Structure of PDB 4nm6 Chain A

Receptor sequence

>4nm6A (length=407) Species: 9606 (Homo sapiens)

SCRCEGPFYTHLGAGPNVAAIREIMEERFGQKGKAIRIERVIYTGKEGKS
SQGCPIAKWVVRRSSSEEKLLCLVRERAGHTCEAAVIVILILVWEGIPLS
LADKLYSELTETLRKYGTLTNRRCALNEERTCACQGLDPETCGASFSFGC
SWSMYYNGCKFARSKIPRKFKLLGDDPKEEEKLESHLQNLSTLMAPTYKK
LAPDAYNNQIEYEHRAPECRLGLKEGRPFSGVTACLDFCAHAHRDLHNMQ
NGSTLVCTLTREDNREFGGKPEDEQLHVLPLYKVSDVDEFGSVEAQEEKK
RSGAIQVLSSFRRKVRMLAEPVKTGSDEVWSDSEQSFLDPDIGGVAVAPT
HGSILIECAKRELHATTPLKNPNRNHPTRISLVFYQHKSMNEPKHGLALW
EAKMAEK

3D structure

• PDB: 4nm6 Crystal Structure of TET2-DNA Complex: Insight into TET-Mediated 5mC Oxidation.
• Chain: A
• Resolution: 2.026 Å

Enzymatic activity

• Enzyme Commision number: 1.14.11.80: methylcytosine dioxygenase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	dna	A	R1261 R1262 S1286 S1290 Y1294 K1299 S1303 D1384 Y1902 H1904	R122 R123 S147 S151 Y155 K160 S164 D245 Y385 H387	PDBbind-CN: Kd=1.07uM
BS02	dna	A	W1291 M1293 Y1294 N1296	W152 M154 Y155 N157	PDBbind-CN: Kd=1.07uM
BS03	ZN	A	C1193 C1271 C1273 H1380	C54 C132 C134 H241
BS04	ZN	A	C1135 H1219 C1221	C4 H80 C82
BS05	ZN	A	C1289 C1298 C1358 H1912	C150 C159 C219 H395
BS06	FE2	A	H1382 D1384 H1881	H243 D245 H364

Gene Ontology

Molecular Function

• GO:0070579 5-methylcytosine dioxygenase activity

Biological Process

• GO:0141166 chromosomal 5-methylcytosine DNA demethylation pathway

External links

• PDB: RCSB:4nm6, PDBe:4nm6, PDBj:4nm6
• PDBsum: 4nm6
• PubMed: 24315485
• UniProt: Q6N021|TET2_HUMAN Methylcytosine dioxygenase TET2 (Gene Name=TET2)