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2gdm

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(New page: 200px<br /> <applet load="2gdm" size="450" color="white" frame="true" align="right" spinBox="true" caption="2gdm, resolution 1.7&Aring;" /> '''LEGHEMOGLOBIN (OXY)'...)
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[[Image:2gdm.gif|left|200px]]<br />
 
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<applet load="2gdm" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="2gdm, resolution 1.7&Aring;" />
 
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'''LEGHEMOGLOBIN (OXY)'''<br />
 
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==Overview==
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==LEGHEMOGLOBIN (OXY)==
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The leghaemoglobins have oxygen affinities 11 to 24 times higher than that, of sperm whale myoglobin, due mainly to higher rates of association. To, find out why, we have determined the structures of deoxy- and, oxy-leghaemoglobin II of the lupin at 1.7 A resolution. Results confirm, the general features found in previous X-ray analyses of this protein. The, unique feature that has now emerged is the rotational freedom of the, proximal histidine. In deoxy-leghaemoglobin the imidazole oscillates, between two alternative orientations, eclipsing either the lines N1-N3 or, N2-N4 of the porphyrin; in oxy-leghaemoglobin it is fixed in a staggered, orientation. The iron atom moves from a position 0.30 A from the plane of, the pyrrole nitrogen atoms in deoxy- to a position in the plane in, oxy-leghaemoglobin while the Fe-&lt;N&gt; bond distance remains constant at 2.02, A. The Fe-O-O angle is 152 degrees, as in human haemoglobin. The oxygen is, hydrogen-bonded to the distal histidine at N epsilon 2-O1 and N epsilon, 2-O2 distance of 2.95 A and 2.68 A, respectively. The porphyrin is ruffled, equally in deoxy- and oxy-leghaemoglobins, due to rotations of the pyrrols, about the N-Fe-N bonds, causing the methine bridges to deviate by up to, 0.32 A from the mean porphyrin plane. The only feature capable of, accounting for the high on-rate of the reaction with oxygen are the, mobilities of the proximal histidine and distal histidine residues in, deoxy-leghaemoglobin. The eclipsed positions of the proximal histidine in, deoxy-leghaemoglobin maximize steric hindrance with the porphyrin nitrogen, atoms and minimize pi--&gt;p electron donation, while its staggered position, in oxy-leghaemoglobin reverses both these effects. Together with the, oscillation of the imidazole between the two orientations, these two, factors may reduce the activation energy for the reaction of, leghaemoglobin with oxygen. The distal histidine is in a fixed position in, the haem pocket in the crystal, but must be swinging in and out of the, pocket at a high rate in solution to allow the oxygen to enter.
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<StructureSection load='2gdm' size='340' side='right'caption='[[2gdm]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2gdm]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Lupinus_luteus Lupinus luteus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1gdm 1gdm]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GDM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GDM FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2gdm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gdm OCA], [https://pdbe.org/2gdm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gdm RCSB], [https://www.ebi.ac.uk/pdbsum/2gdm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gdm ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/LGB2_LUPLU LGB2_LUPLU] Provides oxygen to the bacteroids. This role is essential for symbiotic nitrogen fixation.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gd/2gdm_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2gdm ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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2GDM is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Lupinus_luteus Lupinus luteus] with HEM and OXY as [http://en.wikipedia.org/wiki/ligands ligands]. This structure superseeds the now removed PDB entry 1GDM. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2GDM OCA].
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*[[Hemoglobin 3D structures|Hemoglobin 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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The structure of deoxy- and oxy-leghaemoglobin from lupin., Harutyunyan EH, Safonova TN, Kuranova IP, Popov AN, Teplyakov AV, Obmolova GV, Rusakov AA, Vainshtein BK, Dodson GG, Wilson JC, et al., J Mol Biol. 1995 Aug 4;251(1):104-15. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=7643380 7643380]
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[[Category: Large Structures]]
[[Category: Lupinus luteus]]
[[Category: Lupinus luteus]]
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[[Category: Single protein]]
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[[Category: Dodson GG]]
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[[Category: Dodson, G.G.]]
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[[Category: Harutyunyan EH]]
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[[Category: Harutyunyan, E.H.]]
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[[Category: Kuranova IP]]
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[[Category: Kuranova, I.P.]]
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[[Category: Obmolova GV]]
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[[Category: Obmolova, G.V.]]
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[[Category: Perutz MF]]
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[[Category: Perutz, M.F.]]
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[[Category: Popov AN]]
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[[Category: Popov, A.N.]]
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[[Category: Rusakov AA]]
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[[Category: Rusakov, A.A.]]
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[[Category: Safonova TN]]
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[[Category: Safonova, T.N.]]
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[[Category: Teplyakov AV]]
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[[Category: Teplyakov, A.V.]]
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[[Category: Wilson JC]]
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[[Category: Wilson, J.C.]]
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[[Category: HEM]]
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[[Category: OXY]]
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[[Category: leghemoglobin]]
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[[Category: lupine]]
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[[Category: oxygen transport]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Thu Nov 8 13:30:07 2007''
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Current revision

LEGHEMOGLOBIN (OXY)

PDB ID 2gdm

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