Structure of PDB 7nkx Chain B

Receptor sequence

>7nkxB (length=1116) Species: 4932 (Saccharomyces cerevisiae)

DESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTL
IISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKKVFI
GRLPIMLRSKNCYLSEATESDLYKLKECPFDMGGYFIINGSEKVLIAQER
SAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKLYGREGSSAR
TIKATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKPC
VEDGFVIQDRETALDFIGRRGTALGIKKEKRIQYAKDILQKEFLPHITQL
EGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLF
KTLFKKLTKDIFRYMQRTVELAINAKTITSGLKYALATGNWGEQKKAMSS
RAGVSQVLNRYTYSSTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPA
ETPEGQACGLVKNLSLMSCISVGTDPMPIITFLSEWGMEPLEDYVPHQSP
DATRVFVNGVWHGVHRNPARLMETLRTLRRKGDINPEVSMIRDIREKELK
IFTDAGRVYRPLFIVEDDESLGHKELKVRKGHIAKLMATEYQDEYTWSSL
LNEGLVEYIDAEEEESILIAMQPEDLEPVDPAKRIRVSHHATTFTHCEIH
PSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMAN
ILYYPQKPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQS
SIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLD
DDGLIAPGVRVSGEDVIIGKTTPISSKRDASTPLRSTENGIVDQVLVTTN
QDGLKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIV
PDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISK
LLREHGYQSRGFEVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARA
RGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASDA
FRVHICGICGLMTVIAKLNHNQFECKGCDNKIDIYQIHIPYAAKLLFQEL
MAMNITPRLYTDRSRD

3D structure

• PDB: 7nkx Structural basis of nucleosome transcription mediated by Chd1 and FACT.
• Chain: B
• Resolution: 2.9 Å

Enzymatic activity

• Enzyme Commision number: 2.7.7.6: DNA-directed RNA polymerase.

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	B	Y459 A462 K470 K471 T791 R857 R942 R1122 R1129 M1133	Y384 A387 K395 K396 T697 R763 R835 R1015 R1022 M1026
BS02	dna	B	R398 K507	R331 K432
BS03	rna	B	Q481 P528 E529 Q776 R884 K987 H1097 P1110 M1111 R1124	Q406 P453 E454 Q682 R790 K880 H990 P1003 M1004 R1017
BS04	ZN	B	C1163 C1166 C1182 C1185	C1056 C1059 C1075 C1078

Gene Ontology

Molecular Function

• GO:0001055 RNA polymerase II activity
• GO:0003677 DNA binding
• GO:0003729 mRNA binding
• GO:0003899 DNA-directed 5'-3' RNA polymerase activity
• GO:0003968 RNA-dependent RNA polymerase activity
• GO:0005515 protein binding
• GO:0008270 zinc ion binding
• GO:0016779 nucleotidyltransferase activity
• GO:0032549 ribonucleoside binding
• GO:0034062 5'-3' RNA polymerase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0001172 RNA-templated transcription
• GO:0006351 DNA-templated transcription
• GO:0006366 transcription by RNA polymerase II
• GO:0006367 transcription initiation at RNA polymerase II promoter
• GO:0006368 transcription elongation by RNA polymerase II

Cellular Component

• GO:0000428 DNA-directed RNA polymerase complex
• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005665 RNA polymerase II, core complex
• GO:0005739 mitochondrion
• GO:0010494 cytoplasmic stress granule

External links

• PDB: RCSB:7nkx, PDBe:7nkx, PDBj:7nkx
• PDBsum: 7nkx
• PubMed: 33846633
• UniProt: P08518|RPB2_YEAST DNA-directed RNA polymerase II subunit RPB2 (Gene Name=RPB2)