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Nickel in PDB 6g5x: Crystal Structure of KDM4A with Compound Yp-02-145

Protein crystallography data

The structure of Crystal Structure of KDM4A with Compound Yp-02-145, PDB code: 6g5x was solved by P.H.Malecki, D.M.Carter, U.Gohlke, E.Specker, M.Nazare, M.S.Weiss, U.Heinemann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.84 / 1.78
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 99.137, 148.615, 56.910, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 20.3

Other elements in 6g5x:

The structure of Crystal Structure of KDM4A with Compound Yp-02-145 also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of KDM4A with Compound Yp-02-145 (pdb code 6g5x). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Crystal Structure of KDM4A with Compound Yp-02-145, PDB code: 6g5x:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in 6g5x

Go back to Nickel Binding Sites List in 6g5x
Nickel binding site 1 out of 4 in the Crystal Structure of KDM4A with Compound Yp-02-145


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 KDM4A with Compound Yp-02-145 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni402

b:31.8
occ:1.00
O5 A:CIT408 2.0 34.7 1.0
N18 B:MY7406 2.1 26.6 1.0
O7 A:CIT408 2.2 33.5 1.0
O A:HOH668 2.2 35.3 1.0
N10 B:MY7406 2.2 33.9 1.0
O2 A:CIT408 2.2 30.9 1.0
C6 A:CIT408 2.7 39.0 1.0
C14 B:MY7406 2.7 31.4 1.0
N9 B:MY7406 2.8 30.8 1.0
C3 A:CIT408 2.8 34.5 1.0
C1 A:CIT408 3.1 33.6 1.0
C17 B:MY7406 3.3 32.2 1.0
C11 B:MY7406 3.4 41.6 1.0
C2 A:CIT408 3.4 37.0 1.0
O6 A:CIT408 3.9 34.0 1.0
C12 B:MY7406 4.0 38.9 1.0
C19 B:MY7406 4.0 30.9 1.0
N15 B:MY7406 4.0 30.1 1.0
O B:HOH690 4.0 35.9 1.0
C8 B:MY7406 4.1 38.5 1.0
NH2 A:ARG218 4.2 27.6 1.0
O3 A:CIT408 4.2 43.1 1.0
C16 B:MY7406 4.2 33.3 1.0
C4 A:CIT408 4.2 43.5 1.0
O1 A:CIT408 4.3 28.4 1.0
C7 B:MY7406 4.4 40.5 1.0
O B:HOH707 4.5 39.2 1.0
CD A:ARG218 4.5 31.1 1.0
C5 A:CIT408 4.7 48.5 1.0
CB B:PHE114 4.8 31.7 1.0
CG B:GLU115 4.8 40.4 1.0
CZ A:ARG218 5.0 33.2 1.0

Nickel binding site 2 out of 4 in 6g5x

Go back to Nickel Binding Sites List in 6g5x
Nickel binding site 2 out of 4 in the Crystal Structure of KDM4A with Compound Yp-02-145


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 KDM4A with Compound Yp-02-145 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni403

b:50.4
occ:0.50
O A:HOH724 2.3 53.8 1.0
NE2 A:HIS215 2.4 26.4 1.0
O A:HOH742 2.6 45.3 1.0
O B:HOH718 3.2 41.9 1.0
CE1 A:HIS215 3.2 29.8 1.0
CD2 A:HIS215 3.4 34.0 1.0
O B:HOH760 3.5 50.9 1.0
O A:HOH746 3.5 42.4 1.0
O A:HOH521 4.2 36.1 1.0
OE1 A:GLU214 4.2 31.6 1.0
O B:HOH707 4.4 39.2 1.0
ND1 A:HIS215 4.4 26.3 1.0
CG A:HIS215 4.5 29.0 1.0
C19 B:MY7406 5.0 30.9 1.0
C20 B:MY7406 5.0 41.6 1.0

Nickel binding site 3 out of 4 in 6g5x

Go back to Nickel Binding Sites List in 6g5x
Nickel binding site 3 out of 4 in the Crystal Structure of KDM4A with Compound Yp-02-145


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of KDM4A with Compound Yp-02-145 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni404

b:26.0
occ:1.00
OE1 A:GLU190 2.1 23.7 1.0
NE2 A:HIS188 2.1 25.7 1.0
NE2 A:HIS276 2.1 21.7 1.0
O4 A:CIT407 2.2 24.6 1.0
O A:HOH588 2.2 23.9 1.0
O A:HOH506 2.3 27.4 1.0
CE1 A:HIS188 3.0 27.5 1.0
CE1 A:HIS276 3.0 22.5 1.0
CD A:GLU190 3.1 25.3 1.0
C5 A:CIT407 3.1 29.0 1.0
CD2 A:HIS188 3.2 22.6 1.0
CD2 A:HIS276 3.2 23.2 1.0
O3 A:CIT407 3.3 30.1 1.0
OE2 A:GLU190 3.4 22.9 1.0
ND1 A:HIS188 4.1 21.4 1.0
O A:HOH624 4.1 41.5 1.0
ND1 A:HIS276 4.2 23.2 1.0
CG A:HIS188 4.2 22.4 1.0
O A:HOH597 4.3 37.4 1.0
CG A:HIS276 4.3 25.2 1.0
OG A:SER196 4.4 26.4 1.0
CG A:GLU190 4.4 22.4 1.0
C4 A:CIT407 4.5 25.4 1.0
O A:HOH683 4.8 40.8 1.0
O7 A:CIT407 5.0 33.9 1.0
CB A:SER196 5.0 24.5 1.0

Nickel binding site 4 out of 4 in 6g5x

Go back to Nickel Binding Sites List in 6g5x
Nickel binding site 4 out of 4 in the Crystal Structure of KDM4A with Compound Yp-02-145


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of KDM4A with Compound Yp-02-145 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni402

b:26.3
occ:1.00
OE1 B:GLU190 2.0 24.9 1.0
O B:HOH503 2.1 29.6 1.0
NE2 B:HIS276 2.1 21.3 1.0
O4 B:CIT405 2.1 23.8 1.0
NE2 B:HIS188 2.2 24.7 1.0
O B:HOH580 2.2 24.6 1.0
CE1 B:HIS276 3.0 25.0 1.0
C5 B:CIT405 3.0 29.4 1.0
CE1 B:HIS188 3.0 25.6 1.0
CD B:GLU190 3.1 27.3 1.0
O3 B:CIT405 3.1 37.3 1.0
CD2 B:HIS188 3.2 25.6 1.0
CD2 B:HIS276 3.2 24.9 1.0
OE2 B:GLU190 3.4 24.7 1.0
O B:HOH659 4.0 37.7 1.0
ND1 B:HIS188 4.1 24.1 1.0
ND1 B:HIS276 4.1 22.8 1.0
O B:HOH615 4.2 40.8 1.0
CG B:HIS188 4.3 20.4 1.0
CG B:HIS276 4.3 21.9 1.0
C4 B:CIT405 4.4 22.3 1.0
CG B:GLU190 4.4 22.7 1.0
OG B:SER196 4.5 22.7 1.0
NZ B:LYS241 4.8 97.2 1.0

Reference:

P.H.Malecki, D.M.Carter, U.Gohlke, E.Specker, M.Nazare, M.S.Weiss, U.Heinemann. Crystal Structure of KDM4A with Compound Yp-02-145 To Be Published.
Page generated: Wed Dec 16 01:51:16 2020

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