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(-) Description

Title :  TERANRY COMPLEX OF HUMAN DNA POLYMERASE IOTA R96G INSERTING DCMPNPP OPPOSITE TEMPLATE G IN THE PRESENCE OF MN2+
 
Authors :  J. Y. Choi, A. Patra, M. Yeom, Y. S. Lee, Q. Zhang, M. Egli, F. P. Guengeric
Date :  11 Jul 16  (Deposition) - 31 Aug 16  (Release) - 19 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,P,T
Keywords :  Dna Polymerase, Poli, R96G, Manganese, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Y. Choi, A. Patra, M. Yeom, Y. S. Lee, Q. Zhang, M. Egli, F. P. Guengerich
Kinetic And Structural Impact Of Metal Ions And Genetic Variations On Human Dna Polymerase Iota.
J. Biol. Chem. V. 291 21063 2016
PubMed-ID: 27555320  |  Reference-DOI: 10.1074/JBC.M116.748285

(-) Compounds

Molecule 1 - DNA (5'-D(*CP*TP*GP*GP*GP*GP*TP*CP*CP*T)-3')
    Chains: T
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 2 - DNA (5'-D(P*AP*GP*GP*AP*CP*CP*C)-3')
    Chains: P
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA POLYMERASE IOTA
    Chains: A
    EC Number: 2.7.7.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1-445
    Gene: POLI, RAD30B
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ETA2,RAD30 HOMOLOG B

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : APT

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
10KX1Ligand/Ion2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]CYTIDINE
2MN2Ligand/IonMANGANESE (II) ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:59 , ASP A:151 , GLU A:152 , 0KX A:501 , MN A:502 , DC P:873binding site for residue MN P 901
2AC2SOFTWAREASP A:59 , LEU A:60 , ASP A:61 , CYS A:62 , PHE A:63 , TYR A:64 , VAL A:89 , THR A:90 , LYS A:102 , ASP A:151 , LYS A:239 , MN A:502 , DC P:873 , MN P:901 , DG T:840 , DG T:841binding site for residue 0KX A 501
3AC3SOFTWAREASP A:59 , LEU A:60 , ASP A:151 , 0KX A:501 , MN P:901binding site for residue MN A 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5KT5)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Lys A:239 -Pro A:240

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5KT5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5KT5)

(-) Exons   (0, 0)

(no "Exon" information available for 5KT5)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:379
                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.hhhhhhhhhhhhhhh...eeeee..eeeeehhhhhhh.....eehhhhhhhh...eeee...hhhhhhhhhhhhhhhhhhh..eeee...eeeeehhhhhhhhhhhhhhhhhh......ee.hhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhh......eee.hhhhhhhhhhhh.hhhhh...hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............eeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeee...eeeeeee.hhhhhhhh...hhhhhhhhhhhhhhhhh.....eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kt5 A  51 SSRVIVHVDLDCFYAQVEMISNPELKDKPLGVQQKYLVVTCNYEAGKLGVKKLMNVRDAKEKCPQLVLVNGEDLTRYREMSYKVTELLEEFSPVVERLGFDENFVDLTEMVEKRLQQLQSDELSAVTVSGHVYNNQSINLLDVLHIRLLVGSQIAAEMREAMYNQLGLTGCAGVASNKLLAKLVSGVFKPNQQTVLLPESCQHLIHSLNHIKEIPGIGYKTAKCLEALGINSVRDLQTFSPKILEKELGISVAQRIQKLSFGEDNSPVILSGPPQSFSEEDSFKKCSSEVEAKNKIEELLASLLNRVCQDGRKPHTVRLIIRRYSGRESRQCPIPSHVIQKLGYDVMTPMVDILMKLFRNMVNVKFHLTLLSVCFCNLK 439
                                    60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370    || 385       395  ||   408       418    || 430         
                                                                                                                                                                                                                                                                                                                                                              375|              398|                  423|             
                                                                                                                                                                                                                                                                                                                                                               381               402                   426             


Chain P from PDB  Type:DNA  Length:7
                                       
                 5kt5 P 867 AGGACCC 873


Chain T from PDB  Type:DNA  Length:10
                                          
                 5kt5 T 838 CTGGGGTCCT 847
                                   847
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  - → Gap (green background, '-', border residues have a numbering label)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5KT5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5KT5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5KT5)

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)

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  2.7.7.7
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        POLI_HUMAN | Q9UNA4: 1t3n 1zet 2alz 2dpi 2dpj 2fll 2fln 2flp 2khu 2khw 2ktf 2l0f 2l0g 2mbb 3epg 3epi 3g6v 3g6x 3g6y 3gv5 3gv7 3gv8 3h40 3h4b 3h4d 3ngd 3osn 3q8p 3q8q 3q8r 3q8s 4ebc 4ebd 4ebe 4eyh 4eyi 4fs1 4fs2 5kt2 5kt3 5kt4 5kt6 5kt7 5ulw 5ulx

(-) Related Entries Specified in the PDB File

5kt2 5kt3 5kt4 5kt6 5kt7