First-second shell interactions in metal binding sites in proteins: a PDB survey and DFT/CDM calculations.

scientific article

First-second shell interactions in metal binding sites in proteins: a PDB survey and DFT/CDM calculations. is …
instance of (P31):
scholarly articleQ13442814

External links are
P356DOI10.1021/JA0209722
P698PubMed publication ID12617685

P50authorCarmay LimQ45916099
P2093author name stringYen-lin Lin
Todor Dudev
Minko Dudev
P2860cites workThe Protein Data Bank: a computer-based archival file for macromolecular structuresQ27860989
P433issue10
P407language of work or nameEnglishQ1860
P304page(s)3168-3180
P577publication date2003-03-01
P1433published inJournal of the American Chemical SocietyQ898902
P1476titleFirst-second shell interactions in metal binding sites in proteins: a PDB survey and DFT/CDM calculations
P478volume125

Reverse relations

cites work (P2860)
Q46394009A Database of Transition-Metal-Coordinated Peptide Cross-Sections: Selective Interaction with Specific Amino Acid Residues
Q33533342A computational study of a recreated G protein-GEF reaction intermediate competent for nucleotide exchange: fate of the Mg ion
Q96136751A novel tetrapeptide fluorescence sensor for early diagnosis of prostate cancer based on imaging Zn2+ in healthy versus cancerous cells
Q51705450A peptide-based fluorescent chemosensor for measuring cadmium ions in aqueous solutions and live cells.
Q30343061A united residue force-field for calcium-protein interactions.
Q36965903Activation of Slo1 BK channels by Mg2+ coordinated between the voltage sensor and RCK1 domains
Q52338976Active site remodeling during the catalytic cycle in metal-dependent fructose-1,6-bisphosphate aldolases.
Q36683451BION web server: predicting non-specifically bound surface ions
Q37808952Bioinformatics in bioinorganic chemistry
Q34984656Calcium exchange and structural changes during the photosynthetic oxygen evolving cycle
Q34350493Calcium ligation in photosystem II under inhibiting conditions
Q88618180Coupling between an electrostatic network and the Zn2+ binding site modulates Hv1 activation
Q37287914Crystal Structure of the Metallo-β-Lactamase GOB in the Periplasmic Dizinc Form Reveals an Unusual Metal Site
Q33670085Determination of the structure form of the fourth ligand of zinc in Acutolysin A using combined quantum mechanical and molecular mechanical simulation
Q33280171Discovering structural motifs using a structural alphabet: application to magnesium-binding sites
Q39686303Factors controlling the selectivity for Na(+) over Mg(2+) in sodium transporters and enzymes.
Q30406816First- and second-shell metal binding residues in human proteins are disproportionately associated with disease-related SNPs
Q46423830How the extra methylene group affects the ligation properties of Glu vs. Asp and Gln vs. Asn amino acids: a DFT/PCM study
Q44703982Identification of ion-selectivity determinants in heavy-metal transport P1B-type ATPases.
Q45034273Insights into the role of an active site aspartate in Ty1 reverse transcriptase polymerization
Q30393133Integration of Diverse Research Methods to Analyze and Engineer Ca2+- Binding Proteins: From Prediction to Production
Q36842363Intracellular Mg2+ is a voltage-dependent pore blocker of HCN channels
Q38379384Ion binding to biological macromolecules
Q54649400Iron porphyrins with a hydrogen bonding cavity: effect of weak interactions on their electronic structure and reactivity.
Q40925014Kinetic and CD/MCD spectroscopic studies of the atypical, three-His-ligated, non-heme Fe2+ center in diketone dioxygenase: the role of hydrophilic outer shell residues in catalysis
Q37301039Ligation of water to magnesium chelates of biological importance
Q56639725Many-body effect determines the selectivity for Ca and Mg in proteins
Q46194663Metal-histidine-glutamate as a regulator of enzymatic cycles: a case study of carbonic anhydrase.
Q26751494Minimal Functional Sites in Metalloproteins and Their Usage in Structural Bioinformatics
Q30408808Minimal functional sites allow a classification of zinc sites in proteins
Q38429683Molecular Dynamics Investigation of Dipeptide - Transition Metal Salts in Aqueous Solutions
Q37323081Molecular mechanism of Zn2+ inhibition of a voltage-gated proton channel
Q56896955Mutation of outer-shell residues modulates metal ion co-ordination strength in a metalloenzyme
Q28539398NMR characterization of the interaction of the endonuclease domain of MutL with divalent metal ions and ATP
Q28082109Overcoming differences: The catalytic mechanism of metallo-β-lactamases
Q50475143Pi-pi interaction between aromatic ring and copper-coordinated His81 imidazole regulates the blue copper active-site structure.
Q41557386Predicting Ca2+ -binding sites using refined carbon clusters
Q36047365Predicting nonspecific ion binding using DelPhi
Q30389971Probing the minimal determinants of zinc binding with computational protein design
Q80827528Protein side chains facilitate Mg/Al exchange in model protein binding sites
Q36786978Quantum effects in cation interactions with first and second coordination shell ligands in metalloproteins
Q53421901Role of a remote leucine residue in the catalytic function of polyol dehydrogenase.
Q36003830Role of conserved glycine in zinc-dependent medium chain dehydrogenase/reductase superfamily
Q27675892Solution Structure of RING Finger-like Domain of Retinoblastoma-binding Protein-6 (RBBP6) Suggests It Functions as a U-box
Q44497207Statistical analysis of structural characteristics of protein Ca2+-binding sites
Q50788857Statistical investigation of surface bound ions and further development of BION server to include pH and salt dependence.
Q89206165Structural basis for relief of phospholamban-mediated inhibition of the sarcoplasmic reticulum Ca2+-ATPase at saturating Ca2+ conditions
Q42137993Structural differences between Pb2+- and Ca2+-binding sites in proteins: implications with respect to toxicity
Q28478520The Plasmodium falciparum malaria M1 alanyl aminopeptidase (PfA-M1): insights of catalytic mechanism and function from MD simulations
Q60959847The Role of the Second Coordination Sphere in the Biological Activity of Arene Ruthenium Metalla-Assemblies
Q38258839The mechanical role of metal ions in biogenic protein-based materials
Q40079802The role of a dipeptide outer-coordination sphere on H2-production catalysts: influence on catalytic rates and electron transfer.
Q30397217The structural role of the zinc ion can be dispensable in prokaryotic zinc-finger domains
Q40155467Towards predicting Ca2+-binding sites with different coordination numbers in proteins with atomic resolution
Q33953108Transamidase subunit GAA1/GPAA1 is a M28 family metallo-peptide-synthetase that catalyzes the peptide bond formation between the substrate protein's omega-site and the GPI lipid anchor's phosphoethanolamine
Q47114778Transition metal binding selectivity in proteins and its correlation with the phylogenomic classification of the cation diffusion facilitator protein family.
Q27650934Zinc Coordination Geometry and Ligand Binding Affinity: The Structural and Kinetic Analysis of the Second-Shell Serine 228 Residue and the Methionine 180 Residue of the Aminopeptidase from Vibrio proteolyticus †
Q92930337β-Lactamases and β-Lactamase Inhibitors in the 21st Century

Search more.