https://www.fc.up.pt/PortoBioComp/database/ 2026-04-08T23:15:23+01:00 https://www.fc.up.pt/PortoBioComp/database/ https://www.fc.up.pt/PortoBioComp/database/lib/tpl/dokuwiki/images/favicon.ico text/html 2013-10-03T19:00:42+01:00 https://www.fc.up.pt/PortoBioComp/database/doku.php?id=mm:parameters:lipids:phosphatidylethanolamines_pe&rev=1380823242&do=diff For each phospholipid, its name, 4-letter code, composition of aliphatic chains (sn1/sn2), and parameter files are presented. In addition, the values for volume per lipid (VL), area per lipid (AL), and bilayer thickness (DHH) in a bilayer setting are given, together with experimental data (when available). These parameters were obtained under the General Amber Force Field (GAFF) terminology and general parameters. text/html 2013-10-03T19:00:15+01:00 https://www.fc.up.pt/PortoBioComp/database/doku.php?id=mm:parameters:lipids:phosphatidylcholines_pc&rev=1380823215&do=diff For each phospholipid, its name, 4-letter code, composition of aliphatic chains (sn1/sn2), and parameter files are presented. In addition, the values for volume per lipid (VL), area per lipid (AL), and bilayer thickness (DHH) in a bilayer setting are given, together with experimental data (when available). For the DOPC phospholipid, order parameters for the acyl chains are displayed and compared with experiment. These parameters were obtained under the General Amber Force Field (GAFF) terminolog… text/html 2013-07-25T19:24:42+01:00 https://www.fc.up.pt/PortoBioComp/database/doku.php?id=mm:parameters:lipids:example_page&rev=1374776682&do=diff The following charge parameters for 12 distinct phospholipids were determined, following an AMBER compatible approach. These parameters were validated by building a bilayer system for each phospholipid type and by comparing structural and dynamical values with experimental data available. Some validation results are displayed at the end of the page, and for the DOPC phospholipid a good correlation with experimental available data was obtained. text/html 2013-10-03T18:59:50+01:00 https://www.fc.up.pt/PortoBioComp/database/doku.php?id=mm:parameters:iron:cc_c_2&rev=1380823190&do=diff Desulforedoxin is a mononuclear iron tetrahedral metal center coordinated with two directly linked cysteines and and two cysteines that are not linked. COORDINATION SPHERE Oxidation State: Fe(III) Spin Multiplicity: 6 ---------- Structure chosen to parameterize TEST PROTEIN Protein Desulforedoxin PDB Code 1DXG Crystallographic Resolution 1.80 Å Organism Desulfovibrio gigas [Archer, 1995] Parameters Determined Atom Types ATOM TYPE NEW ATOM TYPE … text/html 2013-10-03T18:54:49+01:00 https://www.fc.up.pt/PortoBioComp/database/doku.php?id=mm:parameters:manganese:hdewawawa&rev=1380822889&do=diff In Citochrome c Oxidase the manganese ion has a nonredox role. Manganese(II) is bonded to residues from different subunits: a glutamate, an aspartate and histidine ligands and possibly one to three water molecules. The glutamate ligand is also coordinated to a copper atom and the histidine is hydrogen bonded to a heme a3 propionate. COORDINATION SPHERE Oxidation State: Mn(II) Spin Multiplicity: 6 text/html 2013-08-05T14:53:46+01:00 https://www.fc.up.pt/PortoBioComp/database/doku.php?id=mm:parameters:zinc:hdc_fp&rev=1375710826&do=diff The metal center of Farnesyltransferase for the product complex is hereby presented, in which the Zinc atom is bonded to 1 histidine, 1 cysteine, 1 aspartate (monodentate), and to the product. Coordination Sphere Oxidation state: Zn(II) Spin multiplicity: 1 text/html 2013-08-06T15:33:59+01:00 https://www.fc.up.pt/PortoBioComp/database/doku.php?id=mm:parameters:zinc:hdc&rev=1375799639&do=diff The metal center of Farnesyltransferase in the resting state is hereby presented, in which the Zinc atom is bonded to 1 histidine, 1 cysteine and to 1 aspartate (bidentate). Validation for the binary complex is additionally provided. Coordination Sphere Oxidation state: Zn(II) Spin multiplicity: 1 JMOL text/html 2013-10-03T18:46:30+01:00 https://www.fc.up.pt/PortoBioComp/database/doku.php?id=mm:parameters:manganese:ddwawawawa&rev=1380822390&do=diff