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2ITB

CRYSTAL STRUCTURE OF A PUTATIVE TRNA-(MS(2)IO(6)A)-HYDROXYLASE (PP_2188) FROM PSEUDOMONAS PUTIDA KT2440 AT 2.05 A RESOLUTION

Functional Information from GO Data
ChainGOidnamespacecontents
A0004497molecular_functionmonooxygenase activity
A0006400biological_processtRNA modification
A0008033biological_processtRNA processing
A0045301molecular_functiontRNA-(2-methylthio-N-6-(cis-hydroxy)isopentenyl adenosine)-hydroxylase activity
A0046872molecular_functionmetal ion binding
B0004497molecular_functionmonooxygenase activity
B0006400biological_processtRNA modification
B0008033biological_processtRNA processing
B0045301molecular_functiontRNA-(2-methylthio-N-6-(cis-hydroxy)isopentenyl adenosine)-hydroxylase activity
B0046872molecular_functionmetal ion binding
Functional Information from PDB Data
site_idAC1
Number of Residues8
DetailsBINDING SITE FOR RESIDUE FE A 501
ChainResidue
AGLU38
AGLU69
AHIS72
AGLU151
AFE502
APER503
AHOH511
AHOH512

site_idAC2
Number of Residues7
DetailsBINDING SITE FOR RESIDUE FE A 502
ChainResidue
AGLU69
AGLU122
AGLU151
AHIS154
AFE501
APER503
AHOH512

site_idAC3
Number of Residues7
DetailsBINDING SITE FOR RESIDUE FE B 501
ChainResidue
BGLU38
BGLU69
BHIS72
BGLU151
BFE502
BUNL503
BHOH514

site_idAC4
Number of Residues6
DetailsBINDING SITE FOR RESIDUE FE B 502
ChainResidue
BGLU69
BGLU122
BGLU151
BHIS154
BFE501
BUNL503

site_idAC5
Number of Residues6
DetailsBINDING SITE FOR RESIDUE PER A 503
ChainResidue
AGLU38
AGLU69
AGLU122
AGLU151
AFE501
AFE502

site_idAC6
Number of Residues10
DetailsBINDING SITE FOR RESIDUE UNL B 503
ChainResidue
BCYS37
BGLU38
BALA41
BGLU69
BGLU122
BGLU151
BFE501
BFE502
BEDO510
BHOH514

site_idAC7
Number of Residues3
DetailsBINDING SITE FOR RESIDUE EDO B 504
ChainResidue
BCYS37
BHIS196
BHOH595

site_idAC8
Number of Residues7
DetailsBINDING SITE FOR RESIDUE EDO B 505
ChainResidue
BGLY12
BGLN75
BARG78
BARG82
BPHE143
BMSE183
BHOH522

site_idAC9
Number of Residues6
DetailsBINDING SITE FOR RESIDUE EDO A 504
ChainResidue
ALEU102
AARG104
AASP113
ACYS174
AHOH519
AHOH551

site_idBC1
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO B 506
ChainResidue
BASN36
BEDO513
BHOH531
BHOH567
BHOH620

site_idBC2
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO A 505
ChainResidue
AHIS55
AHOH531
BALA169
BARG173

site_idBC3
Number of Residues7
DetailsBINDING SITE FOR RESIDUE EDO A 506
ChainResidue
ATHR44
AARG100
ATHR114
AVAL117
AGLY118
AILE121
AEDO510

site_idBC4
Number of Residues6
DetailsBINDING SITE FOR RESIDUE EDO B 507
ChainResidue
BASN164
BGLY166
BASP167
AASN53
BPRO89
BHIS163

site_idBC5
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO B 508
ChainResidue
BLEU102
BARG104
BASP113
BLEU177
BHOH546

site_idBC6
Number of Residues6
DetailsBINDING SITE FOR RESIDUE EDO B 509
ChainResidue
BASP33
BASN36
BLYS40
BALA92
BGLY93
BHOH517

site_idBC7
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO B 510
ChainResidue
BTHR44
BGLU69
BGLU122
BTYR158
BUNL503

site_idBC8
Number of Residues6
DetailsBINDING SITE FOR RESIDUE EDO A 507
ChainResidue
AASP33
AASN36
ACYS37
AALA92
AGLY93
AHOH526

site_idBC9
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO B 511
ChainResidue
BGLN75
BPHE143
BGLY146
BMSE183
BGLN187

site_idCC1
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO B 512
ChainResidue
AGLU107
BARG82
BALA172
BGLU176
BARG179

site_idCC2
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO A 508
ChainResidue
ALYS35
AASN36
AHIS73
AHOH532

site_idCC3
Number of Residues3
DetailsBINDING SITE FOR RESIDUE EDO A 509
ChainResidue
AASP170
AARG173
BARG83

site_idCC4
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO B 513
ChainResidue
AILE49
AASN53
BLYS35
BHIS73
BEDO506

site_idCC5
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO A 510
ChainResidue
AGLU122
ATYR158
AEDO506
AHOH535

site_idFEA
Number of Residues10
DetailsDI-IRON METAL BINDING SITE FROM CHAIN A. A PEROXIDE ION (PER A503) WAS MODELED BRIDGING THE TWO IRON ATOMS. THE ASSIGNMENT OF THE PEROXIDE ION IS TENTATIVE AND IS BASED ON THE ENZYME FUNCTION AND THE ELECTRON DENSITY. HOWEVER, WE DON'T HAVE SPECTROSCOPIC DATA AT THIS TIME.
ChainResidue
AGLU38
AHOH512
AGLU69
AHIS72
AGLU122
AHIS154
AFE501
AFE502
APER503
AHOH511

site_idFEB
Number of Residues10
DetailsDI-IRON METAL BINDING SITE FROM CHAIN B. NOTE THAT SITE FEB DIFFERS FROM SITE FEA. THE DENSITY FOR THE MODELED UNKNOWN LIAGND (UNL) DIFFERS FROM THE NCS DENSITY IN SITE FEA THAT WAS MODELED AS A PEROXIDE ION.
ChainResidue
BGLU38
BGLU69
BHIS72
BGLU122
BGLU151
BHIS154
BFE501
BFE502
BUNL503
BHOH514

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues10
DetailsBINDING: BINDING => ECO:0000269|PubMed:32785618, ECO:0000269|Ref.2, ECO:0007744|PDB:2ITB, ECO:0007744|PDB:6ZMA, ECO:0007744|PDB:6ZMB, ECO:0007744|PDB:6ZMC
ChainResidueDetails
AGLU38
AGLU69
AHIS72
AGLU122
AHIS154
BGLU38
BGLU69
BHIS72
BGLU122
BHIS154

site_idSWS_FT_FI2
Number of Residues2
DetailsBINDING: BINDING => ECO:0000269|PubMed:32785618, ECO:0007744|PDB:6ZMA, ECO:0007744|PDB:6ZMB, ECO:0007744|PDB:6ZMC
ChainResidueDetails
AGLU151
BGLU151

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PDB entries from 2024-06-12

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