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6CDK

Characterization of the P1+ intermediate state of nitrogenase P-cluster

Replaces:  5IJY
Functional Information from GO Data
ChainGOidnamespacecontents
A0000166molecular_functionnucleotide binding
A0005524molecular_functionATP binding
A0009399biological_processnitrogen fixation
A0016163molecular_functionnitrogenase activity
A0016491molecular_functionoxidoreductase activity
A0016612cellular_componentmolybdenum-iron nitrogenase complex
A0046872molecular_functionmetal ion binding
A0051536molecular_functioniron-sulfur cluster binding
B0000166molecular_functionnucleotide binding
B0005524molecular_functionATP binding
B0009399biological_processnitrogen fixation
B0016163molecular_functionnitrogenase activity
B0016491molecular_functionoxidoreductase activity
B0016612cellular_componentmolybdenum-iron nitrogenase complex
B0046872molecular_functionmetal ion binding
B0051536molecular_functioniron-sulfur cluster binding
C0000166molecular_functionnucleotide binding
C0005524molecular_functionATP binding
C0009399biological_processnitrogen fixation
C0016163molecular_functionnitrogenase activity
C0016491molecular_functionoxidoreductase activity
C0016612cellular_componentmolybdenum-iron nitrogenase complex
C0046872molecular_functionmetal ion binding
C0051536molecular_functioniron-sulfur cluster binding
D0000166molecular_functionnucleotide binding
D0005524molecular_functionATP binding
D0009399biological_processnitrogen fixation
D0016163molecular_functionnitrogenase activity
D0016491molecular_functionoxidoreductase activity
D0016612cellular_componentmolybdenum-iron nitrogenase complex
D0046872molecular_functionmetal ion binding
D0051536molecular_functioniron-sulfur cluster binding
Functional Information from PDB Data
site_idAC1
Number of Residues16
Detailsbinding site for residue HCA A 501
ChainResidue
AALA65
AHOH662
AHOH663
AHOH668
AHOH700
AHOH715
AHOH716
AHOH720
AGLN191
AGLY424
AILE425
AHIS442
AICS502
AHOH634
AHOH635
AHOH650

site_idAC2
Number of Residues12
Detailsbinding site for residue ICS A 502
ChainResidue
AVAL70
AARG96
AHIS195
ATYR229
ACYS275
AGLY356
AGLY357
ALEU358
AARG359
APHE381
AHIS442
AHCA501

site_idAC3
Number of Residues12
Detailsbinding site for residue CLF A 503
ChainResidue
ACYS62
ATYR64
APRO85
AGLY87
ACYS88
ACYS154
AGLY185
BCYS70
BSER92
BCYS95
BCYS153
BSER188

site_idAC4
Number of Residues6
Detailsbinding site for residue FE B 601
ChainResidue
BASP353
BASP357
BHOH725
DARG108
DGLU109
DHOH795

site_idAC5
Number of Residues6
Detailsbinding site for residue FE B 602
ChainResidue
BARG108
BGLU109
DASP353
DASP357
DHOH819
DHOH846

site_idAC6
Number of Residues16
Detailsbinding site for residue HCA C 501
ChainResidue
CALA65
CGLN191
CGLY424
CILE425
CHIS442
CICS502
CHOH614
CHOH619
CHOH643
CHOH666
CHOH675
CHOH677
CHOH678
CHOH718
DHOH737
DHOH756

site_idAC7
Number of Residues12
Detailsbinding site for residue ICS C 502
ChainResidue
CVAL70
CARG96
CHIS195
CTYR229
CILE231
CCYS275
CGLY356
CGLY357
CARG359
CPHE381
CHIS442
CHCA501

site_idAC8
Number of Residues12
Detailsbinding site for residue CLF C 503
ChainResidue
CCYS62
CTYR64
CGLY87
CCYS88
CTYR91
CCYS154
CGLY185
DCYS70
DGLY94
DCYS95
DCYS153
DSER188

Functional Information from PROSITE/UniProt
site_idPS00090
Number of Residues15
DetailsNITROGENASE_1_2 Nitrogenases component 1 alpha and beta subunits signature 2. TTCmaeviGDDLnAF
ChainResidueDetails
BTHR151-PHE165
ASER152-VAL166

site_idPS00699
Number of Residues8
DetailsNITROGENASE_1_1 Nitrogenases component 1 alpha and beta subunits signature 1. YVHGSQGC
ChainResidueDetails
BTYR88-CYS95
AILE81-CYS88

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues18
DetailsBinding site: {}
ChainResidueDetails

Catalytic Information from CSA
site_idMCSA1
Number of Residues2
DetailsM-CSA 212
ChainResidueDetails
BCYS153metal ligand
BVAL157polar interaction, single electron acceptor, single electron donor, single electron relay
AARG96activator, hydrogen bond donor
AHIS195activator, polar interaction

site_idMCSA2
Number of Residues2
DetailsM-CSA 212
ChainResidueDetails
DCYS153metal ligand
DVAL157polar interaction, single electron acceptor, single electron donor, single electron relay
CARG96activator, hydrogen bond donor
CHIS195activator, polar interaction

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PDB entries from 2025-08-27

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