3PU8: PHF2 Jumonji-NOG-Fe(II) complex

PHF2 Jumonji-NOG-Fe(II) complex. Determined by X-ray diffraction at 1.94 Å resolution. Released 26 Jan 2011.

Method: X-ray diffraction
Resolution: 1.94 Å
Organism: Homo sapiens
Chains: 2
Atoms: 6,256
Mol. weight: 91.47 kDa
Ligands: FE, OGA, OXY
Released: 26 Jan 2011

Explore 3PU8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3PU8 contains 45 α-helices and 32 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 21 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	87-94	8
β-strand	100	1	4
α-helix	101-103	3
β-strand	106-107	2	5
α-helix	110-112	3
α-helix	115-121	7
β-strand	127-129	3	5
β-strand	138	1	6
α-helix	146-153	8
β-strand	158-163	6	5
β-strand	168-173	6	5
α-helix	174-181	8
β-strand	190-196	7	5
α-helix	201-205	5
β-strand	207	1	6
α-helix	210-215	6
α-helix	217-221	5
α-helix	229-231	3
β-strand	236-240	5	5
β-strand	244-249	6	4
α-helix	252-254	3
β-strand	256-263	8	5
β-strand	266-271	6	4
α-helix	275-286	12
α-helix	290-292	3
α-helix	295-298	4
β-strand	303-307	5	4
β-strand	312-315	4	5
β-strand	320-325	6	4
β-strand	329-336	8	5
α-helix	342-355	14
α-helix	366-387	22
α-helix	390-392	3
α-helix	393-409	17
α-helix	415-419	5
α-helix	422-423	2
α-helix	428-442	15

Chain B: 24 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	81-83	3
α-helix	87-95	9
β-strand	100	1	1
α-helix	101-103	3
β-strand	106-107	2	2
α-helix	110-112	3
α-helix	115-121	7
β-strand	127-129	3	2
β-strand	138	1	3
α-helix	146-153	8
β-strand	158-163	6	2
β-strand	168-173	6	2
α-helix	174-181	8
β-strand	190-196	7	2
α-helix	201-205	5
β-strand	207	1	3
α-helix	210-215	6
α-helix	217-221	5
α-helix	229-231	3
β-strand	236-240	5	2
β-strand	244-249	6	1
α-helix	252-254	3
β-strand	256-263	8	2
β-strand	265-271	7	1
α-helix	275-286	12
α-helix	290-292	3
α-helix	295-298	4
β-strand	303-308	6	1
β-strand	312-315	4	2
β-strand	320-325	6	1
β-strand	329-336	8	2
α-helix	339-341	3
α-helix	342-355	14
α-helix	366-387	22
α-helix	390-392	3
α-helix	393-410	18
α-helix	415-418	4
α-helix	419-421	3
α-helix	422-423	2
α-helix	428-443	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
PHD finger protein 2	A, B	protein	392	Homo sapiens	O75151 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3PU8_1 PHD finger protein 2 (chains A, B)
STLKKKRTWHKHGPGQAPDVKPVQNGSQLFIKELRSRTFPSAEDVVARVPGSQLTLGYME
EHGFTEPILVPKKDGLGLAVPAPTFYVSDVENYVGPERSVDVTDVTKQKDCKMKLKEFVD
YYYSTNRKRVLNVTNLEFSDTRMSSFVEPPDIVKKLSWVENYWPDDALLAKPKVTKYCLI
CVKDSYTDFHIDSGGASAWYHVLKGEKTFYLIRPASANISLYERWRSASNHSEMFFADQV
DKCYKCIVKQGQTLFIPSGWIYATLTPVDCLAFAGHFLHSLSVEMQMRAYEVERRLKLGS
LTQFPNFETACWYMGKHLLEAFKGSHKSGKQLPPHLVQGAKILNGAFRSWTKKQALAEHE
DELPEHFKPSQLIKDLAKEIRLSENASKAVRP

Ligands and cofactors

ID	Name	Formula	Copies
FE	FE (III) ion	Fe	2
OGA	N-oxalylglycine	C4 H5 N O5	2
OXY	Oxygen molecule	O2	2

Water and common crystallization additives (SO4, CL, EDO) are not listed.

Primary citation

Structural basis for human PHF2 Jumonji domain interaction with metal ions. Horton, J.R., Upadhyay, A.K., Hashimoto, H. et al. J Mol Biol (2011) 406:1-8. DOI 10.1016/j.jmb.2010.12.013 · PubMed

Other PDB entries of the same protein (UniProt O75151 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7M10 1.15 Å, PHF2 PHD Domain Complexed with Peptide From N-terminus of VRK1
3KQI 1.78 Å, crystal structure of PHF2 PHD domain complexed with H3K4Me3 peptide
3PUA 1.89 Å, PHF2 Jumonji-NOG-Ni(II)
3PU3 1.95 Å, PHF2 Jumonji domain-NOG complex
3PTR 1.95 Å, PHF2 Jumonji domain
3PUS 2.08 Å, PHF2 Jumonji-NOG-Ni(II)
8F8Y 3.06 Å, PHF2 (PHD+JMJ) in Complex with VRK1 N-Terminal Peptide
8F8Z 3.3 Å, PHF2 (PHD+JMJ) in Complex with H3 Histone N-Terminal Peptide

Browse structure collections

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