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Nickel in PDB 3pus: PHF2 Jumonji-Nog-Ni(II)

Protein crystallography data

The structure of PHF2 Jumonji-Nog-Ni(II), PDB code: 3pus was solved by J.R.Horton, A.K.Upadhyay, H.Hashimoto, X.Zhang, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.53 / 2.08
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 65.353, 96.979, 66.194, 90.00, 89.78, 90.00
R / Rfree (%) 17.5 / 23.2

Nickel Binding Sites:

The binding sites of Nickel atom in the PHF2 Jumonji-Nog-Ni(II) (pdb code 3pus). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the PHF2 Jumonji-Nog-Ni(II), PDB code: 3pus:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 3pus

Go back to Nickel Binding Sites List in 3pus
Nickel binding site 1 out of 2 in the PHF2 Jumonji-Nog-Ni(II)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of PHF2 Jumonji-Nog-Ni(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni452

b:31.6
occ:1.00
O2 A:OGA453 2.1 45.0 1.0
NE2 A:HIS249 2.1 21.5 1.0
OD1 A:ASP251 2.2 27.6 1.0
O2' A:OGA453 2.3 26.0 1.0
OH A:TYR321 2.4 22.2 1.0
O A:HOH500 2.5 42.1 1.0
C1 A:OGA453 2.8 44.8 1.0
C2 A:OGA453 2.8 39.5 1.0
CD2 A:HIS249 3.0 22.9 1.0
CG A:ASP251 3.1 31.1 1.0
CE1 A:HIS249 3.2 22.7 1.0
CZ A:TYR321 3.2 24.2 1.0
OD2 A:ASP251 3.2 34.0 1.0
CE1 A:TYR321 3.9 27.4 1.0
O1 A:OGA453 4.0 40.7 1.0
CE2 A:TYR321 4.1 21.9 1.0
N1 A:OGA453 4.2 37.7 1.0
CG A:HIS249 4.2 24.7 1.0
ND1 A:HIS249 4.3 24.8 1.0
O A:HOH543 4.4 45.4 1.0
CB A:ASP251 4.5 28.3 1.0
CE1 A:HIS335 4.6 30.7 1.0
CA A:ASP251 4.8 28.1 1.0
O A:HOH515 4.9 51.6 1.0
C4 A:OGA453 4.9 34.8 1.0

Nickel binding site 2 out of 2 in 3pus

Go back to Nickel Binding Sites List in 3pus
Nickel binding site 2 out of 2 in the PHF2 Jumonji-Nog-Ni(II)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of PHF2 Jumonji-Nog-Ni(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni1

b:30.9
occ:1.00
NE2 B:HIS249 2.1 23.5 1.0
O2 B:OGA453 2.2 44.2 1.0
OD1 B:ASP251 2.2 26.2 1.0
OH B:TYR321 2.3 33.0 1.0
O2' B:OGA453 2.3 31.7 1.0
O B:HOH486 2.5 37.6 1.0
C1 B:OGA453 2.9 43.5 1.0
C2 B:OGA453 2.9 39.6 1.0
CD2 B:HIS249 3.0 29.1 1.0
CZ B:TYR321 3.1 30.9 1.0
CG B:ASP251 3.1 31.0 1.0
CE1 B:HIS249 3.2 28.8 1.0
OD2 B:ASP251 3.3 35.2 1.0
CE1 B:TYR321 3.8 30.0 1.0
CE2 B:TYR321 4.0 27.0 1.0
O1 B:OGA453 4.1 42.4 1.0
CG B:HIS249 4.2 28.7 1.0
ND1 B:HIS249 4.2 32.0 1.0
N1 B:OGA453 4.3 45.1 1.0
CB B:ASP251 4.5 29.1 1.0
CE1 B:HIS335 4.8 34.8 1.0
CA B:ASP251 4.8 30.4 1.0
C4 B:OGA453 4.9 43.5 1.0
CD1 B:TYR321 5.0 23.8 1.0

Reference:

J.R.Horton, A.K.Upadhyay, H.Hashimoto, X.Zhang, X.Cheng. Structural Basis For Human PHF2 Jumonji Domain Interaction with Metal Ions. J.Mol.Biol. V. 406 1 2011.
ISSN: ISSN 0022-2836
PubMed: 21167174
DOI: 10.1016/J.JMB.2010.12.013
Page generated: Fri Sep 25 08:31:56 2020
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