The avian viral S integrase shows preference by manganese(II) over magnesium. In both cases the metal atom is bonded to two aspartates and four water molecules. COORDINATION SPHERE Oxidation state: Mn(II) Spin multiplicity: 6 ---------- Structure chosen to parameterize TEST PROTEIN Protein Integrase PDB Code 1A5V Crystallographic Resolution 1.90 Å Organism Rous Sarcoma Virus [Lubkowski, 1998] Parameters Determined Atom Types ATOM TYPE NEW ATOM … text/html 2013-10-03T18:50:44+01:00 https://www.fc.up.pt/PortoBioComp/database/doku.php?id=mm:parameters:manganese:ded_cl&rev=1380822644&do=diff The metal atom of Chloromuconate Cycloisomerase is shown to be bonded to two aspartates, a glutamate and chloride ion. COORDINATION SPHERE Oxidation State: Mn(II) Spin Multiplicity: 6 ---------- Structure chosen to parameterize TEST PROTEIN Protein Chloromuconate Cycloisomerase PDB Code 2CHR Crystallographic Resolution 3.00 Å Organism Cupriavidus necator [Kleywegt, 1996] Parameters Determined Atom Types ATOM TYPE NEW ATOM TYPE MASS STRUCTU… text/html 2013-10-03T18:51:33+01:00 https://www.fc.up.pt/PortoBioComp/database/doku.php?id=mm:parameters:manganese:dedwawawa&rev=1380822693&do=diff Muconate Cycloisomerase shows preference on manganese(II) over the magnesium ion to perform. Its coordination sphere is similar to the one found in chloromuconate cycloisomerase, with two aspartates and a glutamate. COORDINATION SPHERE Oxidation State: Mn(II) Spin Multiplicity: 6 text/html 2013-10-03T18:52:37+01:00 https://www.fc.up.pt/PortoBioComp/database/doku.php?id=mm:parameters:manganese:dee_so2&rev=1380822757&do=diff Crystal structures from Mandelate Racemase show that it is octameric. The manganese(II) atom in this enzyme is bonded to the side chains of an aspartate, two glutamates and it is bidentate either to a sulfate ion or a S-altrolactate. COORDINATION SPHERE Oxidation State: Mn(II) Spin Multiplicity: 6 text/html 2013-10-03T18:53:33+01:00 https://www.fc.up.pt/PortoBioComp/database/doku.php?id=mm:parameters:manganese:denwawawa&rev=1380822813&do=diff D-Glutarate Dehydratase is analogous to mandelate racemase and enolase. The manganese coordination sphere has a manganese(II) atom bonded to a glutamate, an aspartate and an asparagine from the same subunit. COORDINATION SPHERE Oxidation State: Mn(II) Spin Multiplicity: 6 text/html 2013-10-03T18:55:04+01:00 https://www.fc.up.pt/PortoBioComp/database/doku.php?id=mm:parameters:manganese:ed_py2_wawa&rev=1380822904&do=diff In Pyruvate Kinase manganese(II) mediates the allosteric communication between the phosphoenolpyruvate and fructose-1,6-bisphosphate. Crystal structures suggest that manganese(II) bonds to aspartate, glutamate and the oxygen from a carbonyl and carboxylate groups from a pyruvate ligand. A water molecule is referred as participating in the octahedral coordination of manganese(II). COORDINATION SPHERE Oxidation State: Mn(II) Spin Multiplicity: 6 text/html 2013-10-03T18:59:21+01:00 https://www.fc.up.pt/PortoBioComp/database/doku.php?id=mm:parameters:zinc:hdc_czl&rev=1380823161&do=diff The metal center of Farnesyltransferase for the product complex is hereby presented, in which the Zinc atom is bonded to 1 histidine, 1 cysteine, 1 aspartate (monodentate), and to the product (CZL). COORDINATION SPHERE Oxidation state: Zn(II) Spin multiplicity: 1 text/html 2013-10-03T18:55:50+01:00 https://www.fc.up.pt/PortoBioComp/database/doku.php?id=mm:parameters:manganese:hhdh_ho&rev=1380822950&do=diff The coordination sphere of Manganese Superoxide Dismutase is located in a hydrophobic pocket formed by two subunits. In the resting state the manganese coordination geometry presents distorted trigonal bipyramidal geometry with two histidine and an aspartate equatorial ligands and a histidine and water/hydroxide in axial positions. COORDINATION SPHERE Oxidation State: Mn(III) Spin Multiplicity: 5 text/html 2013-10-03T19:00:23+01:00 https://www.fc.up.pt/PortoBioComp/database/doku.php?id=mm:parameters:iron:cc_fe_ss_fe_cc&rev=1380823223&do=diff Ferredoxin is a binuclear iron center with four cysteine residues and two sulfurs, having a redox potential of
