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NMR processing:
MDD
NMR assignment:
Backbone:
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MARS
UNIO Match
PINE
Side-chains:
UNIO ATNOS-Ascan
NOEs:
UNIO ATNOS-Candid
UNIO Candid
ASDP
Structure from NMR restraints:
Ab initio:
GeNMR
Cyana
XPLOR-NIH
ASDP
UNIO ATNOS-Candid
UNIO Candid
Fragment-based:
BMRB CS-Rosetta
Rosetta-NMR (Robetta)
Template-based:
GeNMR
I-TASSER
Refinement:
Amber
Structure from chemical shifts:
Fragment-based:
WeNMR CS-Rosetta
BMRB CS-Rosetta
Homology-based:
CS23D
Simshift
Torsion angles from chemical shifts:
Preditor
TALOS
Promega- Proline
Secondary structure from chemical shifts:
CSI (via RCI server)
TALOS
MICS caps, β-turns
d2D
PECAN
Flexibility from chemical shifts:
RCI
Interactions from chemical shifts:
HADDOCK
Chemical shifts re-referencing:
Shiftcor
UNIO Shiftinspector
LACS
CheckShift
RefDB
NMR model quality:
NOEs, other restraints:
PROSESS
PSVS
RPF scores
iCing
Chemical shifts:
PROSESS
CheShift2
Vasco
iCing
RDCs:
DC
Anisofit
Pseudocontact shifts:
Anisofit
Protein geomtery:
Resolution-by-Proxy
PROSESS
What-If
iCing
PSVS
MolProbity
SAVES2 or SAVES4
Vadar
Prosa
ProQ
MetaMQAPII
PSQS
Eval123D
STAN
Ramachandran Plot
Rampage
ERRAT
Verify_3D
Harmony
Quality Control Check
NMR spectrum prediction:
FANDAS
MestReS
V-NMR
Flexibility from structure:
Backbone S2
Methyl S2
B-factor
Molecular dynamics:
Gromacs
Amber
Antechamber
Chemical shifts prediction:
From structure:
Shiftx2
Sparta+
Camshift
CH3shift- Methyl
ArShift- Aromatic
ShiftS
Proshift
PPM
CheShift-2- Cα
From sequence:
Shifty
Camcoil
Poulsen_rc_CS
Disordered proteins:
MAXOCC
Format conversion & validation:
CCPN
From NMR-STAR 3.1
Validate NMR-STAR 3.1
NMR sample preparation:
Protein disorder:
DisMeta
Protein solubility:
camLILA
ccSOL
Camfold
camGroEL
Zyggregator
Isotope labeling:
UPLABEL
Solid-state NMR:
sedNMR


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Default Structural characterization of the divalent cation sites of bacterial phosphotriester

Structural characterization of the divalent cation sites of bacterial phosphotriesterase by 113Cd NMR spectroscopy.

Related Articles Structural characterization of the divalent cation sites of bacterial phosphotriesterase by 113Cd NMR spectroscopy.

Biochemistry. 1993 Sep 7;32(35):9148-55

Authors: Omburo GA, Mullins LS, Raushel FM

The phosphotriesterase from Pseudomonas diminuta catalyzes the hydrolysis of organophosphate esters. The isolated native protein contains zinc, and removal of this metal abolishes the enzymatic activity. Reconstitution of the apoenzyme requires 2 mol of cadmium per mol of protein for full catalytic activity. The kcat and Km values for the hydrolysis of paraoxon for the cadmium-substituted enzyme are 4300 s-1 and 390 microM, respectively. These values compare favorably with the kinetic constants observed for the zinc-substituted enzyme (2300 s-1 and 78 microM). A hybrid enzyme containing one zinc and one cadmium ion is catalytically active, and the kinetic constants are nearly identical to the values obtained with the all-zinc-containing enzyme. The NMR spectrum of protein reconstituted with two 113Cd2+ ions per enzyme molecule exhibits cadmium resonances at 212 and 116 ppm downfield from Cd(ClO4)2. The two metal ions are, therefore, in significantly different chemical environments. These two binding sites have been designated the M alpha and M beta sites for the low- and high-field signals, respectively. Protein substituted with a single cadmium ion also shows two cadmium resonances, and thus one site is not completely filled prior to the binding of metal to the other site. The Cd/Zn hybrid protein shows a single cadmium resonance at 115 ppm, and thus the cadmium is occupying the M beta site while zinc is occupying the M alpha site. The positions of the observed chemical shifts for the two cadmium signals indicate that the ligands to both metals are composed of a mixture of oxygen and nitrogen atoms.(ABSTRACT TRUNCATED AT 250 WORDS)

PMID: 8396425 [PubMed - indexed for MEDLINE]



Source: PubMed
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