Structure of PDB 8scr Chain D

Receptor sequence

>8scrD (length=579) Species: 1422 (Geobacillus stearothermophilus) [Search protein sequence]

KMAFTLADRVTEEMLADKAALVVEVVEENYHDAPIVGIAVVNEHGRFFLR
PETALADPQFVAWLGDETKKKSMFDSKRAAVALKWKGIELCGVSFDLLLA
AYLLDPAQGVDDVAAAAKMKQYEAVRPDEAVYGKGAKRAVPDEPVLAEHL
VRKAAAIWELERPFLDELRRNEQDRLLVELEQPLSSILAEMEFAGVKVDT
KRLEQMGKELAEQLGTVEQRIYELAGQEFNINSPKQLGVILFEKLQLPVL
KKTKTGYSTSADVLEKLAPYHEIVENILHYRQLGKLQSTYIEGLLKVVRP
ATKKVHTIFNQALTQTGRLSSTEPNLQNIPIRLEEGRKIRQAFVPSESDW
LIFAADYSQIELRVLAHIAEDDNLMEAFRRDLDIHTKTAMDIFQVSEDEV
TPNMRRQAKAVNFGIVYGISDYGLAQNLNISRKEAAEFIERYFESFPGVK
RYMENIVQEAKQKGYVTTLLHRRRYLPDITSRNFNVRSFAERMAMNTPIQ
GSAADIIKKAMIDLNARLKEERLQAHLLLQVHDELILEAPKEEMERLCRL
VPEVMEQAVTLRVPLKVDYHYGSTWYDAK

3D structure

PDB

8scr Trivalent rare earth metal cofactors confer rapid NP-DNA polymerase activity

Chain

Resolution

2.0 Å

3D
structure

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Enzymatic activity

Enzyme Commision number

2.7.7.7: DNA-directed DNA 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)
BS01	dna	D	T550 K551 S555 T556 S557 A558 R578 K582 Y587 R615 Q624 N625 I626 P627 I628 R629 I657 E658 F710 V828 H829 D830 E831	T253 K254 S258 T259 S260 A261 R281 K285 Y290 R318 Q327 N328 I329 P330 I331 R332 I360 E361 F413 V531 H532 D533 E534
BS02	dna	D	N529 S530 K532 T552 G553 Y554 S585 T586 L610 T611 Q612 T613 R615 S617 S618 T619 E620 N622 G711 Y714 I716 S717 Y719 R729 R771 R789 N793 Q797	N232 S233 K235 T255 G256 Y257 S288 T289 L313 T314 Q315 T316 R318 S320 S321 T322 E323 N325 G414 Y417 I419 S420 Y422 R432 R474 R492 N496 Q500
BS03	DGT	D	R615 Y654 Q656 I657 E658 H682 R702 K706 F710 Y714 D830	R318 Y357 Q359 I360 E361 H385 R405 K409 F413 Y417 D533
BS04	CA	D	D653 Y654 D830	D356 Y357 D533

Gene Ontology

	Molecular Function
GO:0000166	nucleotide binding
GO:0003676	nucleic acid binding
GO:0003677	DNA binding
GO:0003887	DNA-directed DNA polymerase activity
GO:0004518	nuclease activity
GO:0008408	3'-5' exonuclease activity
GO:0046872	metal ion binding

	Biological Process
GO:0006139	nucleobase-containing compound metabolic process
GO:0006260	DNA replication
GO:0006261	DNA-templated DNA replication
GO:0006281	DNA repair
GO:0006302	double-strand break repair
GO:0006974	DNA damage response
GO:0071897	DNA biosynthetic process

View graph for
Molecular Function

View graph for
Biological Process

External links

PDB	RCSB:8scr, PDBe:8scr, PDBj:8scr
PDBsum	8scr
PubMed	37883544
UniProt	D9N168

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