Estimation of precipitation data by using deterministic interpolation methods: A case study in Penang Island

Yin, Lim Hui; Ting, Ng Yee; Shan, Fam Pei; Shimizu, Kunio; Lateh, Habibah

doi:10.1063/1.5136406

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Calculation Methods1

Weighting Schemes For Proteins At Different Resolutions1

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2022

2023

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Cited by 2 publications

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“…Parameter p is an exponential parameter usually set to around 0.5–3.0 by the user. 55,61 By comparing different w i by using different p values from a small amount of VFe protein data as shown in Table 2, we adopt p = 1, 62 which also generate balanced w i for MoFe protein data of all various resolutions as in Fig. S1 †…”

Section: Calculation Methodsmentioning

confidence: 99%

Statistical analysis of P^N clusters in Mo/VFe protein crystals using a bond valence method toward their electronic structures

2022

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Section: Calculation Methodsmentioning

confidence: 99%

Statistical analysis of P^N clusters in Mo/VFe protein crystals using a bond valence method toward their electronic structures

2022

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“…S1. We adopt p = 1 (Yin et al, 2019), generating a concordant balanced w i distribution in the P 2+ clusters of 18 MoFe proteins. Detailed bond-valence calculations for all adopted and abandoned P 2+ clusters can be found in the supporting information.…”

Section: Weighting Schemes For Proteins At Different Resolutionsmentioning

confidence: 99%

Statistical analyses of the oxidized P-clusters in MoFe proteins using the bond-valence method: towards their electron transfer in nitrogenases

Xie

Chen

Zhou

2023

Acta Cryst Sect D Struct Biol

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26 well selected oxidized P-clusters (P2+) from the crystallographic data deposited in the Protein Data Bank have been analysed statistically by the bond-valence sum method with weighting schemes for MoFe proteins at different resolutions. Interestingly, the oxidation states of P2+ clusters correspond to Fe2 3+Fe6 2+ with high electron delocalization, showing the same oxidation states as the resting states of P-clusters (PN) in nitrogenases. The previously uncertain reduction of P2+ to PN clusters by two electrons was assigned as a double protonation of P2+, in which decoordination of the serine residue and the peptide chain of cysteine take place, in MoFe proteins. This is further supported by the obviously shorter α-alkoxy C—O bond (average of 1.398 Å) in P2+ clusters and longer α-hydroxy C—O bond (average of 1.422 Å) in PN clusters, while no change is observed in the electronic structures of Fe8S7 Fe atoms in P-clusters. Spatially, the calculations show that Fe3 and Fe6, the most oxidized and most reduced Fe atoms, have the shortest distances of 9.329 Å from the homocitrate in the FeMo cofactor and 14.947 Å from the [Fe4S4] cluster, respectively, and may well function as important electron-transport sites.

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Estimation of precipitation data by using deterministic interpolation methods: A case study in Penang Island

Cited by 2 publications

References 20 publications

Statistical analysis of P^N clusters in Mo/VFe protein crystals using a bond valence method toward their electronic structures

Statistical analysis of P^N clusters in Mo/VFe protein crystals using a bond valence method toward their electronic structures

Statistical analyses of the oxidized P-clusters in MoFe proteins using the bond-valence method: towards their electron transfer in nitrogenases

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Estimation of precipitation data by using deterministic interpolation methods: A case study in Penang Island

Cited by 2 publications

References 20 publications

Statistical analysis of PN clusters in Mo/VFe protein crystals using a bond valence method toward their electronic structures

Statistical analysis of PN clusters in Mo/VFe protein crystals using a bond valence method toward their electronic structures

Statistical analyses of the oxidized P-clusters in MoFe proteins using the bond-valence method: towards their electron transfer in nitrogenases

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Statistical analysis of P^N clusters in Mo/VFe protein crystals using a bond valence method toward their electronic structures

Statistical analysis of P^N clusters in Mo/VFe protein crystals using a bond valence method toward their electronic structures