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Nickel in PDB 4gd4: Crystal Structure of JMJD2A Complexed with Inhibitor

Protein crystallography data

The structure of Crystal Structure of JMJD2A Complexed with Inhibitor, PDB code: 4gd4 was solved by O.N.F.King, T.Krojer, C.H.Arrowsmith, A.Edwards, C.Bountra, M.A.Mcdonough, C.J.Schofield, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 83.64 / 2.33
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 100.750, 150.030, 57.490, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 21.8

Other elements in 4gd4:

The structure of Crystal Structure of JMJD2A Complexed with Inhibitor also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
Zinc (Zn) 2 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of JMJD2A Complexed with Inhibitor (pdb code 4gd4). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of JMJD2A Complexed with Inhibitor, PDB code: 4gd4:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 4gd4

Go back to Nickel Binding Sites List in 4gd4
Nickel binding site 1 out of 2 in the Crystal Structure of JMJD2A Complexed with Inhibitor


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 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni501

b:52.1
occ:1.00
NE2 A:HIS276 2.2 26.2 1.0
N A:0WS504 2.2 68.5 1.0
OE2 A:GLU190 2.2 34.2 1.0
NE2 A:HIS188 2.3 30.4 1.0
O A:HOH739 2.5 52.3 1.0
N1 A:0WS504 2.5 67.9 1.0
C6 A:0WS504 3.1 69.5 1.0
C3 A:0WS504 3.1 69.9 1.0
CE1 A:HIS276 3.1 25.9 1.0
H3 A:0WS504 3.2 66.4 1.0
C4 A:0WS504 3.2 66.2 1.0
CD2 A:HIS276 3.2 27.2 1.0
CD A:GLU190 3.2 38.3 1.0
CE1 A:HIS188 3.3 30.4 1.0
CD2 A:HIS188 3.3 29.7 1.0
OE1 A:GLU190 3.5 32.3 1.0
N2 A:0WS504 3.6 69.2 1.0
H A:0WS504 3.9 69.0 1.0
OG A:SER196 4.3 39.3 1.0
ND1 A:HIS276 4.3 28.5 1.0
CG A:HIS276 4.3 27.4 1.0
C8 A:0WS504 4.3 70.7 1.0
ND1 A:HIS188 4.4 31.2 1.0
CG A:HIS188 4.4 28.3 1.0
C2 A:0WS504 4.4 69.6 1.0
O A:HOH738 4.5 42.1 1.0
C5 A:0WS504 4.5 65.7 1.0
CG A:GLU190 4.6 30.7 1.0
C7 A:0WS504 4.6 70.5 1.0
CG2 A:THR270 4.8 28.9 1.0
OG1 A:THR270 4.9 30.9 1.0
O A:HOH719 5.0 47.4 1.0

Nickel binding site 2 out of 2 in 4gd4

Go back to Nickel Binding Sites List in 4gd4
Nickel binding site 2 out of 2 in the Crystal Structure of JMJD2A Complexed with Inhibitor


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of JMJD2A Complexed with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni501

b:54.4
occ:1.00
OE2 B:GLU190 2.2 36.4 1.0
N B:0WS506 2.2 69.0 1.0
NE2 B:HIS276 2.3 26.7 1.0
NE2 B:HIS188 2.4 31.3 1.0
N1 B:0WS506 2.6 72.2 1.0
O B:HOH728 2.7 50.0 1.0
H3 B:0WS506 3.1 66.9 1.0
C3 B:0WS506 3.1 70.5 1.0
C4 B:0WS506 3.1 66.6 1.0
CD B:GLU190 3.1 36.8 1.0
C6 B:0WS506 3.1 72.4 1.0
CE1 B:HIS276 3.2 26.2 1.0
CE1 B:HIS188 3.3 30.8 1.0
CD2 B:HIS188 3.3 30.9 1.0
CD2 B:HIS276 3.3 26.6 1.0
OE1 B:GLU190 3.4 29.0 1.0
N2 B:0WS506 3.7 74.6 1.0
H B:0WS506 4.0 75.0 1.0
OG B:SER196 4.3 41.3 1.0
O B:HOH658 4.3 47.5 1.0
ND1 B:HIS276 4.4 28.7 1.0
ND1 B:HIS188 4.4 32.0 1.0
CG B:HIS188 4.4 29.4 1.0
C2 B:0WS506 4.4 69.0 1.0
C8 B:0WS506 4.4 74.2 1.0
CG B:HIS276 4.4 26.9 1.0
C5 B:0WS506 4.4 65.7 1.0
CG B:GLU190 4.5 28.6 1.0
C7 B:0WS506 4.7 75.4 1.0
CG2 B:THR270 4.9 28.9 1.0
OG1 B:THR270 5.0 37.5 1.0
C1 B:0WS506 5.0 67.4 1.0
CB B:SER196 5.0 31.2 1.0

Reference:

O.N.F.King, T.Krojer, C.H.Arrowsmith, A.Edwards, C.Bountra, M.A.Mcdonough, C.J.Schofield, Structural Genomics Consortium (Sgc). Crystal Structure of JMJD2A Complexed with Inhibitor To Be Published.
Page generated: Wed Dec 16 01:30:14 2020

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