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(-) Description

Title :  S100Z FROM ZEBRAFISH IN COMPLEX WITH CALCIUM
 
Authors :  O. V. Moroz, I. B. Bronstein, K. S. Wilson
Date :  13 Jan 11  (Deposition) - 27 Jul 11  (Release) - 24 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.03
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Keywords :  Metal-Binding Protein, Ef-Hand, Calcium Regulation, Oligomerisation, Neuronal Development, Spine2, Structural Proteomics In Europe 2 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. V. Moroz, I. B. Bronstein, K. S. Wilson
The Crystal Structure Of Zebrafish S100Z: Implications For Calcium-Promoted S100 Protein Oligomerisation.
J. Mol. Biol. V. 411 1072 2011
PubMed-ID: 21756915  |  Reference-DOI: 10.1016/J.JMB.2011.06.048

(-) Compounds

Molecule 1 - S100 CALCIUM BINDING PROTEIN Z
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET22B
    Expression System Vector Type: PLASMID
    Organism Common: ZEBRAFISH
    Organism Scientific: DANIO RERIO
    Organism Taxid: 7955
    Synonym: S100Z

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): AB    
Biological Unit 2 (1x):   CD  
Biological Unit 3 (1x):     EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 18)

Asymmetric Unit (2, 18)
No.NameCountTypeFull Name
1CA12Ligand/IonCALCIUM ION
2IPA6Ligand/IonISOPROPYL ALCOHOL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2IPA1Ligand/IonISOPROPYL ALCOHOL
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2IPA2Ligand/IonISOPROPYL ALCOHOL
Biological Unit 3 (1, 3)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2IPA3Ligand/IonISOPROPYL ALCOHOL

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:20 , GLU A:23 , ASP A:25 , LYS A:28 , GLU A:33 , HOH A:2076BINDING SITE FOR RESIDUE CA A 101
02AC2SOFTWAREASP A:63 , ASN A:65 , ASP A:67 , GLU A:69 , GLU A:74 , HOH A:2072BINDING SITE FOR RESIDUE CA A 102
03AC3SOFTWARESER B:20 , GLU B:23 , ASP B:25 , LYS B:28 , GLU B:33 , HOH B:2077BINDING SITE FOR RESIDUE CA B 101
04AC4SOFTWAREASP B:63 , ASN B:65 , ASP B:67 , GLU B:69 , GLU B:74 , HOH B:2073BINDING SITE FOR RESIDUE CA B 102
05AC5SOFTWARESER C:20 , GLU C:23 , ASP C:25 , LYS C:28 , GLU C:33 , HOH C:2060BINDING SITE FOR RESIDUE CA C 101
06AC6SOFTWAREASP C:63 , ASN C:65 , ASP C:67 , GLU C:69 , GLU C:74 , HOH C:2055BINDING SITE FOR RESIDUE CA C 102
07AC7SOFTWARESER D:20 , GLU D:23 , ASP D:25 , LYS D:28 , GLU D:33 , HOH D:2058BINDING SITE FOR RESIDUE CA D 101
08AC8SOFTWAREASP D:63 , ASN D:65 , ASP D:67 , GLU D:69 , GLU D:74 , HOH D:2053BINDING SITE FOR RESIDUE CA D 102
09AC9SOFTWARESER E:20 , GLU E:23 , ASP E:25 , LYS E:28 , GLU E:33 , HOH E:2071BINDING SITE FOR RESIDUE CA E 101
10BC1SOFTWAREASP E:63 , ASN E:65 , ASP E:67 , GLU E:69 , GLU E:74 , HOH E:2065BINDING SITE FOR RESIDUE CA E 102
11BC2SOFTWARESER F:20 , GLU F:23 , ASP F:25 , LYS F:28 , GLU F:33 , HOH F:2056BINDING SITE FOR RESIDUE CA F 101
12BC3SOFTWAREASP F:63 , ASN F:65 , ASP F:67 , GLU F:69 , GLU F:74 , HOH F:2053BINDING SITE FOR RESIDUE CA F 102
13BC4SOFTWAREARG A:97 , HOH A:2090BINDING SITE FOR RESIDUE IPA A1100
14BC5SOFTWAREARG C:97 , HOH C:2077 , ILE E:58BINDING SITE FOR RESIDUE IPA C1100
15BC6SOFTWAREPHE B:90 , CYS D:86BINDING SITE FOR RESIDUE IPA D1100
16BC7SOFTWARECYS C:86 , HOH C:2018 , PHE E:89 , PHE E:90BINDING SITE FOR RESIDUE IPA E1099
17BC8SOFTWARECYS A:86 , PHE A:89 , CYS F:86 , PHE F:89 , PHE F:90BINDING SITE FOR RESIDUE IPA F1100
18BC9SOFTWAREILE A:58 , ARG F:97 , HOH F:2068BINDING SITE FOR RESIDUE IPA F1101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Y5I)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Y5I)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Y5I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Y5I)

(-) Exons   (0, 0)

(no "Exon" information available for 2Y5I)

(-) Sequences/Alignments

Asymmetric 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:97
 aligned with Q503K9_DANRE | Q503K9 from UniProtKB/TrEMBL  Length:99

