Structure of PDB 3f2d Chain A

Receptor sequence

>3f2dA (length=993) Species: 1462 (Geobacillus kaustophilus)

VRRLETIVEEERRVVVQGYVFDAEVSELKSGRTLLTMKITDYTNSILVKM
FSRDKEDAELMSGVKKGMWVKVRGSVQNDTFVRDLVIIANDLNEIAANER
QDTAPEGEKRVELHLHTPMSQMDAVTSVTKLIEQAKKWGHPAIAVTDHAV
VQSFPEAYSAAKKHGMKVIYGLEANIVDDPFHVTLLAQNETGLKNLFKLV
SLSHIQYFHRVPRIPRSVLVKHRDGLLVGSGCDKGELFDNVEDIARFYDF
LEVHPPDVYKPLVKDEEMIKNIIRSIVALGEKLDIPVVATGNVHYLNPED
KIYRKILIHSQGGANPLNRHELPDVYFRTTNEMLDCFSFLGPEKAKEIVV
DNTQKIASLIGDVKPIKDELYTPRIEGADEEIREMSYRRAKEIYGDPLPK
LVEERLEKELKSIIGHGFAVIYLISHKLVKKSLDDGYLVGSRGSVGSSFV
ATMTEITEVNPLPPHYVCPNCKHSEFFNDGSVGSGFDLPDKNCPRCGTKY
KKDGHDIPFETFLGFKGDKVPDIDLNFSGEYQPRAHNYTKVLFGEDNVYR
AGTIGTVADKTAYGFVKAYASDHNLELRGAEIDRLAAGCTGVKRTTGQHP
GGIIVVPDYMEIYDFTPIQYPADDTSSEWRTTHFDFHSIHDNLLKLDILG
HDDPTVIRMLQDLSGIDPKTIPTDDPDVMGIFSSTEPLGVTPEQIMCNVG
TIGIPEFGTRFVRQMLEETRPKTFSELVQISGLSHGTDVWLGNAQELIQN
GTCTLSEVIGCRDDIMVYLIYRGLEPSLAFKIMESVRKGKGLTPEFEAEM
RKHDVPEWYIDSCKKIKYMFPKAHAAAYVLMAVRIAYFKVHHPLLYYASY
FTVRAEDFDLDAMIKGSAAIRKRIEEINAKGIQATAKEKSLLTVLEVALE
MCERGFSFKNIDLYRSQATEFVIDGNSLIPPFNAIPGLGTNVAQAIVRAR
EEGEFLSKEDLQQRGKLSKTLLEYLESRGCLDSLPDHNQLSLF

3D structure

• PDB: 3f2d Structure of PolC reveals unique DNA binding and fidelity determinants.
• Chain: A
• Resolution: 2.51 Å

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)	Binding affinity
BS01	dna	A	R893 I1005 T1007 A1009 T1012 H1050 D1098 K1338 G1388 G1390	R442 I554 T556 A558 T561 H599 D647 K887 G937 G939
BS02	dna	A	Q983 R1001 Q1049 A1073 G1101 H1102 D1103 E1157 T1160 F1162 S1185 H1186 G1187 L1192 G1332 I1333 S1419 T1421	Q532 R550 Q598 A622 G650 H651 D652 E706 T709 F711 S734 H735 G736 L741 G881 I882 S968 T970
BS03	MN	A	D973 D975	D522 D524
BS04	MN	A	E405 H620 C670	E173 H182 C232
BS05	MN	A	H346 H348 E405 N743	H114 H116 E173 N292
BS06	ZN	A	C919 C922 C944 C947	C468 C471 C493 C496
BS07	ZN	A	D355 H380 H745	D123 H148 H294
BS08	DGT	A	R893 G894 S895 K970 D973 D975 R1213 Y1269 F1271 P1272 H1275	R442 G443 S444 K519 D522 D524 R762 Y818 F820 P821 H824

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0003677 DNA binding
• GO:0003824 catalytic activity
• GO:0003887 DNA-directed DNA polymerase activity
• GO:0008408 3'-5' exonuclease activity

Biological Process

• GO:0006260 DNA replication

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:3f2d, PDBe:3f2d, PDBj:3f2d
• PDBsum: 3f2d
• PubMed: 19106298
• UniProt: Q5L0J3