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4H2H

Crystal structure of an enolase (mandalate racemase subgroup, target EFI-502101) from Pelagibaca bermudensis htcc2601, with bound mg and l-4-hydroxyproline betaine (betonicine)

Functional Information from GO Data
ChainGOidnamespacecontents
A0000287molecular_functionmagnesium ion binding
A0006579biological_processamino-acid betaine catabolic process
A0016853molecular_functionisomerase activity
A0016854molecular_functionracemase and epimerase activity
A0016855molecular_functionracemase and epimerase activity, acting on amino acids and derivatives
A0036361molecular_functionracemase activity, acting on amino acids and derivatives
A0046872molecular_functionmetal ion binding
B0000287molecular_functionmagnesium ion binding
B0006579biological_processamino-acid betaine catabolic process
B0016853molecular_functionisomerase activity
B0016854molecular_functionracemase and epimerase activity
B0016855molecular_functionracemase and epimerase activity, acting on amino acids and derivatives
B0036361molecular_functionracemase activity, acting on amino acids and derivatives
B0046872molecular_functionmetal ion binding
C0000287molecular_functionmagnesium ion binding
C0006579biological_processamino-acid betaine catabolic process
C0016853molecular_functionisomerase activity
C0016854molecular_functionracemase and epimerase activity
C0016855molecular_functionracemase and epimerase activity, acting on amino acids and derivatives
C0036361molecular_functionracemase activity, acting on amino acids and derivatives
C0046872molecular_functionmetal ion binding
D0000287molecular_functionmagnesium ion binding
D0006579biological_processamino-acid betaine catabolic process
D0016853molecular_functionisomerase activity
D0016854molecular_functionracemase and epimerase activity
D0016855molecular_functionracemase and epimerase activity, acting on amino acids and derivatives
D0036361molecular_functionracemase activity, acting on amino acids and derivatives
D0046872molecular_functionmetal ion binding
E0000287molecular_functionmagnesium ion binding
E0006579biological_processamino-acid betaine catabolic process
E0016853molecular_functionisomerase activity
E0016854molecular_functionracemase and epimerase activity
E0016855molecular_functionracemase and epimerase activity, acting on amino acids and derivatives
E0036361molecular_functionracemase activity, acting on amino acids and derivatives
E0046872molecular_functionmetal ion binding
F0000287molecular_functionmagnesium ion binding
F0006579biological_processamino-acid betaine catabolic process
F0016853molecular_functionisomerase activity
F0016854molecular_functionracemase and epimerase activity
F0016855molecular_functionracemase and epimerase activity, acting on amino acids and derivatives
F0036361molecular_functionracemase activity, acting on amino acids and derivatives
F0046872molecular_functionmetal ion binding
G0000287molecular_functionmagnesium ion binding
G0006579biological_processamino-acid betaine catabolic process
G0016853molecular_functionisomerase activity
G0016854molecular_functionracemase and epimerase activity
G0016855molecular_functionracemase and epimerase activity, acting on amino acids and derivatives
G0036361molecular_functionracemase activity, acting on amino acids and derivatives
G0046872molecular_functionmetal ion binding
H0000287molecular_functionmagnesium ion binding
H0006579biological_processamino-acid betaine catabolic process
H0016853molecular_functionisomerase activity
H0016854molecular_functionracemase and epimerase activity
H0016855molecular_functionracemase and epimerase activity, acting on amino acids and derivatives
H0036361molecular_functionracemase activity, acting on amino acids and derivatives
H0046872molecular_functionmetal ion binding
Functional Information from PDB Data
site_idAC1
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MG A 401
ChainResidue
AGLN161
AASP193
AGLU218
AASP241
A0XW403
AHOH550

site_idAC2
Number of Residues6
DetailsBINDING SITE FOR RESIDUE NI A 402
ChainResidue
CHOH507
EHIS235
HHIS235
AHIS235
CHIS235
CHOH505

site_idAC3
Number of Residues13
DetailsBINDING SITE FOR RESIDUE 0XW A 403
ChainResidue
ATYR20
ATYR56
ATYR134
AGLN161
ALYS163
AASP193
AASN195
AGLU218
AASP241
ALYS265
AALA294
ATRP320
AMG401

site_idAC4
Number of Residues3
DetailsBINDING SITE FOR RESIDUE IOD A 404
ChainResidue
AGLY185
AGLY187
CHOH549

site_idAC5
Number of Residues3
DetailsBINDING SITE FOR RESIDUE IOD A 405
ChainResidue
ASER246
ALEU247
AASN248

site_idAC6
Number of Residues1
DetailsBINDING SITE FOR RESIDUE IOD A 406
ChainResidue
AARG314

site_idAC7
Number of Residues1
DetailsBINDING SITE FOR RESIDUE IOD A 407
ChainResidue
AHOH663