    Alignment length:97
                                    12        22        32        42        52        62        72        82        92       
          Q503K9_DANRE    3 SKLEGAMDALITVFHNYSGSEGDKYKLSKGELKELLNAELTDFLMSQKDPMLVEKIMNDLDSNKDNEVDFNEFVVLVAALTVACNDFFQEQQKKRSK 99
               SCOP domains d2y5ia_ A: automated matches                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh......eehhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh......eehhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                  2y5i A  3 SKLEGAMDALITVFHNYSGSEGDKYKLSKGELKELLNAELTDFLMSQKDPMLVEKIMNDLDSNKDNEVDFNEFVVLVAALTVACNDFFQEQQKKRSK 99
                                    12        22        32        42        52        62        72        82        92       


Chain B from PDB  Type:PROTEIN  Length:96
 aligned with Q503K9_DANRE | Q503K9 from UniProtKB/TrEMBL  Length:99

    Alignment length:96
                                    12        22        32        42        52        62        72        82        92      
          Q503K9_DANRE    3 SKLEGAMDALITVFHNYSGSEGDKYKLSKGELKELLNAELTDFLMSQKDPMLVEKIMNDLDSNKDNEVDFNEFVVLVAALTVACNDFFQEQQKKRS 98
               SCOP domains d2y5ib_ B: automated matches                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh......eehhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh......eehhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                  2y5i B  3 SKLEGAMDALITVFHNYSGSEGDKYKLSKGELKELLNAELTDFLMSQKDPMLVEKIMNDLDSNKDNEVDFNEFVVLVAALTVACNDFFQEQQKKRS 98
                                    12        22        32        42        52        62        72        82        92      


Chain C from PDB  Type:PROTEIN  Length:98
 aligned with Q503K9_DANRE | Q503K9 from UniProtKB/TrEMBL  Length:99

    Alignment length:98
                                    11        21        31        41        51        61        71        81        91        
          Q503K9_DANRE    2 PSKLEGAMDALITVFHNYSGSEGDKYKLSKGELKELLNAELTDFLMSQKDPMLVEKIMNDLDSNKDNEVDFNEFVVLVAALTVACNDFFQEQQKKRSK 99
               SCOP domains d2y5ic_ C: automated matches                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh......eehhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh......eehhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                  2y5i C  2 PSKLEGAMDALITVFHNYSGSEGDKYKLSKGELKELLNAELTDFLMSQKDPMLVEKIMNDLDSNKDNEVDFNEFVVLVAALTVACNDFFQEQQKKRSK 99
                                    11        21        31        41        51        61        71        81        91        


Chain D from PDB  Type:PROTEIN  Length:98
 aligned with Q503K9_DANRE | Q503K9 from UniProtKB/TrEMBL  Length:99

    Alignment length:98
                                    11        21        31        41        51        61        71        81        91        
          Q503K9_DANRE    2 PSKLEGAMDALITVFHNYSGSEGDKYKLSKGELKELLNAELTDFLMSQKDPMLVEKIMNDLDSNKDNEVDFNEFVVLVAALTVACNDFFQEQQKKRSK 99
               SCOP domains d2y5id_ D: automated matches                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh......eehhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh......eehhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                  2y5i D  2 PSKLEGAMDALITVFHNYSGSEGDKYKLSKGELKELLNAELTDFLMSQKDPMLVEKIMNDLDSNKDNEVDFNEFVVLVAALTVACNDFFQEQQKKRSK 99
                                    11        21        31        41        51        61        71        81        91        


Chain E from PDB  Type:PROTEIN  Length:97
 aligned with Q503K9_DANRE | Q503K9 from UniProtKB/TrEMBL  Length:99

    Alignment length:97
                                    11        21        31        41        51        61        71        81        91       
          Q503K9_DANRE    2 PSKLEGAMDALITVFHNYSGSEGDKYKLSKGELKELLNAELTDFLMSQKDPMLVEKIMNDLDSNKDNEVDFNEFVVLVAALTVACNDFFQEQQKKRS 98
               SCOP domains d2y5ie_ E: automated matches                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh......eehhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh......eehhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                  2y5i E  2 PSKLEGAMDALITVFHNYSGSEGDKYKLSKGELKELLNAELTDFLMSQKDPMLVEKIMNDLDSNKDNEVDFNEFVVLVAALTVACNDFFQEQQKKRS 98
                                    11        21        31        41        51        61        71        81        91       


Chain F from PDB  Type:PROTEIN  Length:98
 aligned with Q503K9_DANRE | Q503K9 from UniProtKB/TrEMBL  Length:99

    Alignment length:98
                                    11        21        31        41        51        61        71        81        91        
          Q503K9_DANRE    2 PSKLEGAMDALITVFHNYSGSEGDKYKLSKGELKELLNAELTDFLMSQKDPMLVEKIMNDLDSNKDNEVDFNEFVVLVAALTVACNDFFQEQQKKRSK 99
               SCOP domains d2y5if_ F: automated matches                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh......eehhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh......eehhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                  2y5i F  2 PSKLEGAMDALITVFHNYSGSEGDKYKLSKGELKELLNAELTDFLMSQKDPMLVEKIMNDLDSNKDNEVDFNEFVVLVAALTVACNDFFQEQQKKRSK 99
                                    11        21        31        41        51        61        71        81        91
   Legend:   → Mismatch (orange background)
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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  (1, 6)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Y5I)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2Y5I)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (Q503K9_DANRE | Q503K9)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

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