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Iron in PDB 4xdp: Crystal Structure of Human KDM4C Catalytic Domain Bound to Tris

Protein crystallography data

The structure of Crystal Structure of Human KDM4C Catalytic Domain Bound to Tris, PDB code: 4xdp was solved by K.K.Swinger, P.A.Boriack-Sjodin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.42 / 2.07
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 93.870, 89.750, 98.280, 90.00, 96.31, 90.00
R / Rfree (%) 20.7 / 24.2

Other elements in 4xdp:

The structure of Crystal Structure of Human KDM4C Catalytic Domain Bound to Tris also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms
Zinc (Zn) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Human KDM4C Catalytic Domain Bound to Tris (pdb code 4xdp). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure of Human KDM4C Catalytic Domain Bound to Tris, PDB code: 4xdp:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 4xdp

Go back to Iron Binding Sites List in 4xdp
Iron binding site 1 out of 2 in the Crystal Structure of Human KDM4C Catalytic Domain Bound to Tris


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Human KDM4C Catalytic Domain Bound to Tris within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:16.0
occ:1.00
NE2 A:HIS278 1.9 16.8 1.0
NE2 A:HIS190 1.9 17.1 1.0
O2 A:TRS403 2.0 21.3 1.0
OE2 A:GLU192 2.0 16.8 1.0
O3 A:TRS403 2.0 19.8 1.0
O1 A:TRS403 2.1 19.8 1.0
CE1 A:HIS278 2.8 16.2 1.0
CE1 A:HIS190 2.8 16.4 1.0
CD2 A:HIS190 3.0 16.7 1.0
CD2 A:HIS278 3.0 15.6 1.0
CD A:GLU192 3.0 15.7 1.0
C2 A:TRS403 3.2 22.6 1.0
C3 A:TRS403 3.2 21.1 1.0
C1 A:TRS403 3.3 21.5 1.0
C A:TRS403 3.4 21.9 1.0
OE1 A:GLU192 3.4 16.1 1.0
ND1 A:HIS278 3.9 15.7 1.0
ND1 A:HIS190 3.9 16.1 1.0
CG A:HIS190 4.1 16.2 1.0
CG A:HIS278 4.1 15.1 1.0
O A:HOH610 4.2 19.9 1.0
CG A:GLU192 4.3 15.5 1.0
OG A:SER198 4.4 15.6 1.0
NZ A:LYS243 4.7 23.0 1.0
CG2 A:THR272 4.9 12.8 1.0
N A:TRS403 4.9 23.0 1.0
OG1 A:THR272 5.0 13.0 1.0

Iron binding site 2 out of 2 in 4xdp

Go back to Iron Binding Sites List in 4xdp
Iron binding site 2 out of 2 in the Crystal Structure of Human KDM4C Catalytic Domain Bound to Tris


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Human KDM4C Catalytic Domain Bound to Tris within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe402

b:20.9
occ:1.00
NE2 B:HIS278 1.9 22.7 1.0
NE2 B:HIS190 1.9 25.0 1.0
O3 B:TRS403 2.0 27.0 1.0
O1 B:TRS403 2.0 25.4 1.0
OE2 B:GLU192 2.0 26.1 1.0
O2 B:TRS403 2.1 24.9 1.0
CE1 B:HIS278 2.7 21.7 1.0
CE1 B:HIS190 2.8 23.9 1.0
CD2 B:HIS190 3.0 24.4 1.0
CD B:GLU192 3.0 23.9 1.0
C1 B:TRS403 3.0 26.5 1.0
CD2 B:HIS278 3.0 20.7 1.0
C2 B:TRS403 3.1 25.8 1.0
C3 B:TRS403 3.1 29.4 1.0
C B:TRS403 3.2 27.2 1.0
OE1 B:GLU192 3.4 24.4 1.0
ND1 B:HIS278 3.9 20.4 1.0
ND1 B:HIS190 3.9 23.3 1.0
CG B:HIS190 4.1 23.3 1.0
CG B:HIS278 4.1 19.5 1.0
CG B:GLU192 4.3 23.3 1.0
OG B:SER198 4.4 21.1 1.0
N B:TRS403 4.6 28.6 1.0
CG2 B:THR272 4.8 17.4 1.0

Reference:

T.J.Wigle, K.K.Swinger, J.E.Campbell, M.D.Scholle, J.Sherrill, E.A.Admirand, P.A.Boriack-Sjodin, K.W.Kuntz, R.Chesworth, M.P.Moyer, M.P.Scott, R.A.Copeland. A High-Throughput Mass Spectrometry Assay Coupled with Redox Activity Testing Reduces Artifacts and False Positives in Lysine Demethylase Screening. J Biomol Screen 2015.
ISSN: ESSN 1552-454X
PubMed: 25755264
DOI: 10.1177/1087057115575689
Page generated: Sun Dec 13 15:51:47 2020

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