site_idAC8
Number of Residues1
DetailsBINDING SITE FOR RESIDUE IOD A 409
ChainResidue
ALYS36

site_idAC9
Number of Residues1
DetailsBINDING SITE FOR RESIDUE IOD A 410
ChainResidue
AHIS329

site_idBC1
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MG B 401
ChainResidue
BGLN161
BASP193
BGLU218
BASP241
B0XW403
BHOH551

site_idBC2
Number of Residues6
DetailsBINDING SITE FOR RESIDUE NI B 402
ChainResidue
BHIS235
DHIS235
DHOH528
FHIS235
FHOH510
GHIS235

site_idBC3
Number of Residues14
DetailsBINDING SITE FOR RESIDUE 0XW B 403
ChainResidue
BTYR20
BTYR56
BTYR134
BSER136
BGLN161
BLYS163
BASP193
BASN195
BGLU218
BASP241
BLYS265
BALA294
BTRP320
BMG401

site_idBC4
Number of Residues3
DetailsBINDING SITE FOR RESIDUE IOD B 404
ChainResidue
BGLY185
BGLY187
FHOH566

site_idBC5
Number of Residues1
DetailsBINDING SITE FOR RESIDUE IOD B 405
ChainResidue
BARG314

site_idBC6
Number of Residues1
DetailsBINDING SITE FOR RESIDUE IOD B 407
ChainResidue
BARG88

site_idBC7
Number of Residues1
DetailsBINDING SITE FOR RESIDUE IOD B 408
ChainResidue
BHOH787

site_idBC8
Number of Residues1
DetailsBINDING SITE FOR RESIDUE IOD B 409
ChainResidue
BHIS329

site_idBC9
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MG C 401
ChainResidue
CGLN161
CASP193
CGLU218
CASP241
C0XW402
CHOH514

site_idCC1
Number of Residues14
DetailsBINDING SITE FOR RESIDUE 0XW C 402
ChainResidue
CTYR20
CVAL52
CTYR56
CTYR134
CGLN161
CLYS163
CASP193
CASN195
CGLU218
CASP241
CLYS265
CALA294
CTRP320
CMG401

site_idCC2
Number of Residues7
DetailsBINDING SITE FOR RESIDUE MPD C 403
ChainResidue
CLYS178
CGLU181
FALA146
FLYS178
FGLU181
FALA182
FHOH663

site_idCC3
Number of Residues2
DetailsBINDING SITE FOR RESIDUE IOD C 404
ChainResidue
CGLU141
CARG167

site_idCC4
Number of Residues1
DetailsBINDING SITE FOR RESIDUE IOD C 405
ChainResidue
CHOH709

site_idCC5
Number of Residues1
DetailsBINDING SITE FOR RESIDUE IOD C 406
ChainResidue
CARG314

site_idCC6
Number of Residues1
DetailsBINDING SITE FOR RESIDUE IOD C 407
ChainResidue
CARG147

site_idCC7
Number of Residues3
DetailsBINDING SITE FOR RESIDUE IOD C 410
ChainResidue
CGLY185
CGLY187
HHOH591

site_idCC8
Number of Residues1
DetailsBINDING SITE FOR RESIDUE IOD C 412
ChainResidue
CGLU141

site_idCC9
Number of Residues1
DetailsBINDING SITE FOR RESIDUE IOD C 413
ChainResidue
CHIS329

site_idDC1
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MG D 401
ChainResidue
DGLN161
DASP193
DGLU218
DASP241
D0XW402
DHOH524

site_idDC2
Number of Residues15
DetailsBINDING SITE FOR RESIDUE 0XW D 402
ChainResidue
DTYR20
DVAL52
DTYR56
DTYR134
DSER136
DGLN161
DLYS163
DASP193
DASN195
DGLU218
DASP241
DLYS265
DALA294
DTRP320
DMG401

site_idDC3
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MPD D 403
ChainResidue
CPHE224
CGLU228
DPHE224
DHOH623
DHOH631

site_idDC4
Number of Residues1
DetailsBINDING SITE FOR RESIDUE IOD D 404
ChainResidue
DARG167

site_idDC5
Number of Residues3
DetailsBINDING SITE FOR RESIDUE IOD D 405
ChainResidue
BHOH609
DGLY185
DGLY187

site_idDC6
Number of Residues1
DetailsBINDING SITE FOR RESIDUE IOD D 406
ChainResidue
DHOH638

site_idDC7
Number of Residues1
DetailsBINDING SITE FOR RESIDUE IOD D 407
ChainResidue
DARG314

site_idDC8
Number of Residues1
DetailsBINDING SITE FOR RESIDUE IOD D 408
ChainResidue
DARG88

site_idDC9
Number of Residues5
DetailsBINDING SITE FOR RESIDUE IOD D 409
ChainResidue
DPRO19
DTYR20
DARG21
DGLY138
DHOH713

