2Z8A - JenaLib

Title :   LIGAND MIGRATION AND BINDING IN THE DIMERIC HEMOGLOBIN OF SCAPHARCA INAEQUIVALVIS: I25W WITH CO BOUND TO HEME AND IN THE PRESENCE OF 3 ATOMS OF XE

Authors :   J. E. Knapp, W. E. Royer Jr. , K. Nienhaus, P. Palladino, G. U. Nienhaus

Date :   04 Sep 07 (Deposition) - 27 Nov 07 (Release) - 24 Mar 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.06

Chains :   Asym./Biol. Unit : A,B

Keywords :   Oxygen Transport, Allostery, Oxygen Affinity, Cytoplasm, Heme, Iron, Metal-Binding, Oxygen Storage/Transport, Oxygen Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Nienhaus, J. E. Knapp, P. Palladino, W. E. Royer Jr. , G. U. Nienhaus
Ligand Migration And Binding In The Dimeric Hemoglobin Of Scapharca Inaequivalvis
Biochemistry V. 46 14018 2007
PubMed-ID: 18001141 | Reference-DOI: 10.1021/BI7016798
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 9)

Sites (8, 8)

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR B:2011 , ASP B:2013 , HOH B:9038 , HOH B:9197 , HOH B:9366 , HOH B:9379	BINDING SITE FOR RESIDUE PO4 B 5402
2	AC2	SOFTWARE	TYR A:1050 , PHE A:1051 , ARG A:1053 , HIS A:1069 , LEU A:1073 , LEU A:1077 , PHE A:1097 , ASN A:1100 , HIS A:1101 , ARG A:1104 , GLU A:1110 , PHE A:1111 , CMO A:1148 , XE A:5505 , HOH A:9012 , HOH A:9033 , HOH A:9068 , HOH A:9075 , HOH A:9076 , LYS B:2096 , ASN B:2100 , HOH B:9044	BINDING SITE FOR RESIDUE HEM A 1147
3	AC3	SOFTWARE	LYS A:1096 , ASN A:1100 , HOH A:9001 , HOH A:9069 , TYR B:2050 , PHE B:2051 , ARG B:2053 , HIS B:2069 , LEU B:2073 , PHE B:2097 , ASN B:2100 , HIS B:2101 , ARG B:2104 , GLU B:2110 , PHE B:2111 , CMO B:2148 , XE B:5506 , HOH B:9011 , HOH B:9040 , HOH B:9044 , HOH B:9110	BINDING SITE FOR RESIDUE HEM B 2147
4	AC4	SOFTWARE	MET A:1037 , PHE A:1051 , HIS A:1069 , LEU A:1073 , HEM A:1147	BINDING SITE FOR RESIDUE CMO A 1148
5	AC5	SOFTWARE	MET B:2037 , PHE B:2051 , HIS B:2069 , LEU B:2073 , HEM B:2147	BINDING SITE FOR RESIDUE CMO B 2148
6	AC6	SOFTWARE	LEU B:2077	BINDING SITE FOR RESIDUE XE B 5502
7	AC7	SOFTWARE	PHE A:1097 , PHE A:1111 , HEM A:1147	BINDING SITE FOR RESIDUE XE A 5505
8	AC8	SOFTWARE	PHE B:2097 , PHE B:2111 , HEM B:2147	BINDING SITE FOR RESIDUE XE B 5506

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Asymmetric/Biological 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
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Chain A from PDB  Type:PROTEIN  Length:145
 aligned with GLB1_ANAIN | P02213 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:145
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141     
          GLB1_ANAIN      2 SVYDAAAQLTADVKKDLRDSWKVIGSDKKGNGVALMTTLFADNQETIGYFKRLGDVSQGMANDKLRGHSITLMYALQNFIDQLDNPDDLVCVVEKFAVNHITRKISAAEFGKINGPIKKVLASKNFGDKYANAWAKLVAVVQAAL  146
               SCOP domains d2z8aa_ A: Hemoglobin I                                                                                                                           SCOP domains
               CATH domains 2z8aA00 A:1002-1146 Globins                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhh.hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh..hhhhhh.hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------GLOBIN  PDB: A:1010-1146 UniProt: 10-146                                                                                                  PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2z8a A 1002 SVYDAAAQLTADVKKDLRDSWKVWGSDKKGNGVALMTTLFADNQETIGYFKRLGDVSQGMANDKLRGHSITLMYALQNFIDQLDNPDDLVCVVEKFAVNHITRKISAAEFGKINGPIKKVLASKNFGDKYANAWAKLVAVVQAAL 1146
                                  1011      1021      1031      1041      1051      1061      1071      1081      1091      1101      1111      1121      1131      1141

Chain B from PDB  Type:PROTEIN  Length:146
 aligned with GLB1_ANAIN | P02213 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140      
          GLB1_ANAIN      1 PSVYDAAAQLTADVKKDLRDSWKVIGSDKKGNGVALMTTLFADNQETIGYFKRLGDVSQGMANDKLRGHSITLMYALQNFIDQLDNPDDLVCVVEKFAVNHITRKISAAEFGKINGPIKKVLASKNFGDKYANAWAKLVAVVQAAL  146
               SCOP domains d2z8ab_ B: Hemoglobin I                                                                                                                            SCOP domains
               CATH domains 2z8aB00 B:2001-2146 Globins                                                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh.hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...hhhhhh.hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------GLOBIN  PDB: B:2010-2146 UniProt: 10-146                                                                                                  PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2z8a B 2001 PSVYDAAAQLTADVKKDLRDSWKVWGSDKKGNGVALMTTLFADNQETIGYFKRLGDVSQGMANDKLRGHSITLMYALQNFIDQLDNPDDLVCVVEKFAVNHITRKISAAEFGKINGPIKKVLASKNFGDKYANAWAKLVAVVQAAL 2146
                                  2010      2020      2030      2040      2050      2060      2070      2080      2090      2100      2110      2120      2130      2140

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	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, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (GLB1_ANAIN | P02213)

molecular function
	GO:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0019825	oxygen binding	Interacting selectively and non-covalently with oxygen (O2).
	GO:0005344	oxygen transporter activity	Enables the directed movement of oxygen into, out of or within a cell, or between cells.
biological process
	GO:0015671	oxygen transport	The directed movement of oxygen (O2) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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