400 mV. COORDINATION SPHERE Oxidation State: Fe(III)/Fe(III) Spin Multiplicity: 1 ---------- Structure chosen to parameterize TEST PROTEIN Protein [2Fe-2S] Ferredoxin PDB Code 4FXC Crystallographic Resolution 2.50 Å Organism Spirulina platensis [Fukuyama, 1995] Parameters Determined Atom Types ATOM TYPE NEW ATOM TYPE MASS STRUC… text/html 2013-10-03T18:57:04+01:00 https://www.fc.up.pt/PortoBioComp/database/doku.php?id=mm:parameters:manganese:hhdhwa&rev=1380823024&do=diff The coordination sphere of Manganese Superoxide Dismutase is located in a hydrophobic pocket formed by two subunits. In the resting state the manganese coordination geometry presents distorted trigonal bipyramidal geometry with two histidine and an aspartate equatorial ligands and a histidine and water/hydroxide in axial positions. COORDINATION SPHERE Oxidation State: Mn(III) Spin Multiplicity: 5 text/html 2013-10-03T18:57:45+01:00 https://www.fc.up.pt/PortoBioComp/database/doku.php?id=mm:parameters:manganese:hhe_d2&rev=1380823065&do=diff During the crystallographic refinements of Pneumococcal Surface Antigen Adhesin A the metal ion was modeled as zinc, with attempts to model manganese(II) failed. The metal atom is expected to be tetrahedral bonded to two histidines, a glutamate and an aspartate, with angles ranging from 93o to 131o. COORDINATION SPHERE Oxidation State: Mn(II) Spin Multiplicity: 6 text/html 2013-10-03T18:57:53+01:00 https://www.fc.up.pt/PortoBioComp/database/doku.php?id=mm:parameters:zinc:hdcc&rev=1380823073&do=diff The metal center of Farnesyltransferase for the ternary complex is hereby presented, in which the Zinc atom is bonded to 1 histidine, 2 cysteine residues (1 from the peptide inhibitor) and to 1 aspartate (monodentate). COORDINATION SPHERE Oxidation state: Zn(II) Spin multiplicity: 1 text/html 2013-10-03T18:58:12+01:00 https://www.fc.up.pt/PortoBioComp/database/doku.php?id=mm:parameters:zinc:hc_d2&rev=1380823092&do=diff The metal center of Farnesyltransferase in the resting state is hereby presented, in which the Zinc atom is bonded to 1 histidine, 1 cysteine and to 1 aspartate (bidentate). Validation for the binary complex is additionally provided. COORDINATION SPHERE Oxidation state: Zn(II) Spin multiplicity: 1 text/html 2013-10-03T18:58:24+01:00 https://www.fc.up.pt/PortoBioComp/database/doku.php?id=mm:parameters:manganese:hhewawa&rev=1380823104&do=diff Homoprotocatechuate-2,3-deoxygenase is shown to have five ligands bonded to the iron(II) ion: a glutamate, two histidines and two waters in a square pyramidal geometry. The ligands in manganese(II) deoxygenases are likely to be the same. Other studies show, however, that it might be hexacoordinated with three solvent molecules occupying ligand positions. COORDINATION SPHERE Oxidation State: Mn(II) Spin Multiplicity: 5 text/html 2013-10-03T18:59:10+01:00 https://www.fc.up.pt/PortoBioComp/database/doku.php?id=mm:parameters:iron:cccc&rev=1380823150&do=diff Rubredoxin is a mononuclear iron tetrahedral metal center coordinated with four cysteines that are not directly connected in the backbone of the protein. COORDINATION SPHERE Oxidation State: Fe(III) Spin Multiplicity: 6 ---------- Structure chosen to parameterize TEST PROTEIN Protein Rubredoxin PDB Code 1IRO Crystallographic Resolution 1.10 Å Organism Clostridium pasteurianum [Dauter, 1996] Parameters Determined Atom Types ATOM TYPE NEW ATOM TY… text/html 2013-10-03T18:56:25+01:00 https://www.fc.up.pt/PortoBioComp/database/doku.php?id=mm:parameters:manganese:hhdh_ho_o&rev=1380822985&do=diff Electronic spectroscopy studies on the resting and enzyme-substrates states of Manganese Superoxide Dismutase support the hypothesis of a side-on peroxo complex with the superoxide anion. The superoxide anion coordinates to the manganese ion between two histidines. The spin multiplicity of the coordination sphere has been reported as a quartet, due to an antiferromagnetic coupling between the superoxide and manganese species. COORDINATION SPHERE Oxidation State: Mn(III) Spin Multiplic…