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Iron in PDB 3puq: CEKDM7A From C.Elegans, Complex with Alpha-Kg

Enzymatic activity of CEKDM7A From C.Elegans, Complex with Alpha-Kg

All present enzymatic activity of CEKDM7A From C.Elegans, Complex with Alpha-Kg:
1.14.11.27;

Protein crystallography data

The structure of CEKDM7A From C.Elegans, Complex with Alpha-Kg, PDB code: 3puq was solved by Y.Yang, P.Wang, W.Xu, Y.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.25
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 93.592, 78.138, 102.930, 90.00, 92.07, 90.00
R / Rfree (%) 18.8 / 22.4

Other elements in 3puq:

The structure of CEKDM7A From C.Elegans, Complex with Alpha-Kg also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the CEKDM7A From C.Elegans, Complex with Alpha-Kg (pdb code 3puq). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the CEKDM7A From C.Elegans, Complex with Alpha-Kg, PDB code: 3puq:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 3puq

Go back to Iron Binding Sites List in 3puq
Iron binding site 1 out of 2 in the CEKDM7A From C.Elegans, Complex with Alpha-Kg


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of CEKDM7A From C.Elegans, Complex with Alpha-Kg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1

b:17.7
occ:1.00
O1 A:AKG4 2.0 23.6 1.0
NE2 A:HIS567 2.1 18.0 1.0
O5 A:AKG4 2.1 21.5 1.0
OD2 A:ASP497 2.2 18.9 1.0
O A:HOH1006 2.2 22.0 1.0
NE2 A:HIS495 2.2 20.6 1.0
C1 A:AKG4 2.7 27.6 1.0
C2 A:AKG4 2.7 25.6 1.0
CE1 A:HIS567 2.8 19.8 1.0
CG A:ASP497 3.1 22.9 1.0
CD2 A:HIS495 3.1 22.8 1.0
CE1 A:HIS495 3.3 22.6 1.0
CD2 A:HIS567 3.3 23.4 1.0
OD1 A:ASP497 3.3 25.4 1.0
O2 A:AKG4 3.9 32.0 1.0
OH A:TYR505 4.0 29.5 1.0
ND1 A:HIS567 4.0 17.2 1.0
O A:HOH1125 4.1 28.3 1.0
C3 A:AKG4 4.2 26.4 1.0
CG A:HIS567 4.3 19.6 1.0
CG A:HIS495 4.3 23.9 1.0
ND1 A:HIS495 4.3 22.9 1.0
CB A:ASP497 4.5 22.5 1.0
CA A:ASP497 4.8 23.6 1.0
O1 A:GOL5 4.9 29.7 1.0
N A:ASP497 4.9 20.1 1.0

Iron binding site 2 out of 2 in 3puq

Go back to Iron Binding Sites List in 3puq
Iron binding site 2 out of 2 in the CEKDM7A From C.Elegans, Complex with Alpha-Kg


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of CEKDM7A From C.Elegans, Complex with Alpha-Kg within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1

b:17.3
occ:1.00
O1 C:AKG4 2.0 24.6 1.0
NE2 C:HIS567 2.1 15.5 1.0
O5 C:AKG4 2.1 22.3 1.0
OD2 C:ASP497 2.2 20.1 1.0
NE2 C:HIS495 2.3 24.2 1.0
O C:HOH1012 2.3 19.3 1.0
C1 C:AKG4 2.7 26.3 1.0
C2 C:AKG4 2.7 26.5 1.0
CE1 C:HIS567 2.9 18.1 1.0
CG C:ASP497 3.1 21.4 1.0
CD2 C:HIS495 3.1 23.2 1.0
CD2 C:HIS567 3.2 19.9 1.0
OD1 C:ASP497 3.3 24.8 1.0
CE1 C:HIS495 3.3 25.3 1.0
O2 C:AKG4 3.9 29.3 1.0
O C:HOH1102 4.0 29.9 1.0
ND1 C:HIS567 4.0 19.1 1.0
C3 C:AKG4 4.0 36.1 1.0
OH C:TYR505 4.2 26.1 1.0
CG C:HIS567 4.2 16.3 1.0
CG C:HIS495 4.3 23.6 1.0
ND1 C:HIS495 4.3 23.7 1.0
CB C:ASP497 4.4 18.9 1.0
CA C:ASP497 4.8 19.2 1.0
N C:ASP497 4.9 16.9 1.0
O1 C:GOL5 5.0 28.9 1.0

Reference:

W.Xu, H.Yang, Y.Liu, Y.Yang, P.Wang, S.-H.Kim, S.Ito, C.Yang, P.Wang, M.-T.Xiao, L.-X.Liu, W.-Q.Jiang, J.Liu, J.-Y.Zhang, B.Wang, S.Frye, Y.Zhang, Y.-H.Xu, Q.-Y.Lei, K.-L.Guan, S.-M.Zhao, Y.Xiong. Oncometabolite 2-Hydroxyglutarate Is A Competitive Inhibitor of Alpha-Ketoglutarate-Dependent Dioxygenases Cancer Cell V. 19 17 2011.
ISSN: ISSN 1535-6108
PubMed: 21251613
DOI: 10.1016/J.CCR.2010.12.014
Page generated: Sun Dec 13 15:18:19 2020

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