site_idEC1
Number of Residues1
DetailsBINDING SITE FOR RESIDUE IOD D 410
ChainResidue
DASN17

site_idEC2
Number of Residues2
DetailsBINDING SITE FOR RESIDUE IOD D 411
ChainResidue
DILE44
DLYS113

site_idEC3
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MG E 401
ChainResidue
EGLN161
EASP193
EGLU218
EASP241
E0XW402
EHOH738

site_idEC4
Number of Residues12
DetailsBINDING SITE FOR RESIDUE 0XW E 402
ChainResidue
EVAL52
ETYR56
ETYR134
ESER136
EGLN161
ELYS163
EASP193
EGLU218
EASP241
ELYS265
EALA294
EMG401

site_idEC5
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MPD E 403
ChainResidue
EPHE224
EGLU228
EHOH616
EHOH649
FPHE224
FGLU228

site_idEC6
Number of Residues1
DetailsBINDING SITE FOR RESIDUE IOD E 404
ChainResidue
EARG167

site_idEC7
Number of Residues1
DetailsBINDING SITE FOR RESIDUE IOD E 405
ChainResidue
EARG314

site_idEC8
Number of Residues1
DetailsBINDING SITE FOR RESIDUE IOD E 406
ChainResidue
EHOH693

site_idEC9
Number of Residues1
DetailsBINDING SITE FOR RESIDUE IOD E 407
ChainResidue
EARG88

site_idFC1
Number of Residues1
DetailsBINDING SITE FOR RESIDUE IOD E 408
ChainResidue
EVAL139

site_idFC2
Number of Residues4
DetailsBINDING SITE FOR RESIDUE IOD E 409
ChainResidue
EILE44
ELYS113
EHOH710
EHOH735

site_idFC3
Number of Residues3
DetailsBINDING SITE FOR RESIDUE IOD E 410
ChainResidue
AHOH602
EGLY185
EGLY187

site_idFC4
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MG F 401
ChainResidue
FGLN161
FASP193
FGLU218
FASP241
F0XW402
FHOH571

site_idFC5
Number of Residues14
DetailsBINDING SITE FOR RESIDUE 0XW F 402
ChainResidue
FTYR20
FVAL52
FTYR56
FTYR134
FGLN161
FLYS163
FASP193
FASN195
FGLU218
FASP241
FLYS265
FALA294
FTRP320
FMG401

site_idFC6
Number of Residues1
DetailsBINDING SITE FOR RESIDUE IOD F 403
ChainResidue
FHOH667

site_idFC7
Number of Residues1
DetailsBINDING SITE FOR RESIDUE IOD F 404
ChainResidue
FARG167

site_idFC8
Number of Residues2
DetailsBINDING SITE FOR RESIDUE IOD F 406
ChainResidue
FGLY185
FGLY187

site_idFC9
Number of Residues1
DetailsBINDING SITE FOR RESIDUE IOD F 407
ChainResidue
FARG314

site_idGC1
Number of Residues2
DetailsBINDING SITE FOR RESIDUE IOD F 410
ChainResidue
FMET140
FGLU141

site_idGC2
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MG G 401
ChainResidue
GGLN161
GASP193
GGLU218
GASP241
G0XW402
GHOH517

site_idGC3
Number of Residues13
DetailsBINDING SITE FOR RESIDUE 0XW G 402
ChainResidue
GVAL52
GTYR56
GTYR134
GGLN161
GLYS163
GASP193
GASN195
GGLU218
GASP241
GLYS265
GALA294
GTRP320
GMG401

site_idGC4
Number of Residues1
DetailsBINDING SITE FOR RESIDUE IOD G 403
ChainResidue
GARG314

site_idGC5
Number of Residues1
DetailsBINDING SITE FOR RESIDUE IOD G 404
ChainResidue
GHOH614

site_idGC6
Number of Residues1
DetailsBINDING SITE FOR RESIDUE IOD G 405
ChainResidue
GARG167

site_idGC7
Number of Residues1
DetailsBINDING SITE FOR RESIDUE IOD G 406
ChainResidue
GHIS329

site_idGC8
Number of Residues2
DetailsBINDING SITE FOR RESIDUE IOD G 407
ChainResidue
GILE44
GLYS113

site_idGC9
Number of Residues1
DetailsBINDING SITE FOR RESIDUE IOD G 408
ChainResidue
GARG88

site_idHC1
Number of Residues3
DetailsBINDING SITE FOR RESIDUE IOD G 409
ChainResidue
DHOH641
GGLY185
GGLY187

site_idHC2
Number of Residues1
DetailsBINDING SITE FOR RESIDUE IOD G 410
ChainResidue
GGLU141

