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Iron in PDB 3kva: Structure of KIAA1718 Jumonji Domain in Complex with Alpha- Ketoglutarate

Protein crystallography data

The structure of Structure of KIAA1718 Jumonji Domain in Complex with Alpha- Ketoglutarate, PDB code: 3kva was solved by J.R.Horton, A.K.Upadhyay, H.H.Qi, X.Zhang, Y.Shi, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.40 / 2.79
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 78.100, 78.100, 290.800, 90.00, 90.00, 120.00
R / Rfree (%) 20.3 / 26.9

Iron Binding Sites:

The binding sites of Iron atom in the Structure of KIAA1718 Jumonji Domain in Complex with Alpha- Ketoglutarate (pdb code 3kva). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Structure of KIAA1718 Jumonji Domain in Complex with Alpha- Ketoglutarate, PDB code: 3kva:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 3kva

Go back to Iron Binding Sites List in 3kva
Iron binding site 1 out of 2 in the Structure of KIAA1718 Jumonji Domain in Complex with Alpha- Ketoglutarate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of KIAA1718 Jumonji Domain in Complex with Alpha- Ketoglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe489

b:63.5
occ:1.00
NE2 A:HIS282 2.2 33.5 1.0
O5 A:AKG701 2.3 69.6 1.0
O2 A:AKG701 2.4 71.8 1.0
NE2 A:HIS354 2.5 40.2 1.0
OD1 A:ASP284 2.6 42.4 1.0
CE1 A:HIS282 2.9 33.4 1.0
CE1 A:HIS354 3.0 38.8 1.0
OD2 A:ASP284 3.0 44.1 1.0
CG A:ASP284 3.0 41.3 1.0
C2 A:AKG701 3.1 70.5 1.0
C1 A:AKG701 3.1 71.7 1.0
CD2 A:HIS282 3.3 32.8 1.0
CD2 A:HIS354 3.6 39.0 1.0
ND1 A:HIS282 4.0 33.8 1.0
ND1 A:HIS354 4.1 38.6 1.0
CG A:HIS282 4.3 32.7 1.0
O1 A:AKG701 4.3 72.0 1.0
CB A:ASP284 4.3 37.0 1.0
CG A:HIS354 4.5 37.7 1.0
CA A:ASP284 4.5 35.1 1.0
N A:ASP284 4.6 34.2 1.0
C3 A:AKG701 4.6 68.7 1.0

Iron binding site 2 out of 2 in 3kva

Go back to Iron Binding Sites List in 3kva
Iron binding site 2 out of 2 in the Structure of KIAA1718 Jumonji Domain in Complex with Alpha- Ketoglutarate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of KIAA1718 Jumonji Domain in Complex with Alpha- Ketoglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe490

b:53.6
occ:1.00
OG A:SER249 3.2 41.4 1.0
N A:TRP250 3.2 37.7 1.0
N A:LEU370 3.2 34.9 1.0
N A:VAL251 3.2 37.5 1.0
CG2 A:VAL251 3.7 36.2 1.0
CA A:PHE369 3.8 35.5 1.0
CB A:VAL251 3.8 37.9 1.0
CA A:SER249 3.8 40.1 1.0
C A:SER249 3.8 39.0 1.0
CB A:SER249 3.9 40.6 1.0
O A:LEU370 3.9 35.2 1.0
CA A:TRP250 3.9 36.3 1.0
CB A:TRP250 3.9 34.0 1.0
C A:PHE369 4.0 35.7 1.0
C A:TRP250 4.1 36.8 1.0
CB A:LEU370 4.1 34.2 1.0
CA A:LEU370 4.1 34.7 1.0
CA A:VAL251 4.1 38.8 1.0
CB A:PHE369 4.1 35.9 1.0
CG A:LEU370 4.5 34.3 1.0
C A:LEU370 4.5 35.0 1.0
CZ A:PHE396 4.5 49.2 1.0
O A:ASN368 4.8 35.4 1.0
CE1 A:PHE396 4.8 50.1 1.0
O A:SER249 4.8 39.0 1.0
CD1 A:LEU370 4.9 32.5 1.0
N A:PHE369 5.0 35.6 1.0

Reference:

J.R.Horton, A.K.Upadhyay, H.H.Qi, X.Zhang, Y.Shi, X.Cheng. Enzymatic and Structural Insights For Substrate Specificity of A Family of Jumonji Histone Lysine Demethylases. Nat.Struct.Mol.Biol. V. 17 38 2010.
ISSN: ISSN 1545-9993
PubMed: 20023638
DOI: 10.1038/NSMB.1753
Page generated: Sun Dec 13 15:10:32 2020

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