PortoBioComp

vmdmagazinedatabase

2017-06-30T11:58:38+01:00

Contents : Note: All the data present in this database are derived from theoretical and computational calculations or obtained from experimental sources. ---------- Allotropy is the property of some chemical elements to exist in two or more different forms, known as allotropes of these elements. Allotropes of the same element can exhibit quite different physical properties and chemical behaviours.Allotropes of carbon include diamond (where the carbon atoms are bon…

mm:parameters:manganese:hdewawawa

2013-10-03T18:54:49+01:00

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

mm:parameters:zinc:hdc_czl

2013-10-03T18:59:21+01:00

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

mm:parameters:copper_zinc:hhh_cu_h_zn_dhh

2013-10-03T18:58:39+01:00

The metal center of Cu, Zn Superoxide Dismutase is hereby presented, in which the zinc atom is bonded to 3 histidines, and 1 aspartate (monodentate) and the copper atom to 4 histidines. Validation for this metal centre in the protein environment is additionally provided. COORDINATION SPHERE Oxidation state: Cu(II) / Zn(II) Spin multiplicity: 1

mm:parameters:manganese:hhewawa

2013-10-03T18:58:24+01:00

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

mm:parameters:zinc:hc_d2

2013-10-03T18:58:12+01:00

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

mm:parameters:zinc:hdcc

2013-10-03T18:57:53+01:00

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

mm:parameters:manganese:hhe_d2

2013-10-03T18:57:45+01:00

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

mm:parameters:manganese:denwawawa

2013-10-03T18:53:33+01:00

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

mm:parameters:manganese:dee_so2

2013-10-03T18:52:37+01:00

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

mm:parameters:manganese:ded_cl

2013-10-03T18:50:44+01:00

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…

mm:parameters:manganese:ddwawawawa

2013-10-03T18:46:30+01:00

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 …

mm:parameters:zinc:hdc

2013-08-06T15:33:59+01:00

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

mm:parameters:zinc:hdc_fp

2013-08-05T14:53:46+01:00

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