site_idHC3
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MG H 401
ChainResidue
HGLN161
HASP193
HGLU218
HASP241
H0XW402
HHOH515

site_idHC4
Number of Residues13
DetailsBINDING SITE FOR RESIDUE 0XW H 402
ChainResidue
HTYR20
HVAL52
HTYR56
HGLN161
HLYS163
HASP193
HASN195
HGLU218
HASP241
HLYS265
HALA294
HTRP320
HMG401

site_idHC5
Number of Residues1
DetailsBINDING SITE FOR RESIDUE IOD H 403
ChainResidue
HARG314

site_idHC6
Number of Residues1
DetailsBINDING SITE FOR RESIDUE IOD H 404
ChainResidue
HHOH645

site_idHC7
Number of Residues1
DetailsBINDING SITE FOR RESIDUE IOD H 405
ChainResidue
HARG167

site_idHC8
Number of Residues2
DetailsBINDING SITE FOR RESIDUE IOD H 406
ChainResidue
HMET140
HGLU141

site_idHC9
Number of Residues3
DetailsBINDING SITE FOR RESIDUE IOD H 408
ChainResidue
EHOH591
HGLY185
HGLY187

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues16
DetailsACT_SITE: Proton donor/acceptor => ECO:0000250
ChainResidueDetails
ALYS163
ELYS265
FLYS163
FLYS265
GLYS163
GLYS265
HLYS163
HLYS265
ALYS265
BLYS163
BLYS265
CLYS163
CLYS265
DLYS163
DLYS265
ELYS163

site_idSWS_FT_FI2
Number of Residues48
DetailsBINDING:
ChainResidueDetails
ATYR56
BGLU218
BASP241
BALA294
CTYR56
CGLN161
CASP193
CGLU218
CASP241
CALA294
DTYR56
AGLN161
DGLN161
DASP193
DGLU218
DASP241
DALA294
ETYR56
EGLN161
EASP193
EGLU218
EASP241
AASP193
EALA294
FTYR56
FGLN161
FASP193
FGLU218
FASP241
FALA294
GTYR56
GGLN161
GASP193
AGLU218
GGLU218
GASP241
GALA294
HTYR56
HGLN161
HASP193
HGLU218
HASP241
HALA294
AASP241
AALA294
BTYR56
BGLN161
BASP193

Catalytic Information from CSA
site_idMCSA1
Number of Residues6
DetailsM-CSA 940
ChainResidueDetails
ALYS163proton shuttle (general acid/base)
AASP193metal ligand
AGLU218metal ligand
AASP241metal ligand
ALYS265proton shuttle (general acid/base)
ATRP320electrostatic stabiliser

site_idMCSA2
Number of Residues6
DetailsM-CSA 940
ChainResidueDetails
BLYS163proton shuttle (general acid/base)
BASP193metal ligand
BGLU218metal ligand
BASP241metal ligand
BLYS265proton shuttle (general acid/base)
BTRP320electrostatic stabiliser

site_idMCSA3
Number of Residues6
DetailsM-CSA 940
ChainResidueDetails
CLYS163proton shuttle (general acid/base)
CASP193metal ligand
CGLU218metal ligand
CASP241metal ligand
CLYS265proton shuttle (general acid/base)
CTRP320electrostatic stabiliser

site_idMCSA4
Number of Residues6
DetailsM-CSA 940
ChainResidueDetails
DLYS163proton shuttle (general acid/base)
DASP193metal ligand
DGLU218metal ligand
DASP241metal ligand
DLYS265proton shuttle (general acid/base)
DTRP320electrostatic stabiliser

site_idMCSA5
Number of Residues6
DetailsM-CSA 940
ChainResidueDetails
ELYS163proton shuttle (general acid/base)
EASP193metal ligand
EGLU218metal ligand
EASP241metal ligand
ELYS265proton shuttle (general acid/base)
ETRP320electrostatic stabiliser

site_idMCSA6
Number of Residues6
DetailsM-CSA 940
ChainResidueDetails
FLYS163proton shuttle (general acid/base)
FASP193metal ligand
FGLU218metal ligand
FASP241metal ligand
FLYS265proton shuttle (general acid/base)
FTRP320electrostatic stabiliser

site_idMCSA7
Number of Residues6
DetailsM-CSA 940
ChainResidueDetails
GLYS163proton shuttle (general acid/base)
GASP193metal ligand
GGLU218metal ligand
GASP241metal ligand
GLYS265proton shuttle (general acid/base)
GTRP320electrostatic stabiliser

site_idMCSA8
Number of Residues6
DetailsM-CSA 940
ChainResidueDetails
HLYS163proton shuttle (general acid/base)
HASP193metal ligand
HGLU218metal ligand
HASP241metal ligand
HLYS265proton shuttle (general acid/base)
HTRP320electrostatic stabiliser

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PDB entries from 2024-07-10

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