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Iron in PDB 3ldb: Structure of JMJD6 Complexd with Alpha-Ketoglutarate and Fab Fragment.

Protein crystallography data

The structure of Structure of JMJD6 Complexd with Alpha-Ketoglutarate and Fab Fragment., PDB code: 3ldb was solved by X.Hong, J.Zang, J.White, J.W.Kappler, C.Wang, G.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.28 / 2.70
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 138.381, 138.381, 183.622, 90.00, 90.00, 90.00
R / Rfree (%) 25 / 28.5

Other elements in 3ldb:

The structure of Structure of JMJD6 Complexd with Alpha-Ketoglutarate and Fab Fragment. also contains other interesting chemical elements:

Mercury (Hg) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Structure of JMJD6 Complexd with Alpha-Ketoglutarate and Fab Fragment. (pdb code 3ldb). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total only one binding site of Iron was determined in the Structure of JMJD6 Complexd with Alpha-Ketoglutarate and Fab Fragment., PDB code: 3ldb:

Iron binding site 1 out of 1 in 3ldb

Go back to Iron Binding Sites List in 3ldb
Iron binding site 1 out of 1 in the Structure of JMJD6 Complexd with Alpha-Ketoglutarate and Fab Fragment.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of JMJD6 Complexd with Alpha-Ketoglutarate and Fab Fragment. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:0.8
occ:1.00
NE2 A:HIS273 2.5 66.0 1.0
NE2 A:HIS187 2.8 94.1 1.0
CE1 A:HIS187 2.9 93.7 1.0
OD1 A:ASP189 3.0 86.8 1.0
CE1 A:HIS273 3.3 66.3 1.0
C2 A:AKG600 3.5 0.1 1.0
O5 A:AKG600 3.5 0.3 1.0
C1 A:AKG600 3.5 0.5 1.0
O2 A:AKG600 3.6 0.0 1.0
CD2 A:HIS273 3.6 64.5 1.0
CG A:ASP189 3.7 84.2 1.0
OD2 A:ASP189 3.7 86.7 1.0
CD2 A:HIS187 4.0 91.4 1.0
ND1 A:HIS187 4.1 91.8 1.0
O1 A:AKG600 4.1 0.8 1.0
C3 A:AKG600 4.2 0.6 1.0
ND1 A:HIS273 4.5 65.3 1.0
CG A:HIS187 4.7 88.8 1.0
CG A:HIS273 4.7 63.8 1.0
C4 A:AKG600 4.9 0.0 1.0

Reference:

X.Hong, J.Zang, J.White, C.Wang, C.H.Pan, R.Zhao, R.C.Murphy, S.Dai, P.Henson, J.W.Kappler, J.Hagman, G.Zhang. Interaction of JMJD6 with Single-Stranded Rna. Proc.Natl.Acad.Sci.Usa V. 107 14568 2010.
ISSN: ISSN 0027-8424
PubMed: 20679243
DOI: 10.1073/PNAS.1008832107
Page generated: Sun Dec 13 15:11:16 2020

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