 90, 120
R / Rfree (%) 16.8 / 22.2

Other elements in 7eqv:

The structure of Crystal Structure of JMJD2A Complexed with 3,4-Dihydroxybenzoic Acid also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Chlorine (Cl) 1 atom

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of JMJD2A Complexed with 3,4-Dihydroxybenzoic Acid (pdb code 7eqv). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total only one binding site of Nickel was determined in the Crystal Structure of JMJD2A Complexed with 3,4-Dihydroxybenzoic Acid, PDB code: 7eqv:

Nickel binding site 1 out of 1 in 7eqv

Go back to Nickel Binding Sites List in 7eqv
Nickel binding site 1 out of 1 in the Crystal Structure of JMJD2A Complexed with 3,4-Dihydroxybenzoic Acid


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of JMJD2A Complexed with 3,4-Dihydroxybenzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni402

b:58.4
occ:1.00
 O4 A:DHB401 1.7 72.8 1.0
OE2 A:GLU190 1.9 44.4 1.0
NE2 A:HIS188 2.3 34.5 1.0
O3 A:DHB401 2.4 60.6 1.0
C4 A:DHB401 2.7 76.8 1.0
O A:HOH507 2.8 43.5 1.0
CD A:GLU190 2.8 35.0 1.0
NE2 A:HIS276 2.9 20.4 1.0
C3 A:DHB401 3.0 69.0 1.0
OE1 A:GLU190 3.1 33.7 1.0
CE1 A:HIS188 3.2 33.1 1.0
CD2 A:HIS188 3.3 33.9 1.0
CE1 A:HIS276 3.5 22.2 1.0
C5 A:DHB401 4.0 83.8 1.0
O A:HOH625 4.1 40.6 1.0
CD2 A:HIS276 4.1 22.3 1.0
CG A:GLU190 4.2 34.8 1.0
ND1 A:HIS188 4.3 32.4 1.0
C2 A:DHB401 4.4 74.7 1.0
CG A:HIS188 4.4 33.6 1.0
NZ A:LYS241 4.6 74.4 1.0
O A:HOH582 4.7 43.6 1.0
ND1 A:HIS276 4.7 18.9 1.0
OG A:SER196 4.9 33.5 1.0

Reference:

J.S.Liu, W.K.Fang, S.M.Yang, M.C.Wu, T.J.Chen, C.M.Chen, T.Y.Lin, K.L.Liu, C.M.Wu, Y.C.Chen, C.P.Chuu, L.Y.Wang, H.P.Hsieh, H.J.Kung, W.C.Wang. Natural Product Myricetin Is A Pan-KDM4 Inhibitor Which with Poly Lactic-Co-Glycolic Acid Formulation Effectively Targets Castration-Resistant Prostate Cancer. J.Biomed.Sci. V. 29 29 2022.
ISSN: ESSN 1423-0127
PubMed: 35534851
DOI: 10.1186/S12929-022-00812-3
Page generated: Thu Oct 10 09:10:53 2024

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