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4MDZ

Crystal structure of a HD-GYP domain (a cyclic-di-GMP phosphodiesterase) containing a tri-nuclear metal centre

Functional Information from GO Data
ChainGOidnamespacecontents
A0000166molecular_functionnucleotide binding
A0016787molecular_functionhydrolase activity
A0046872molecular_functionmetal ion binding
B0000166molecular_functionnucleotide binding
B0016787molecular_functionhydrolase activity
B0046872molecular_functionmetal ion binding
Functional Information from PDB Data
site_idAC1
Number of Residues7
DetailsBINDING SITE FOR RESIDUE FE A 401
ChainResidue
AASP222
AHIS250
AHIS276
AHIS277
AFE402
ASIN404
AHOH501

site_idAC2
Number of Residues8
DetailsBINDING SITE FOR RESIDUE FE A 402
ChainResidue
ALYS225
AFE401
AFE403
ASIN404
ASIN405
AHOH501
AGLU185
AASP222

site_idAC3
Number of Residues8
DetailsBINDING SITE FOR RESIDUE FE A 403
ChainResidue
AGLU185
AHIS189
AHIS221
AASP222
AASP305
AFE402
ASIN405
AHOH508

site_idAC4
Number of Residues10
DetailsBINDING SITE FOR RESIDUE SIN A 404
ChainResidue
AASP222
ALYS225
ALYS238
AHIS250
AHIS277
ATYR285
AFE401
AFE402
AHOH501
AHOH509

site_idAC5
Number of Residues10
DetailsBINDING SITE FOR RESIDUE SIN A 405
ChainResidue
AGLU185
ALYS238
AASP305
AALA309
AFE402
AFE403
AHOH501
AHOH506
AHOH507
AHOH510

site_idAC6
Number of Residues12
DetailsBINDING SITE FOR RESIDUE SIN A 406
ChainResidue
ASER176
AHIS177
ATHR179
ALYS180
AASP183
AGLU185
AILE190
AASP222
AHOH503
AHOH504
AHOH508
AHOH511

site_idAC7
Number of Residues10
DetailsBINDING SITE FOR RESIDUE SIN A 407
ChainResidue
AGLU275
AGLU278
ATRP280
AILE294
AGLY298
AARG299
ASER302
AHIS336
APHE337
AASP338

site_idAC8
Number of Residues12
DetailsBINDING SITE FOR RESIDUE SIN A 408
ChainResidue
ALYS182
ALYS225
AVAL226
AASP230
AHOH530
AHOH531
BLYS182
BLYS225
BVAL226
BLEU233
BHOH536
BHOH541

site_idAC9
Number of Residues5
DetailsBINDING SITE FOR RESIDUE FE B 401
ChainResidue
BASP222
BHIS250
BHIS276
BHIS277
BHOH546

site_idBC1
Number of Residues15
DetailsBINDING SITE FOR RESIDUE C2E B 402
ChainResidue
BLYS235
BGLY237
BLEU239
BTRP244
BHIS277
BTYR285
BASP305
BALA309
BLEU310
BARG314
BPHE328
BHIS336
BHOH502
BHOH504
BHOH511

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PDB entries from 2024-08-07

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